#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
SHOC2	8036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	112745430	112745430	+	Missense_Mutation	SNP	C	C	A			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr10:112745430C>A	ENST00000369452.4	+	3	1093	c.748C>A	c.(748-750)Ctt>Att	p.L250I	SHOC2_ENST00000489390.1_Intron|SHOC2_ENST00000265277.5_Intron	NM_007373.3	NP_031399.2	Q9UQ13	SHOC2_HUMAN	soc-2 suppressor of clear homolog (C. elegans)	250					fibroblast growth factor receptor signaling pathway (GO:0008543)|positive regulation of Ras protein signal transduction (GO:0046579)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein phosphatase type 1 complex (GO:0000164)	protein phosphatase binding (GO:0019903)|protein phosphatase regulator activity (GO:0019888)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(2)	17				Epithelial(162;0.000796)|all cancers(201;0.011)|BRCA - Breast invasive adenocarcinoma(275;0.126)		TCACAATCAACTTGAACACCT	0.368																																																0													94.0	80.0	85.0					10																	112745430		2203	4300	6503	SO:0001583	missense	8036			AB020669	CCDS7568.1, CCDS58095.1	10q25	2014-09-17	2001-11-28		ENSG00000108061	ENSG00000108061			15454	protein-coding gene	gene with protein product		602775	"""soc-2 (suppressor of clear, C.elegans) homolog"""			9618511, 9674433, 10783161	Standard	NM_007373		Approved	KIAA0862, SOC2, SUR-8, SOC-2, SUR8	uc001kzl.4	Q9UQ13	OTTHUMG00000019047	ENST00000369452.4:c.748C>A	10.37:g.112745430C>A	ENSP00000358464:p.Leu250Ile		A8K9W8|B3KR23|O76063|Q5VZS8|Q5VZS9	Missense_Mutation	SNP	ENST00000369452.4	37	CCDS7568.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.112366	0.77210	.	.	ENSG00000108061	ENST00000369452	T	0.61859	0.07	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.62307	0.2417	N	0.17312	0.475	0.80722	D	1	D	0.59357	0.985	P	0.61397	0.888	T	0.62613	-0.6817	10	0.44086	T	0.13	.	20.452	0.99131	0.0:1.0:0.0:0.0	.	250	Q9UQ13	SHOC2_HUMAN	I	250	ENSP00000358464:L250I	ENSP00000358464:L250I	L	+	1	0	SHOC2	112735420	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.125000	0.50469	2.838000	0.97847	0.591000	0.81541	CTT		0.368	SHOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050355.1	NM_007373		9	97	9	97
MRVI1	10335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	10615122	10615122	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr11:10615122C>T	ENST00000436272.1	-	16	2089	c.2011G>A	c.(2011-2013)Gtt>Att	p.V671I	MRVI1-AS1_ENST00000525578.1_RNA|MRVI1_ENST00000558540.1_Missense_Mutation_p.V383I|MRVI1_ENST00000534266.2_Missense_Mutation_p.V383I|MRVI1_ENST00000547195.1_Missense_Mutation_p.V607I|MRVI1_ENST00000545852.1_Missense_Mutation_p.V383I|MRVI1_ENST00000527509.2_Missense_Mutation_p.V607I|MRVI1_ENST00000423302.2_Missense_Mutation_p.V698I|LYVE1_ENST00000531706.1_Intron|MRVI1_ENST00000552103.1_Missense_Mutation_p.V607I|MRVI1-AS1_ENST00000529829.1_RNA|MRVI1_ENST00000531107.1_Missense_Mutation_p.V690I|MRVI1-AS1_ENST00000529979.1_RNA|MRVI1_ENST00000541483.1_Missense_Mutation_p.V492I|MRVI1_ENST00000421747.1_Missense_Mutation_p.V689I|MRVI1_ENST00000424001.1_Missense_Mutation_p.V383I			Q9Y6F6	MRVI1_HUMAN	murine retrovirus integration site 1 homolog	671					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)		ACCACAGCAACGCTGACCCTC	0.517																																																0													102.0	101.0	101.0					11																	10615122		2201	4294	6495	SO:0001583	missense	10335			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.2011G>A	11.37:g.10615122C>T	ENSP00000412229:p.Val671Ile		B7Z3T4|B7Z6I2|B7Z9A3|E9PQY6|F5H6A1|J3KQZ7|Q17S00|Q9UNY1	Missense_Mutation	SNP	ENST00000436272.1	37		.	.	.	.	.	.	.	.	.	.	C	27.5	4.836080	0.91117	.	.	ENSG00000072952	ENST00000421747;ENST00000308763;ENST00000436272;ENST00000547195;ENST00000552103;ENST00000545852;ENST00000424001;ENST00000423302;ENST00000541483;ENST00000531107;ENST00000527509	T;T;T;T;T;T;T;T;T;T	0.13307	2.6;2.6;2.6;2.6;2.6;2.6;2.6;2.6;2.6;2.6	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.24624	0.0597	L	0.28192	0.835	0.58432	D	0.999999	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.81914	0.987;0.995;0.995;0.991	T	0.03630	-1.1018	10	0.10111	T	0.7	-10.6653	19.9357	0.97140	0.0:1.0:0.0:0.0	.	492;671;690;689	F5H6A1;Q9Y6F6;E9PQY6;Q9Y6F6-4	.;MRVI1_HUMAN;.;.	I	689;672;671;607;607;383;383;698;492;690;607	ENSP00000414598:V689I;ENSP00000412229:V671I;ENSP00000448278:V607I;ENSP00000446764:V607I;ENSP00000441971:V383I;ENSP00000401205:V383I;ENSP00000412130:V698I;ENSP00000437784:V492I;ENSP00000432436:V690I;ENSP00000432067:V607I	ENSP00000307885:V672I	V	-	1	0	MRVI1	10571698	1.000000	0.71417	0.996000	0.52242	0.856000	0.48823	7.037000	0.76531	2.715000	0.92844	0.655000	0.94253	GTT		0.517	MRVI1-203	KNOWN	basic	protein_coding	protein_coding		NM_001098579		30	35	30	35
HTR3A	3359	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	113852031	113852031	+	Missense_Mutation	SNP	A	A	T			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr11:113852031A>T	ENST00000504030.2	+	4	816	c.371A>T	c.(370-372)gAg>gTg	p.E124V	HTR3A_ENST00000355556.2_Missense_Mutation_p.E130V|HTR3A_ENST00000375498.2_Missense_Mutation_p.E130V|HTR3A_ENST00000535865.1_5'UTR|HTR3A_ENST00000299961.5_Missense_Mutation_p.E109V|HTR3A_ENST00000506841.2_Missense_Mutation_p.E124V			P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A, ionotropic	124					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)	CTCATCAATGAGTTGTGAGTA	0.512																																																0													104.0	72.0	83.0					11																	113852031		2201	4296	6497	SO:0001583	missense	3359			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.371A>T	11.37:g.113852031A>T	ENSP00000424189:p.Glu124Val		B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Missense_Mutation	SNP	ENST00000504030.2	37		.	.	.	.	.	.	.	.	.	.	A	26.8	4.769632	0.90020	.	.	ENSG00000166736	ENST00000504030;ENST00000355556;ENST00000375498;ENST00000506841;ENST00000299961	T;T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32;-1.32	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	D	0.91670	0.7367	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	0.93510	0.6852	10	0.87932	D	0	-42.0518	15.5476	0.76118	1.0:0.0:0.0:0.0	.	109;130;130	B4DSY6;G5E986;Q7KZM7	.;.;.	V	124;130;130;124;109	ENSP00000424189:E124V;ENSP00000347754:E130V;ENSP00000364648:E130V;ENSP00000424776:E124V;ENSP00000299961:E109V	ENSP00000299961:E109V	E	+	2	0	HTR3A	113357241	1.000000	0.71417	0.996000	0.52242	0.827000	0.46813	9.273000	0.95719	2.071000	0.62044	0.459000	0.35465	GAG		0.512	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869		25	34	25	34
MIPEP	4285	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	24411745	24411745	+	Missense_Mutation	SNP	T	T	C			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr13:24411745T>C	ENST00000382172.3	-	13	1587	c.1489A>G	c.(1489-1491)Atg>Gtg	p.M497V		NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	497					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(12)|prostate(2)|skin(1)	27		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		GCATGTCCCATTTCATGGAAA	0.438																																																0													159.0	150.0	153.0					13																	24411745		2203	4300	6503	SO:0001583	missense	4285				CCDS9303.1	13q12	2011-01-17			ENSG00000027001	ENSG00000027001	3.4.24.59		7104	protein-coding gene	gene with protein product		602241				9073519	Standard	NM_005932		Approved	MIP	uc001uox.4	Q99797	OTTHUMG00000016573	ENST00000382172.3:c.1489A>G	13.37:g.24411745T>C	ENSP00000371607:p.Met497Val		Q5JV15|Q5T9Q9|Q96G65	Missense_Mutation	SNP	ENST00000382172.3	37	CCDS9303.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.343745	0.82022	.	.	ENSG00000027001	ENST00000382172	T	0.08807	3.05	5.82	5.82	0.92795	Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.40171	0.1106	M	0.93507	3.425	0.58432	D	0.999995	D	0.65815	0.995	D	0.74348	0.983	T	0.53514	-0.8428	10	0.72032	D	0.01	.	16.1864	0.81955	0.0:0.0:0.0:1.0	.	497	Q99797	MIPEP_HUMAN	V	497	ENSP00000371607:M497V	ENSP00000371607:M497V	M	-	1	0	MIPEP	23309745	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.928000	0.87587	2.227000	0.72691	0.454000	0.30748	ATG		0.438	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1			60	207	60	207
FRY	10129	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	32811758	32811758	+	Missense_Mutation	SNP	C	C	G			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr13:32811758C>G	ENST00000380250.3	+	44	6549	c.6053C>G	c.(6052-6054)aCc>aGc	p.T2018S		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	2018						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)		TCCTCAAAAACCAGAAGCTCA	0.537																																																0													69.0	71.0	70.0					13																	32811758		1986	4159	6145	SO:0001583	missense	10129			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.6053C>G	13.37:g.32811758C>G	ENSP00000369600:p.Thr2018Ser		Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	C	6.652	0.488748	0.12641	.	.	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.20200	2.09	6.17	5.32	0.75619	.	0.243356	0.47455	D	0.000231	T	0.16041	0.0386	L	0.31476	0.935	0.80722	D	1	B	0.13145	0.007	B	0.13407	0.009	T	0.05451	-1.0884	10	0.07325	T	0.83	.	16.9757	0.86312	0.1287:0.8713:0.0:0.0	.	2018	Q5TBA9	FRY_HUMAN	S	2018;855	ENSP00000369600:T2018S	ENSP00000369600:T2018S	T	+	2	0	FRY	31709758	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.479000	0.60236	1.595000	0.50050	0.655000	0.94253	ACC		0.537	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		16	35	16	35
NBEA	26960	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	35923243	35923243	+	Splice_Site	SNP	A	A	G			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr13:35923243A>G	ENST00000400445.3	+	37	6437		c.e37-1		NBEA_ENST00000379939.2_Splice_Site|NBEA_ENST00000540320.1_Splice_Site|NBEA_ENST00000310336.4_Splice_Site	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin						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)		TTTTCTTTTTAGATTACTGTG	0.313																																																0													60.0	56.0	57.0					13																	35923243		1801	4076	5877	SO:0001630	splice_region_variant	26960			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.5904-1A>G	13.37:g.35923243A>G			B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Splice_Site	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.393525	0.83011	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	.	.	.	5.53	5.53	0.82687	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.653	0.77112	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NBEA	34821243	1.000000	0.71417	0.975000	0.42487	0.955000	0.61496	8.730000	0.91510	2.105000	0.64084	0.528000	0.53228	.		0.313	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	Intron	17	42	17	42
TRPC4	7223	hgsc.bcm.edu;broad.mit.edu	37	13	38320234	38320234	+	Missense_Mutation	SNP	C	C	T	rs200216544		TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr13:38320234C>T	ENST00000379705.3	-	3	1594	c.737G>A	c.(736-738)cGg>cAg	p.R246Q	TRPC4_ENST00000379679.1_Intron|TRPC4_ENST00000379673.2_Missense_Mutation_p.R246Q|TRPC4_ENST00000338947.5_Intron|TRPC4_ENST00000379681.3_Missense_Mutation_p.R246Q|TRPC4_ENST00000355779.2_Missense_Mutation_p.R246Q|TRPC4_ENST00000426868.2_Missense_Mutation_p.R246Q|TRPC4_ENST00000358477.2_Missense_Mutation_p.R246Q|TRPC4_ENST00000447043.1_Missense_Mutation_p.R246Q			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	246					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)			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)		TTTGCACTGCCGTGACAGCTC	0.423													C|||	1	0.000199681	0.0	0.0	5008	,	,		20399	0.001		0.0	False		,,,				2504	0.0															0													157.0	144.0	148.0					13																	38320234		2203	4300	6503	SO:0001583	missense	7223			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.737G>A	13.37:g.38320234C>T	ENSP00000369027:p.Arg246Gln		B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Missense_Mutation	SNP	ENST00000379705.3	37	CCDS9365.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	4.660	0.122762	0.08931	.	.	ENSG00000133107	ENST00000379705;ENST00000379681;ENST00000426868;ENST00000355779;ENST00000358477;ENST00000379673;ENST00000447043	T;T;T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05	6.07	5.23	0.72850	.	0.277600	0.41194	N	0.000928	T	0.31136	0.0787	N	0.01649	-0.78	0.09310	N	1	B;B;B;B;B	0.14012	0.004;0.007;0.009;0.008;0.002	B;B;B;B;B	0.11329	0.002;0.006;0.002;0.006;0.002	T	0.12863	-1.0531	10	0.07990	T	0.79	-11.564	12.3521	0.55155	0.0:0.8652:0.0:0.1348	.	246;246;246;246;246	Q9UBN4-3;Q9UBN4-4;Q9UBN4-5;Q9UBN4-2;Q9UBN4	.;.;.;.;TRPC4_HUMAN	Q	246	ENSP00000369027:R246Q;ENSP00000369003:R246Q;ENSP00000410133:R246Q;ENSP00000348025:R246Q;ENSP00000351264:R246Q;ENSP00000368995:R246Q;ENSP00000414316:R246Q	ENSP00000348025:R246Q	R	-	2	0	TRPC4	37218234	0.880000	0.30214	0.517000	0.27799	0.535000	0.34838	2.094000	0.41719	1.578000	0.49821	0.655000	0.94253	CGG		0.423	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		20	317	20	317
TJP1	7082	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	30024898	30024898	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr15:30024898C>T	ENST00000346128.6	-	14	2332	c.1858G>A	c.(1858-1860)Gat>Aat	p.D620N	TJP1_ENST00000400011.2_Missense_Mutation_p.D624N|TJP1_ENST00000545208.2_Missense_Mutation_p.D620N|TJP1_ENST00000356107.6_Missense_Mutation_p.D620N	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	620	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)		GCGGACAAATCCTCTCTGCTT	0.433																																					Melanoma(77;681 1843 6309 6570)											0													78.0	76.0	76.0					15																	30024898		1837	4091	5928	SO:0001583	missense	7082				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.1858G>A	15.37:g.30024898C>T	ENSP00000281537:p.Asp620Asn		B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	37	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	C	35	5.578969	0.96565	.	.	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	T;T;T;T	0.09350	3.0;3.18;3.11;2.99	5.82	5.82	0.92795	Src homology-3 domain (1);Guanylate kinase/L-type calcium channel (1);	0.000000	0.85682	D	0.000000	T	0.42040	0.1185	M	0.86420	2.815	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	0.31998	-0.9923	9	.	.	.	.	20.1092	0.97906	0.0:1.0:0.0:0.0	.	613;620;620;624	A9CQZ8;Q07157-2;Q07157;G5E9E7	.;.;ZO1_HUMAN;.	N	620;624;620;620;620	ENSP00000281537:D620N;ENSP00000382890:D624N;ENSP00000441202:D620N;ENSP00000348416:D620N	.	D	-	1	0	TJP1	27812190	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.416000	0.80143	2.745000	0.94114	0.655000	0.94253	GAT		0.433	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		47	111	47	111
ZNF592	9640	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	85326612	85326612	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr15:85326612C>T	ENST00000560079.2	+	4	994	c.706C>T	c.(706-708)Cga>Tga	p.R236*	ZNF592_ENST00000299927.3_Nonsense_Mutation_p.R236*	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	236					cell death (GO:0008219)|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(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GGATGCCACTCGATTCTTCGG	0.567																																																0													99.0	114.0	109.0					15																	85326612		2203	4299	6502	SO:0001587	stop_gained	9640			D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"""Zinc fingers, C2H2-type"""	28986	protein-coding gene	gene with protein product		613624	"""spinocerebellar ataxia, autosomal recessive 5"""	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.706C>T	15.37:g.85326612C>T	ENSP00000452877:p.Arg236*		Q2M1T2|Q504Y9	Nonsense_Mutation	SNP	ENST00000560079.2	37	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	C	12.89	2.073506	0.36566	.	.	ENSG00000166716	ENST00000299927	.	.	.	5.87	4.91	0.64330	.	0.839003	0.10876	N	0.624373	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.7518	10.5406	0.45031	0.1372:0.714:0.1488:0.0	.	.	.	.	X	236	.	ENSP00000299927:R236X	R	+	1	2	ZNF592	83127616	0.000000	0.05858	0.022000	0.16811	0.020000	0.10135	0.919000	0.28692	2.780000	0.95670	0.655000	0.94253	CGA		0.567	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630		28	102	28	102
CIITA	4261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	10997737	10997737	+	Nonsense_Mutation	SNP	C	C	T	rs567218474		TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr16:10997737C>T	ENST00000324288.8	+	9	1055	c.922C>T	c.(922-924)Cga>Tga	p.R308*	CIITA_ENST00000381835.5_Nonsense_Mutation_p.R259*|CIITA_ENST00000537380.1_3'UTR	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	308					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						CCTGACCTCCCGAGCAAACAT	0.592			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """								C|||	1	0.000199681	0.0	0.0014	5008	,	,		18878	0.0		0.0	False		,,,				2504	0.0						Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	0													104.0	97.0	100.0					16																	10997737		2197	4300	6497	SO:0001587	stop_gained	4261			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.922C>T	16.37:g.10997737C>T	ENSP00000316328:p.Arg308*		A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Nonsense_Mutation	SNP	ENST00000324288.8	37	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.320743	0.81469	.	.	ENSG00000179583	ENST00000324288;ENST00000381835;ENST00000388910;ENST00000537380	.	.	.	5.47	5.47	0.80525	.	0.450237	0.18613	N	0.136115	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.8224	0.70082	0.0:1.0:0.0:0.0	.	.	.	.	X	308;259;260;308	.	ENSP00000316328:R308X	R	+	1	2	CIITA	10905238	0.969000	0.33509	0.974000	0.42286	0.013000	0.08279	3.279000	0.51670	2.569000	0.86673	0.655000	0.94253	CGA		0.592	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		33	131	33	131
ITGAL	3683	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	30530025	30530025	+	Silent	SNP	C	C	T			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr16:30530025C>T	ENST00000356798.6	+	29	3393	c.3213C>T	c.(3211-3213)aaC>aaT	p.N1071N	ITGAL_ENST00000358164.5_Silent_p.N987N|ITGAL_ENST00000433423.2_Silent_p.N305N	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	1071					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)	ATGGCAGCAACGCCTCCCTGG	0.612																																					NSCLC(110;1462 1641 3311 33990 49495)											0													114.0	89.0	98.0					16																	30530025		2197	4300	6497	SO:0001819	synonymous_variant	3683				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.3213C>T	16.37:g.30530025C>T			O43746|Q45H73|Q96HB1|Q9UBC8	Silent	SNP	ENST00000356798.6	37	CCDS32433.1																																																																																				0.612	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2			13	53	13	53
TRPV3	162514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	3458040	3458040	+	Silent	SNP	G	G	A			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr17:3458040G>A	ENST00000576742.1	-	2	426	c.105C>T	c.(103-105)acC>acT	p.T35T	TRPV3_ENST00000301365.4_Silent_p.T35T|TRPV3_ENST00000572519.1_Silent_p.T35T	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	35					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)	TCTTTGTGGGGGTGATCTCCG	0.657																																																0													40.0	42.0	41.0					17																	3458040		2203	4300	6503	SO:0001819	synonymous_variant	162514			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.105C>T	17.37:g.3458040G>A			Q8NDW7|Q8NET9|Q8NFH2	Silent	SNP	ENST00000576742.1	37	CCDS11029.1																																																																																				0.657	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068		33	33	33	33
ABCC3	8714	hgsc.bcm.edu;broad.mit.edu	37	17	48741328	48741328	+	Missense_Mutation	SNP	C	C	G			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr17:48741328C>G	ENST00000285238.8	+	10	1274	c.1194C>G	c.(1192-1194)aaC>aaG	p.N398K	ABCC3_ENST00000427699.1_Missense_Mutation_p.N398K	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	398	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				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)	TTATCACCAACTCAGTCAAAC	0.587																																																0													141.0	118.0	126.0					17																	48741328		2203	4300	6503	SO:0001583	missense	8714			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.1194C>G	17.37:g.48741328C>G	ENSP00000285238:p.Asn398Lys		B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	37	CCDS32681.1	.	.	.	.	.	.	.	.	.	.	C	15.53	2.862029	0.51482	.	.	ENSG00000108846	ENST00000427699;ENST00000285238	D;D	0.89617	-2.54;-2.54	4.71	-2.86	0.05717	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.054826	0.64402	D	0.000002	D	0.93769	0.8008	M	0.87328	2.875	0.58432	D	0.999998	D;D	0.89917	1.0;0.998	D;D	0.91635	0.999;0.976	D	0.93004	0.6426	10	0.87932	D	0	-8.0011	14.2863	0.66247	0.0:0.6272:0.0:0.3728	.	398;398	O15438;O15438-5	MRP3_HUMAN;.	K	398	ENSP00000395160:N398K;ENSP00000285238:N398K	ENSP00000285238:N398K	N	+	3	2	ABCC3	46096327	0.272000	0.24172	0.963000	0.40424	0.678000	0.39670	-0.172000	0.09868	-0.481000	0.06792	-0.312000	0.09012	AAC		0.587	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038		10	104	10	104
ATP8B3	148229	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	1785266	1785266	+	Silent	SNP	G	G	A			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr19:1785266G>A	ENST00000310127.6	-	27	3662	c.3424C>T	c.(3424-3426)Ctg>Ttg	p.L1142L	ATP8B3_ENST00000539485.1_Silent_p.L1152L|ATP8B3_ENST00000525591.1_Silent_p.L1105L	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	1142					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)		GCCACGCACAGGGCGGTCCAG	0.607																																																0													43.0	53.0	50.0					19																	1785266		2194	4295	6489	SO:0001819	synonymous_variant	148229			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.3424C>T	19.37:g.1785266G>A			Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Silent	SNP	ENST00000310127.6	37	CCDS45901.1																																																																																				0.607	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813		4	17	4	17
SAFB2	9667	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	5587939	5587939	+	Missense_Mutation	SNP	G	G	A	rs376399865		TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr19:5587939G>A	ENST00000252542.4	-	19	2842	c.2578C>T	c.(2578-2580)Cgc>Tgc	p.R860C		NM_014649.2	NP_055464.1	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	860	Gly-rich.|Interacts with SAFB1.				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)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		TGCCAGGCGCGTGCCTGGTGC	0.662																																					Ovarian(127;888 1728 23957 44128 52668)											0													17.0	19.0	18.0					19																	5587939		2203	4298	6501	SO:0001583	missense	9667			D50928	CCDS32879.1	19p13.3	2013-02-12				ENSG00000130254		"""RNA binding motif (RRM) containing"""	21605	protein-coding gene	gene with protein product		608066				12660241	Standard	NM_014649		Approved	KIAA0138	uc002mcd.3	Q14151		ENST00000252542.4:c.2578C>T	19.37:g.5587939G>A	ENSP00000252542:p.Arg860Cys		B4DKG3|Q8TB13	Missense_Mutation	SNP	ENST00000252542.4	37	CCDS32879.1	.	.	.	.	.	.	.	.	.	.	g	12.78	2.039094	0.35989	.	.	ENSG00000130254	ENST00000252542	T	0.13089	2.62	4.41	3.36	0.38483	.	0.111909	0.40469	N	0.001086	T	0.11196	0.0273	L	0.34521	1.04	0.09310	N	0.999996	B	0.19073	0.033	B	0.12156	0.007	T	0.21008	-1.0258	10	0.72032	D	0.01	-4.3184	10.6011	0.45367	0.0911:0.0:0.9089:0.0	.	860	Q14151	SAFB2_HUMAN	C	860	ENSP00000252542:R860C	ENSP00000252542:R860C	R	-	1	0	SAFB2	5538939	0.975000	0.34042	0.002000	0.10522	0.002000	0.02628	5.639000	0.67868	0.829000	0.34733	0.655000	0.94253	CGC		0.662	SAFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451016.1	NM_014649		5	16	5	16
MAG	4099	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	35802842	35802842	+	Silent	SNP	C	C	T			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr19:35802842C>T	ENST00000392213.3	+	10	1797	c.1638C>T	c.(1636-1638)ccC>ccT	p.P546P	MAG_ENST00000593348.1_3'UTR|MAG_ENST00000537831.2_Silent_p.P521P|MAG_ENST00000361922.4_Silent_p.P546P	NM_002361.3	NP_002352.1	P20916	MAG_HUMAN	myelin associated glycoprotein	546					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|substantia nigra development (GO:0021762)	integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)	carbohydrate binding (GO:0030246)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(11)|skin(2)|upper_aerodigestive_tract(2)	34	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CAGAGAGCCCCAGCTTCTCGG	0.607																																																0													50.0	37.0	41.0					19																	35802842		2203	4300	6503	SO:0001819	synonymous_variant	4099			M29273	CCDS12455.1, CCDS12456.1, CCDS56090.1	19q13.1	2013-01-29			ENSG00000105695	ENSG00000105695		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6783	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 4A"""	159460		GMA		2476987, 8432525	Standard	NM_080600		Approved	SIGLEC4A, SIGLEC-4A, S-MAG	uc002nyy.2	P20916		ENST00000392213.3:c.1638C>T	19.37:g.35802842C>T			B7Z2E5|F5GYC0|Q567S4	Silent	SNP	ENST00000392213.3	37	CCDS12455.1																																																																																				0.607	MAG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466071.1	NM_080600		15	2	15	2
ZNF546	339327	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	40520711	40520711	+	Missense_Mutation	SNP	C	C	G			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr19:40520711C>G	ENST00000347077.4	+	7	1750	c.1534C>G	c.(1534-1536)Ctc>Gtc	p.L512V	ZNF546_ENST00000596894.1_Intron|ZNF546_ENST00000600094.1_Missense_Mutation_p.L486V	NM_178544.3	NP_848639.2	Q86UE3	ZN546_HUMAN	zinc finger protein 546	512					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)					TCGCTATCATCTCACTCAACA	0.403																																																0													67.0	59.0	62.0					19																	40520711		2203	4300	6503	SO:0001583	missense	339327			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.1534C>G	19.37:g.40520711C>G	ENSP00000339823:p.Leu512Val		A8K913	Missense_Mutation	SNP	ENST00000347077.4	37	CCDS12548.1	.	.	.	.	.	.	.	.	.	.	c	12.74	2.027705	0.35797	.	.	ENSG00000187187	ENST00000347077;ENST00000392042	T	0.52983	0.64	3.0	3.0	0.34707	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.66982	0.2845	M	0.74389	2.26	0.19575	N	0.999961	D	0.71674	0.998	D	0.85130	0.997	T	0.55444	-0.8140	9	0.87932	D	0	.	12.2301	0.54482	0.0:1.0:0.0:0.0	.	512	Q86UE3	ZN546_HUMAN	V	512;149	ENSP00000339823:L512V	ENSP00000339823:L512V	L	+	1	0	ZNF546	45212551	0.006000	0.16342	0.101000	0.21167	0.766000	0.43426	0.536000	0.23129	1.969000	0.57287	0.655000	0.94253	CTC		0.403	ZNF546-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462495.2	NM_178544		44	16	44	16
SLC17A7	57030	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	49933845	49933845	+	Silent	SNP	C	C	T	rs546442351		TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr19:49933845C>T	ENST00000221485.3	-	12	1785	c.1614G>A	c.(1612-1614)ccG>ccA	p.P538P	SLC17A7_ENST00000600601.1_Silent_p.P471P|SLC17A7_ENST00000543531.1_Silent_p.P526P	NM_020309.3	NP_064705.1	Q9P2U7	VGLU1_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 7	538	Pro-rich.				glutamate secretion (GO:0014047)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|long-term memory (GO:0007616)|neurotransmitter secretion (GO:0007269)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|sequestering of neurotransmitter (GO:0042137)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|clathrin-sculpted glutamate transport vesicle membrane (GO:0060203)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|synaptic vesicle membrane (GO:0030672)	inorganic phosphate transmembrane transporter activity (GO:0005315)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:inorganic phosphate symporter activity (GO:0015319)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(7)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	26		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(486;0.0245)		CATAGGAGGGCGGGGGTGCAG	0.647													C|||	1	0.000199681	0.0	0.0	5008	,	,		12383	0.0		0.0	False		,,,				2504	0.001															0													18.0	20.0	19.0					19																	49933845		2195	4289	6484	SO:0001819	synonymous_variant	57030			AB032436	CCDS12764.1	19q13.33	2013-07-18	2013-07-18		ENSG00000104888	ENSG00000104888		"""Solute carriers"""	16704	protein-coding gene	gene with protein product	"""vesicular glutamate transporter 1"""	605208	"""solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 7"""			8632143, 10820226	Standard	NM_020309		Approved	BNPI, VGLUT1	uc002pnp.3	Q9P2U7		ENST00000221485.3:c.1614G>A	19.37:g.49933845C>T			B4DFR9|B4DG46|Q6PCD0	Silent	SNP	ENST00000221485.3	37	CCDS12764.1																																																																																				0.647	SLC17A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465367.2			10	8	10	8
LRRC7	57554	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	70504174	70504174	+	Silent	SNP	G	G	A			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr1:70504174G>A	ENST00000035383.5	+	19	2583	c.2553G>A	c.(2551-2553)ccG>ccA	p.P851P	LRRC7_ENST00000310961.5_Silent_p.P856P|LRRC7_ENST00000415775.2_Silent_p.P135P	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	851						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						CCCCTAGTCCGTTTGAAGACA	0.478																																																0													74.0	83.0	80.0					1																	70504174		2203	4300	6503	SO:0001819	synonymous_variant	57554				CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.2553G>A	1.37:g.70504174G>A			Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Silent	SNP	ENST00000035383.5	37	CCDS645.1																																																																																				0.478	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		76	12	76	12
NUP210L	91181	hgsc.bcm.edu;ucsc.edu	37	1	154061934	154061934	+	Missense_Mutation	SNP	G	G	A			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr1:154061934G>A	ENST00000368559.3	-	16	2395	c.2324C>T	c.(2323-2325)gCc>gTc	p.A775V	NUP210L_ENST00000271854.3_Missense_Mutation_p.A775V	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	775					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)			ACATGGCTGGGCACCAGCTGG	0.483																																																0													158.0	155.0	156.0					1																	154061934		1965	4162	6127	SO:0001583	missense	91181			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.2324C>T	1.37:g.154061934G>A	ENSP00000357547:p.Ala775Val		E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	37	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	G	9.969	1.224834	0.22457	.	.	ENSG00000143552	ENST00000368559;ENST00000271854	T;T	0.23754	1.89;1.89	4.57	3.66	0.41972	.	0.374745	0.22641	N	0.057448	T	0.07503	0.0189	L	0.36672	1.1	0.24227	N	0.995411	B;B	0.21071	0.051;0.028	B;B	0.12156	0.007;0.007	T	0.20371	-1.0277	10	0.38643	T	0.18	-9.3226	8.5325	0.33344	0.1831:0.0:0.8169:0.0	.	775;775	E7EP56;Q5VU65	.;P210L_HUMAN	V	775	ENSP00000357547:A775V;ENSP00000271854:A775V	ENSP00000271854:A775V	A	-	2	0	NUP210L	152328558	0.934000	0.31675	1.000000	0.80357	0.922000	0.55478	1.278000	0.33179	1.146000	0.42352	0.460000	0.39030	GCC		0.483	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		112	221	112	221
FCRL5	83416	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	157491079	157491079	+	Missense_Mutation	SNP	G	G	A	rs142943534		TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr1:157491079G>A	ENST00000361835.3	-	11	2400	c.2243C>T	c.(2242-2244)cCg>cTg	p.P748L	FCRL5_ENST00000356953.4_Missense_Mutation_p.P748L|FCRL5_ENST00000461387.1_5'UTR	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	748					negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				GCGAGACACCGGAACTGAAAG	0.498													g|||	1	0.000199681	0.0	0.0	5008	,	,		18236	0.0		0.0	False		,,,				2504	0.001															0								G	LEU/PRO,LEU/PRO	2,4400		0,2,2199	24.0	27.0	26.0		2243,2243	4.3	1.0	1	dbSNP_134	26	0,8596		0,0,4298	no	missense,missense	FCRL5	NM_001195388.1,NM_031281.2	98,98	0,2,6497	AA,AG,GG		0.0,0.0454,0.0154	benign,benign	748/999,748/978	157491079	2,12996	2201	4298	6499	SO:0001583	missense	83416			AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.2243C>T	1.37:g.157491079G>A	ENSP00000354691:p.Pro748Leu		A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Missense_Mutation	SNP	ENST00000361835.3	37	CCDS1165.1	.	.	.	.	.	.	.	.	.	.	G	8.706	0.910841	0.17833	4.54E-4	0.0	ENSG00000143297	ENST00000361835;ENST00000356953	T;T	0.56611	0.45;0.46	5.24	4.34	0.51931	Immunoglobulin-like fold (1);	1.319770	0.05694	N	0.592825	T	0.38054	0.1026	M	0.85859	2.78	0.80722	D	1	P;B	0.39044	0.656;0.001	B;B	0.26969	0.075;0.0	T	0.56153	-0.8026	10	0.34782	T	0.22	.	9.8551	0.41082	0.0924:0.0:0.9076:0.0	.	748;748	A6NJE8;Q96RD9	.;FCRL5_HUMAN	L	748	ENSP00000354691:P748L;ENSP00000349434:P748L	ENSP00000349434:P748L	P	-	2	0	FCRL5	155757703	1.000000	0.71417	0.996000	0.52242	0.079000	0.17450	2.662000	0.46766	1.441000	0.47550	-0.143000	0.13931	CCG		0.498	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281		13	63	13	63
ATP1A2	477	hgsc.bcm.edu;broad.mit.edu	37	1	160093040	160093040	+	Missense_Mutation	SNP	G	G	T			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr1:160093040G>T	ENST00000361216.3	+	4	304	c.215G>T	c.(214-216)cGa>cTa	p.R72L	ATP1A2_ENST00000392233.3_Missense_Mutation_p.R72L	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	72					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)	p.R72L(1)		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)			GTTCTGGCTCGAGATGGGCCC	0.642																																																1	Substitution - Missense(1)	kidney(1)											115.0	113.0	113.0					1																	160093040		2203	4300	6503	SO:0001583	missense	477			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.215G>T	1.37:g.160093040G>T	ENSP00000354490:p.Arg72Leu		D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Missense_Mutation	SNP	ENST00000361216.3	37	CCDS1196.1	.	.	.	.	.	.	.	.	.	.	G	12.92	2.081522	0.36758	.	.	ENSG00000018625	ENST00000361216;ENST00000392233	T;T	0.79653	-1.29;-1.29	5.1	5.1	0.69264	ATPase, P-type cation-transporter, N-terminal (2);	0.164660	0.40554	N	0.001076	T	0.71796	0.3382	M	0.75615	2.305	0.47778	D	0.999517	B	0.06786	0.001	B	0.17433	0.018	T	0.74551	-0.3628	10	0.72032	D	0.01	.	10.9404	0.47270	0.0861:0.0:0.9139:0.0	.	72	P50993	AT1A2_HUMAN	L	72	ENSP00000354490:R72L;ENSP00000376066:R72L	ENSP00000354490:R72L	R	+	2	0	ATP1A2	158359664	0.945000	0.32115	1.000000	0.80357	0.123000	0.20343	2.399000	0.44495	2.644000	0.89710	0.561000	0.74099	CGA		0.642	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		17	133	17	133
NCF2	4688	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	183543623	183543623	+	Splice_Site	SNP	C	C	T			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr1:183543623C>T	ENST00000367535.3	-	4	751	c.500G>A	c.(499-501)tGg>tAg	p.W167*	NCF2_ENST00000418089.1_Intron|NCF2_ENST00000413720.1_Intron|NCF2_ENST00000367536.1_Splice_Site_p.W167*	NM_000433.3	NP_000424.2	P19878	NCF2_HUMAN	neutrophil cytosolic factor 2	167					aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cellular response to hormone stimulus (GO:0032870)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron apoptotic process (GO:0043525)|respiratory burst (GO:0045730)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to hyperoxia (GO:0055093)|response to laminar fluid shear stress (GO:0034616)|response to lipopolysaccharide (GO:0032496)|response to progesterone (GO:0032570)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|NADPH oxidase complex (GO:0043020)|nucleolus (GO:0005730)|phagolysosome (GO:0032010)	electron carrier activity (GO:0009055)|protein C-terminus binding (GO:0008022)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30					Dextromethorphan(DB00514)	TACGCTTACCCAGACACACTC	0.463																																																0													346.0	317.0	327.0					1																	183543623		2203	4300	6503	SO:0001630	splice_region_variant	4688			BC001606	CCDS1356.1, CCDS53446.1, CCDS53447.1	1q25	2014-09-17	2008-07-31		ENSG00000116701	ENSG00000116701		"""Tetratricopeptide (TTC) repeat domain containing"""	7661	protein-coding gene	gene with protein product	"""NADPH oxidase activator 2"", ""chronic granulomatous disease, autosomal 2"""	608515	"""neutrophil cytosolic factor 2 (65kD, chronic granulomatous disease, autosomal 2)"""				Standard	NM_000433		Approved	p67phox, NOXA2	uc001gqk.4	P19878	OTTHUMG00000035329	ENST00000367535.3:c.501+1G>A	1.37:g.183543623C>T			B2R6Q1|B4DKQ7|B4DQA7|E9PHJ2|E9PHX3|Q2PP06|Q8NFC7|Q9BV51	Splice_Site	SNP	ENST00000367535.3	37	CCDS1356.1	.	.	.	.	.	.	.	.	.	.	C	38	6.688496	0.97764	.	.	ENSG00000116701	ENST00000367536;ENST00000392014;ENST00000367535	.	.	.	5.32	4.34	0.51931	.	0.060187	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	0.018	11.3984	0.49856	0.3173:0.6826:0.0:0.0	.	.	.	.	X	167;195;167	.	ENSP00000356505:W167X	W	-	2	0	NCF2	181810246	1.000000	0.71417	0.998000	0.56505	0.929000	0.56500	3.715000	0.54897	2.647000	0.89833	0.655000	0.94253	TGG		0.463	NCF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085483.1	NM_000433	Nonsense_Mutation	171	207	171	207
ESRRG	2104	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	216824353	216824353	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr1:216824353C>T	ENST00000408911.3	-	3	704	c.551G>A	c.(550-552)cGc>cAc	p.R184H	ESRRG_ENST00000366937.1_Missense_Mutation_p.R189H|ESRRG_ENST00000463665.1_Intron|ESRRG_ENST00000359162.2_Missense_Mutation_p.R161H|ESRRG_ENST00000487276.1_Missense_Mutation_p.R161H|ESRRG_ENST00000391890.3_Missense_Mutation_p.R161H|ESRRG_ENST00000361395.2_Missense_Mutation_p.R161H|ESRRG_ENST00000493603.1_Missense_Mutation_p.R161H|ESRRG_ENST00000360012.3_Missense_Mutation_p.R161H|ESRRG_ENST00000361525.3_Missense_Mutation_p.R161H|ESRRG_ENST00000366940.2_Missense_Mutation_p.R161H|ESRRG_ENST00000493748.1_Missense_Mutation_p.R161H|ESRRG_ENST00000366938.2_Missense_Mutation_p.R161H	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma	184					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)	CTTCATGAAGCGGCAAGCCTG	0.448																																																0													139.0	132.0	134.0					1																	216824353		2203	4300	6503	SO:0001583	missense	2104			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.551G>A	1.37:g.216824353C>T	ENSP00000386171:p.Arg184His		A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	Missense_Mutation	SNP	ENST00000408911.3	37	CCDS41468.1	.	.	.	.	.	.	.	.	.	.	C	35	5.452979	0.96223	.	.	ENSG00000196482	ENST00000361525;ENST00000366940;ENST00000366937;ENST00000408911;ENST00000359162;ENST00000361395;ENST00000366938;ENST00000360012;ENST00000493603;ENST00000391890;ENST00000487276;ENST00000354407;ENST00000493748;ENST00000475275	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;-5.3	5.74	5.74	0.90152	Zinc finger, NHR/GATA-type (1);Nuclear hormone receptor, ligand-binding (1);Zinc finger, nuclear hormone receptor-type (4);	0.000000	0.85682	D	0.000000	D	0.99667	0.9876	H	0.98866	4.355	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.81914	0.989;0.995	D	0.97420	1.0008	10	0.87932	D	0	.	19.9295	0.97114	0.0:1.0:0.0:0.0	.	189;184	F8W8J3;P62508	.;ERR3_HUMAN	H	161;161;189;184;161;161;161;161;161;161;161;161;161;161	ENSP00000355225:R161H;ENSP00000355907:R161H;ENSP00000355904:R189H;ENSP00000386171:R184H;ENSP00000352077:R161H;ENSP00000354584:R161H;ENSP00000355905:R161H;ENSP00000353108:R161H;ENSP00000419594:R161H;ENSP00000375761:R161H;ENSP00000419155:R161H;ENSP00000417374:R161H;ENSP00000419514:R161H	ENSP00000346386:R161H	R	-	2	0	ESRRG	214890976	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.770000	0.85390	2.695000	0.91970	0.655000	0.94253	CGC		0.448	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	NM_206595		30	163	30	163
CYP24A1	1591	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	20	52779339	52779339	+	Missense_Mutation	SNP	A	A	T			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr20:52779339A>T	ENST00000216862.3	-	7	1300	c.907T>A	c.(907-909)Tgt>Agt	p.C303S	CYP24A1_ENST00000395954.3_Missense_Mutation_p.C161S|CYP24A1_ENST00000395955.3_Missense_Mutation_p.C303S	NM_000782.4	NP_000773.2	Q07973	CP24A_HUMAN	cytochrome P450, family 24, subfamily A, polypeptide 1	303					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)	TAAATGTCACAAAGGAAATCT	0.463																																																0													88.0	81.0	83.0					20																	52779339		2203	4300	6503	SO:0001583	missense	1591			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.907T>A	20.37:g.52779339A>T	ENSP00000216862:p.Cys303Ser		Q15807|Q32ML3|Q5I2W7	Missense_Mutation	SNP	ENST00000216862.3	37	CCDS33491.1	.	.	.	.	.	.	.	.	.	.	A	14.74	2.626026	0.46840	.	.	ENSG00000019186	ENST00000216862;ENST00000395955;ENST00000395954	T;T;T	0.76448	0.26;5.33;-1.02	5.6	1.89	0.25635	.	0.217638	0.49305	D	0.000159	T	0.68081	0.2962	N	0.05487	-0.04	0.39313	D	0.965102	B;B;B	0.33904	0.431;0.128;0.207	P;P;P	0.51657	0.676;0.449;0.449	T	0.58109	-0.7694	10	0.20046	T	0.44	-0.0974	8.0171	0.30387	0.6084:0.2649:0.0:0.1267	.	303;303;161	Q32ML3;Q07973;Q5I2W7	.;CP24A_HUMAN;.	S	303;303;161	ENSP00000216862:C303S;ENSP00000379285:C303S;ENSP00000379284:C161S	ENSP00000216862:C303S	C	-	1	0	CYP24A1	52212746	0.964000	0.33143	0.050000	0.19076	0.842000	0.47809	3.580000	0.53907	0.037000	0.15575	0.533000	0.62120	TGT		0.463	CYP24A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079769.2			53	57	53	57
MICALL1	85377	hgsc.bcm.edu;broad.mit.edu	37	22	38323452	38323452	+	Silent	SNP	G	G	A	rs201808090		TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr22:38323452G>A	ENST00000215957.6	+	9	1626	c.1500G>A	c.(1498-1500)ccG>ccA	p.P500P	MICALL1_ENST00000402631.1_3'UTR	NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	500	Pro-rich.				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)					ACTCGGAGCCGCCCTCGGCCA	0.687													G|||	1	0.000199681	0.0	0.0	5008	,	,		15497	0.001		0.0	False		,,,				2504	0.0															0													27.0	26.0	26.0					22																	38323452		2203	4300	6503	SO:0001819	synonymous_variant	85377			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.1500G>A	22.37:g.38323452G>A			Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Silent	SNP	ENST00000215957.6	37	CCDS13961.1	.	.	.	.	.	.	.	.	.	.	G	10.10	1.257948	0.22965	.	.	ENSG00000100139	ENST00000454685	.	.	.	4.92	-9.83	0.00482	.	.	.	.	.	T	0.31544	0.0800	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39761	-0.9598	4	.	.	.	.	1.1106	0.01704	0.2932:0.1484:0.3289:0.2296	.	.	.	.	T	78	.	.	A	+	1	0	MICALL1	36653398	0.005000	0.15991	0.834000	0.33040	0.909000	0.53808	-1.855000	0.01663	-1.772000	0.01292	-0.477000	0.04895	GCC		0.687	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386		13	19	13	19
REG3G	130120	hgsc.bcm.edu;broad.mit.edu	37	2	79253917	79253917	+	Missense_Mutation	SNP	A	A	G			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr2:79253917A>G	ENST00000272324.5	+	3	339	c.155A>G	c.(154-156)tAt>tGt	p.Y52C	REG3G_ENST00000393897.2_Missense_Mutation_p.Y52C|REG3G_ENST00000409471.1_Missense_Mutation_p.Y52C	NM_001008387.2	NP_001008388.1	Q6UW15	REG3G_HUMAN	regenerating islet-derived 3 gamma	52	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				acute-phase response (GO:0006953)|defense response to Gram-positive bacterium (GO:0050830)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of keratinocyte differentiation (GO:0045617)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of wound healing (GO:0090303)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(27)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TCCCCCTGCTATGCCTTGTTT	0.542																																																0													90.0	88.0	89.0					2																	79253917		2203	4300	6503	SO:0001583	missense	130120			AY359047	CCDS1962.1, CCDS58714.1	2p12	2005-02-11			ENSG00000143954	ENSG00000143954			29595	protein-coding gene	gene with protein product		609933				12975309	Standard	NM_001008387		Approved	UNQ429, LPPM429, PAP1B	uc002snx.4	Q6UW15	OTTHUMG00000130018	ENST00000272324.5:c.155A>G	2.37:g.79253917A>G	ENSP00000272324:p.Tyr52Cys		A8K980|D6W5J6|Q3SYE4|Q3SYE6|Q6FH18	Missense_Mutation	SNP	ENST00000272324.5	37	CCDS1962.1	.	.	.	.	.	.	.	.	.	.	A	14.54	2.564516	0.45694	.	.	ENSG00000143954	ENST00000393897;ENST00000272324;ENST00000409471	T;T;T	0.42513	2.45;2.45;0.97	4.84	3.69	0.42338	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.000000	0.49305	D	0.000148	T	0.73377	0.3579	H	0.98178	4.165	0.33860	D	0.633651	D;D	0.89917	1.0;0.96	D;P	0.97110	1.0;0.711	T	0.82123	-0.0613	10	0.87932	D	0	.	7.3818	0.26859	0.9026:0.0:0.0974:0.0	.	52;52	Q3SYE6;Q6UW15	.;REG3G_HUMAN	C	52	ENSP00000377475:Y52C;ENSP00000272324:Y52C;ENSP00000387105:Y52C	ENSP00000272324:Y52C	Y	+	2	0	REG3G	79107425	1.000000	0.71417	1.000000	0.80357	0.489000	0.33432	2.406000	0.44557	0.993000	0.38866	0.533000	0.62120	TAT		0.542	REG3G-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328247.1	NM_198448		14	26	14	26
SPOPL	339745	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	139308482	139308482	+	Silent	SNP	G	G	A	rs369405867		TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr2:139308482G>A	ENST00000280098.4	+	4	589	c.210G>A	c.(208-210)agG>agA	p.R70R		NM_001001664.2	NP_001001664.1	Q6IQ16	SPOPL_HUMAN	speckle-type POZ protein-like	70	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)		GGTGCCTGAGGGTAAACCCAA	0.378																																																0								G		0,4406		0,0,2203	80.0	84.0	83.0		210	3.8	1.0	2		83	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	SPOPL	NM_001001664.2		0,1,6501	AA,AG,GG		0.0116,0.0,0.0077		70/393	139308482	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	339745				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.210G>A	2.37:g.139308482G>A				Silent	SNP	ENST00000280098.4	37	CCDS33298.1																																																																																				0.378	SPOPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331897.1			35	174	35	174
ITGA6	3655	hgsc.bcm.edu;ucsc.edu	37	2	173366600	173366600	+	Intron	SNP	A	A	T			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr2:173366600A>T	ENST00000264106.6	+	26	3434				ITGA6_ENST00000264107.7_Missense_Mutation_p.D1072V|ITGA6_ENST00000375221.2_Missense_Mutation_p.D1111V|AC093818.1_ENST00000442417.1_RNA|ITGA6_ENST00000409532.1_Missense_Mutation_p.D953V|AC093818.1_ENST00000450443.1_RNA|ITGA6_ENST00000409080.1_Intron|ITGA6_ENST00000343713.4_Missense_Mutation_p.D1067V			P23229	ITA6_HUMAN	integrin, alpha 6						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)			CTTACTTCTGATGCATAGTAT	0.383																																																0													122.0	114.0	117.0					2																	173366600		2203	4300	6503	SO:0001627	intron_variant	3655				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.3232-2219A>T	2.37:g.173366600A>T			B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Missense_Mutation	SNP	ENST00000264106.6	37		.	.	.	.	.	.	.	.	.	.	A	24.2	4.510609	0.85389	.	.	ENSG00000091409	ENST00000409532;ENST00000264107;ENST00000375221;ENST00000343713	T;T;T;T	0.71461	-0.24;-0.57;-0.56;-0.57	6.04	6.04	0.98038	.	.	.	.	.	D	0.83811	0.5335	.	.	.	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.66351	0.943;0.943;0.943	D	0.85810	0.1379	8	0.87932	D	0	.	16.5885	0.84745	1.0:0.0:0.0:0.0	.	1067;1096;1072	P23229-4;P23229-9;P23229-2	.;.;.	V	953;1072;1111;1067	ENSP00000386614:D953V;ENSP00000264107:D1072V;ENSP00000364369:D1111V;ENSP00000341078:D1067V	ENSP00000264107:D1072V	D	+	2	0	ITGA6	173074846	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.720000	0.91442	2.317000	0.78254	0.460000	0.39030	GAT		0.383	ITGA6-201	KNOWN	basic	protein_coding	protein_coding				22	100	22	100
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			65	71	65	71
SUMF1	285362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	4491010	4491010	+	Silent	SNP	G	G	A	rs148557574		TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr3:4491010G>A	ENST00000272902.5	-	3	494	c.459C>T	c.(457-459)ggC>ggT	p.G153G	SUMF1_ENST00000405420.2_Silent_p.G153G|SUMF1_ENST00000458465.2_Intron|SUMF1_ENST00000383843.5_Intron|SUMF1_ENST00000534863.1_Silent_p.G153G	NM_182760.3	NP_877437.2	Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1	153					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)		CAAAGGAGTCGCCAAACTTCT	0.403																																																0								G	,,	0,4406		0,0,2203	126.0	127.0	127.0		,459,459	-8.4	0.7	3	dbSNP_134	127	1,8599	1.2+/-3.3	0,1,4299	no	intron,coding-synonymous,coding-synonymous	SUMF1	NM_001164674.1,NM_001164675.1,NM_182760.3	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	,153/355,153/375	4491010	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	285362			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.459C>T	3.37:g.4491010G>A			B4DXK5|B7XD05|E9PGL0|G5E9B0|Q0VAC6|Q0VAC7|Q2NL78|Q53ZE4|Q6UY39|Q96AK5|Q96DK8	Silent	SNP	ENST00000272902.5	37	CCDS2564.1																																																																																				0.403	SUMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206591.2	NM_182760		114	163	114	163
RBM6	10180	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	50099412	50099412	+	Silent	SNP	C	C	T	rs200245501		TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr3:50099412C>T	ENST00000266022.4	+	15	2716	c.2457C>T	c.(2455-2457)ccC>ccT	p.P819P	RBM6_ENST00000539992.1_Silent_p.P161P|RBM6_ENST00000422955.1_Silent_p.P297P|RBM6_ENST00000441115.1_3'UTR|RBM6_ENST00000443081.1_Silent_p.P687P|RBM6_ENST00000442092.1_Silent_p.P297P	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	819					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)		TCTATGTGCCCCAGGATCCTG	0.438																																																0													83.0	79.0	80.0					3																	50099412		2203	4300	6503	SO:0001819	synonymous_variant	10180			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.2457C>T	3.37:g.50099412C>T			O60549|O75524|Q86SS3	Silent	SNP	ENST00000266022.4	37	CCDS2809.1																																																																																				0.438	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777		20	47	20	47
MCCC1	56922	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	182759530	182759530	+	Silent	SNP	T	T	C			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr3:182759530T>C	ENST00000265594.4	-	11	1238	c.1092A>G	c.(1090-1092)gcA>gcG	p.A364A	MCCC1_ENST00000539926.1_Silent_p.A229A|MCCC1_ENST00000492597.1_Silent_p.A255A	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	364	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)	TCTTCTCTCCTGCTGCAATCT	0.403																																																0													120.0	119.0	119.0					3																	182759530		2203	4300	6503	SO:0001819	synonymous_variant	56922			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.1092A>G	3.37:g.182759530T>C			Q59ES4|Q9H959|Q9NS97	Silent	SNP	ENST00000265594.4	37	CCDS3241.1																																																																																				0.403	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166		92	129	92	129
LRCH3	84859	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	197559180	197559180	+	Missense_Mutation	SNP	A	A	G			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr3:197559180A>G	ENST00000425562.2	+	8	1094	c.1094A>G	c.(1093-1095)aAc>aGc	p.N365S	LRCH3_ENST00000438796.2_Missense_Mutation_p.N365S|LRCH3_ENST00000441090.2_Missense_Mutation_p.N239S|AC055764.1_ENST00000454526.1_RNA|LRCH3_ENST00000536618.1_5'UTR|LRCH3_ENST00000334859.4_Missense_Mutation_p.N365S|LRCH3_ENST00000414675.2_Missense_Mutation_p.N365S			Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 3	365						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)		GTAGTAACAAACGGCGGAGGT	0.408																																																0													69.0	66.0	67.0					3																	197559180		2203	4300	6503	SO:0001583	missense	84859			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.1094A>G	3.37:g.197559180A>G	ENSP00000393579:p.Asn365Ser		B4E0T7|Q96FP9|Q9NT52	Missense_Mutation	SNP	ENST00000425562.2	37		.	.	.	.	.	.	.	.	.	.	A	13.21	2.169946	0.38315	.	.	ENSG00000186001	ENST00000438796;ENST00000441090;ENST00000414675;ENST00000334859;ENST00000425562	T;T;T;T;T	0.30981	2.1;1.51;2.09;2.35;2.12	5.51	5.51	0.81932	.	0.224712	0.43747	D	0.000523	T	0.35038	0.0918	L	0.32530	0.975	0.80722	D	1	P;D;P;P	0.54047	0.925;0.964;0.708;0.941	B;P;B;P	0.53760	0.288;0.683;0.382;0.734	T	0.03807	-1.1002	10	0.17369	T	0.5	-20.1289	15.6494	0.77078	1.0:0.0:0.0:0.0	.	239;365;365;365	E9PD99;B4E0T7;Q96II8-2;Q96II8-3	.;.;.;.	S	365;239;365;365;365	ENSP00000399751:N365S;ENSP00000394609:N239S;ENSP00000394965:N365S;ENSP00000334375:N365S;ENSP00000393579:N365S	ENSP00000334375:N365S	N	+	2	0	LRCH3	199043577	1.000000	0.71417	0.999000	0.59377	0.341000	0.28922	5.381000	0.66208	2.101000	0.63845	0.477000	0.44152	AAC		0.408	LRCH3-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000339965.1	NM_032773		18	70	18	70
KIAA1109	84162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	123192264	123192264	+	Missense_Mutation	SNP	G	G	A	rs375646084		TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr4:123192264G>A	ENST00000264501.4	+	47	7958	c.7585G>A	c.(7585-7587)Gtg>Atg	p.V2529M	KIAA1109_ENST00000388738.3_Missense_Mutation_p.V2529M|KIAA1109_ENST00000455637.1_Missense_Mutation_p.V2529M			Q2LD37	K1109_HUMAN	KIAA1109	2529					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						GGAAAAGTCCGTGTGCACCCC	0.438													G|||	1	0.000199681	0.0	0.0	5008	,	,		17939	0.0		0.0	False		,,,				2504	0.001															0								G	MET/VAL	2,3778		0,2,1888	97.0	97.0	97.0		7585	3.8	0.9	4		97	0,8224		0,0,4112	no	missense	KIAA1109	NM_015312.3	21	0,2,6000	AA,AG,GG		0.0,0.0529,0.0167	benign	2529/5006	123192264	2,12002	1890	4112	6002	SO:0001583	missense	84162			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.7585G>A	4.37:g.123192264G>A	ENSP00000264501:p.Val2529Met		Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.46|11.46	1.645217|1.645217	0.29246|0.29246	5.29E-4|5.29E-4	0.0|0.0	ENSG00000138688|ENSG00000138688	ENST00000419325|ENST00000264501;ENST00000388738;ENST00000455637	.|T;T;T	.|0.23754	.|2.48;2.48;1.89	5.82|5.82	3.85|3.85	0.44370|0.44370	.|.	.|0.368951	.|0.21618	.|U	.|0.071695	T|T	0.10551|0.10551	0.0258|0.0258	N|N	0.03608|0.03608	-0.345|-0.345	0.22342|0.22342	N|N	0.999181|0.999181	.|B;B;B	.|0.12013	.|0.001;0.005;0.002	.|B;B;B	.|0.06405	.|0.002;0.002;0.001	T|T	0.14337|0.14337	-1.0476|-1.0476	5|10	.|0.44086	.|T	.|0.13	.|.	6.719|6.719	0.23321|0.23321	0.3466:0.0:0.6534:0.0|0.3466:0.0:0.6534:0.0	.|.	.|2529;2528;2529	.|Q2LD37-6;Q2LD37-2;Q2LD37	.|.;.;K1109_HUMAN	H|M	486|2529	.|ENSP00000264501:V2529M;ENSP00000373390:V2529M;ENSP00000389925:V2529M	.|ENSP00000264501:V2529M	R|V	+|+	2|1	0|0	KIAA1109|KIAA1109	123411714|123411714	0.992000|0.992000	0.36948|0.36948	0.885000|0.885000	0.34714|0.34714	0.933000|0.933000	0.57130|0.57130	2.684000|2.684000	0.46951|0.46951	1.468000|1.468000	0.48064|0.48064	0.467000|0.467000	0.42956|0.42956	CGT|GTG		0.438	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		52	147	52	147
PIK3R1	5295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	67589138	67589138	+	Missense_Mutation	SNP	G	G	A			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr5:67589138G>A	ENST00000521381.1	+	10	1742	c.1126G>A	c.(1126-1128)Gga>Aga	p.G376R	PIK3R1_ENST00000396611.1_Missense_Mutation_p.G376R|PIK3R1_ENST00000523872.1_Missense_Mutation_p.G13R|PIK3R1_ENST00000320694.8_Missense_Mutation_p.G76R|PIK3R1_ENST00000336483.5_Missense_Mutation_p.G106R|PIK3R1_ENST00000521657.1_Missense_Mutation_p.G376R|PIK3R1_ENST00000274335.5_Missense_Mutation_p.G376R	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	376	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.G376R(5)|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)	CAGGAAAGGGGGAAATAACAA	0.308			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																													Rec	yes		5	5q13.1	5295	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""		"""E, O"""	7	Substitution - Missense(5)|Whole gene deletion(1)|Unknown(1)	central_nervous_system(5)|large_intestine(1)|lung(1)											52.0	58.0	56.0					5																	67589138		2189	4295	6484	SO:0001583	missense	5295			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.1126G>A	5.37:g.67589138G>A	ENSP00000428056:p.Gly376Arg		B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Missense_Mutation	SNP	ENST00000521381.1	37	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.990536	0.93106	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000523807;ENST00000320694;ENST00000521409;ENST00000336483;ENST00000519025;ENST00000523872	T;T;T;T;D;T;T;T;T;T	0.96716	-0.18;-0.18;-0.18;-0.18;-4.1;-0.18;-0.18;-0.18;-0.18;-0.18	5.2	5.2	0.72013	SH2 motif (4);	0.000000	0.85682	D	0.000000	D	0.98153	0.9390	M	0.79926	2.475	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;0.999;1.0	D	0.98655	1.0681	10	0.87932	D	0	-27.7511	19.2944	0.94117	0.0:0.0:1.0:0.0	.	46;106;76;376	B7Z2N8;P27986-2;P27986-3;P27986	.;.;.;P85A_HUMAN	R	376;376;376;376;106;76;13;106;49;13	ENSP00000428056:G376R;ENSP00000429277:G376R;ENSP00000379855:G376R;ENSP00000274335:G376R;ENSP00000430126:G106R;ENSP00000323512:G76R;ENSP00000431058:G13R;ENSP00000338554:G106R;ENSP00000429156:G49R;ENSP00000430098:G13R	ENSP00000274335:G376R	G	+	1	0	PIK3R1	67624894	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.601000	0.98297	2.868000	0.98415	0.555000	0.69702	GGA		0.308	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		41	74	41	74
PCDHB3	56132	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	140481839	140481839	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr5:140481839C>T	ENST00000231130.2	+	1	1606	c.1606C>T	c.(1606-1608)Cgt>Tgt	p.R536C	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	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)			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)			CGCCACAGACCGTGGCTCCCC	0.672																																																0													60.0	63.0	62.0					5																	140481839		2203	4296	6499	SO:0001583	missense	56132			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.1606C>T	5.37:g.140481839C>T	ENSP00000231130:p.Arg536Cys		B2R8P2	Missense_Mutation	SNP	ENST00000231130.2	37	CCDS4245.1	.	.	.	.	.	.	.	.	.	.	C	9.405	1.078948	0.20227	.	.	ENSG00000113205	ENST00000231130	T	0.01767	4.65	4.14	1.24	0.21308	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.04092	0.0114	L	0.33485	1.01	0.20638	N	0.999875	D	0.63046	0.992	P	0.62491	0.903	T	0.45056	-0.9287	9	0.62326	D	0.03	.	8.0177	0.30391	0.2089:0.375:0.4161:0.0	.	536	Q9Y5E6	PCDB3_HUMAN	C	536	ENSP00000231130:R536C	ENSP00000231130:R536C	R	+	1	0	PCDHB3	140462023	0.002000	0.14202	0.093000	0.20910	0.008000	0.06430	0.439000	0.21575	-0.029000	0.13827	0.650000	0.86243	CGT		0.672	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		21	67	21	67
PCDHGA1	56114	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	140711827	140711827	+	Missense_Mutation	SNP	C	C	T	rs547369283	byFrequency	TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr5:140711827C>T	ENST00000517417.1	+	1	1576	c.1576C>T	c.(1576-1578)Cgg>Tgg	p.R526W	AC005618.6_ENST00000606901.1_lincRNA|PCDHGA1_ENST00000378105.3_Missense_Mutation_p.R526W	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	526	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)			TGAGCAGTTCCGGGACATGCA	0.587													C|||	4	0.000798722	0.0	0.0	5008	,	,		19147	0.0		0.0	False		,,,				2504	0.0041															0													185.0	196.0	192.0					5																	140711827		2203	4300	6503	SO:0001583	missense	56114			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.1576C>T	5.37:g.140711827C>T	ENSP00000431083:p.Arg526Trp		Q2M273|Q9Y5D6	Missense_Mutation	SNP	ENST00000517417.1	37	CCDS54922.1	.	.	.	.	.	.	.	.	.	.	C	6.055	0.378515	0.11466	.	.	ENSG00000204956	ENST00000517417;ENST00000378105	T;T	0.61627	0.09;0.09	3.82	1.97	0.26223	Cadherin (5);Cadherin-like (1);	0.978321	0.08324	N	0.963336	T	0.67534	0.2903	H	0.95004	3.61	0.09310	N	1	P;P	0.39696	0.683;0.589	B;B	0.39503	0.218;0.301	T	0.60717	-0.7208	10	0.87932	D	0	.	6.1503	0.20308	0.3276:0.5824:0.0:0.09	.	526;526	Q9Y5H4-2;Q9Y5H4	.;PCDG1_HUMAN	W	526	ENSP00000431083:R526W;ENSP00000367345:R526W	ENSP00000367345:R526W	R	+	1	2	PCDHGA1	140692011	0.000000	0.05858	0.277000	0.24703	0.063000	0.16089	0.236000	0.17967	0.374000	0.24650	0.557000	0.71058	CGG		0.587	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		76	288	76	288
GRPEL2	134266	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	148727842	148727842	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr5:148727842C>T	ENST00000329271.3	+	2	195	c.85C>T	c.(85-87)Ccg>Tcg	p.P29S	GRPEL2_ENST00000416916.2_Missense_Mutation_p.P29S|GRPEL2_ENST00000513661.1_Missense_Mutation_p.P29S|GRPEL2-AS1_ENST00000521295.1_RNA|GRPEL2_ENST00000507562.1_3'UTR	NM_152407.3	NP_689620.2	Q8TAA5	GRPE2_HUMAN	GrpE-like 2, mitochondrial (E. coli)	29					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)			TAGGGGATGGCCGCTTCCATT	0.517																																																0													79.0	78.0	78.0					5																	148727842		2203	4300	6503	SO:0001583	missense	134266			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.85C>T	5.37:g.148727842C>T	ENSP00000329558:p.Pro29Ser		B4DFA6|Q49AJ6	Missense_Mutation	SNP	ENST00000329271.3	37	CCDS4295.1	.	.	.	.	.	.	.	.	.	.	C	12.50	1.956846	0.34565	.	.	ENSG00000164284	ENST00000513661;ENST00000329271;ENST00000416916	.	.	.	5.77	3.83	0.44106	.	0.713016	0.11979	N	0.510975	T	0.16642	0.0400	N	0.08118	0	0.09310	N	1	B;B	0.13145	0.007;0.001	B;B	0.13407	0.009;0.002	T	0.18085	-1.0348	9	0.13108	T	0.6	-0.1598	7.0153	0.24885	0.1366:0.6717:0.1188:0.0728	.	29;29	B4DFA6;Q8TAA5	.;GRPE2_HUMAN	S	29	.	ENSP00000329558:P29S	P	+	1	0	GRPEL2	148708035	0.922000	0.31269	0.904000	0.35570	0.057000	0.15508	1.781000	0.38644	2.732000	0.93576	0.561000	0.74099	CCG		0.517	GRPEL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252327.1	NM_152407		31	114	31	114
NEDD9	4739	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	11190997	11190997	+	Missense_Mutation	SNP	A	A	G			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr6:11190997A>G	ENST00000379446.5	-	5	1271	c.1105T>C	c.(1105-1107)Tct>Cct	p.S369P	RP3-510L9.1_ENST00000500636.2_RNA|NEDD9_ENST00000504387.1_Missense_Mutation_p.S369P	NM_001271033.1|NM_006403.3	NP_001257962.1|NP_006394.1	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally down-regulated 9	369					actin filament bundle assembly (GO:0051017)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|integrin-mediated signaling pathway (GO:0007229)|mitotic nuclear division (GO:0007067)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle pole (GO:0000922)				endometrium(3)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)			CTGGAGAAAGACAATCGGTTG	0.547																																																0													91.0	76.0	81.0					6																	11190997		2203	4300	6503	SO:0001583	missense	4739			L43821	CCDS4520.1, CCDS34340.1, CCDS47373.1, CCDS75400.1	6p25-p24	2011-04-13			ENSG00000111859	ENSG00000111859		"""Cas scaffolding proteins"""	7733	protein-coding gene	gene with protein product	"""Cas scaffolding protein family member 2"", ""Cas-like"""	602265					Standard	NM_182966		Approved	HEF1, CAS-L, CASS2	uc003mzv.2	Q14511	OTTHUMG00000014255	ENST00000379446.5:c.1105T>C	6.37:g.11190997A>G	ENSP00000368759:p.Ser369Pro		A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	Missense_Mutation	SNP	ENST00000379446.5	37	CCDS4520.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.517491	0.85495	.	.	ENSG00000111859	ENST00000379446;ENST00000504387	T;T	0.52983	0.64;0.75	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.64505	0.2604	M	0.81341	2.54	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.996;0.997;0.987	T	0.66626	-0.5876	10	0.44086	T	0.13	-20.8574	16.3662	0.83325	1.0:0.0:0.0:0.0	.	369;369;369	G5E9Y9;A8K9G7;Q14511	.;.;CASL_HUMAN	P	369	ENSP00000368759:S369P;ENSP00000422871:S369P	ENSP00000368759:S369P	S	-	1	0	NEDD9	11298983	1.000000	0.71417	0.662000	0.29724	0.933000	0.57130	8.962000	0.93254	2.274000	0.75844	0.533000	0.62120	TCT		0.547	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039853.2	NM_006403		62	64	62	64
PAQR8	85315	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	52268301	52268301	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr6:52268301C>T	ENST00000442253.2	+	2	464	c.290C>T	c.(289-291)gCc>gTc	p.A97V	PAQR8_ENST00000360726.3_Missense_Mutation_p.A97V	NM_133367.4	NP_588608.1	Q8TEZ7	MPRB_HUMAN	progestin and adipoQ receptor family member VIII	97					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)			endometrium(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|skin(1)|urinary_tract(2)	17	Lung NSC(77;0.0875)					TGGGCCTTTGCCGAGGCTGAG	0.572																																																0													74.0	70.0	72.0					6																	52268301		2203	4300	6503	SO:0001583	missense	85315			AF347029	CCDS4941.1	6p12	2012-08-10	2005-05-20	2005-05-20	ENSG00000170915	ENSG00000170915			15708	protein-coding gene	gene with protein product		607780	"""chromosome 6 open reading frame 33"""	C6orf33		11676489, 12574519	Standard	NM_133367		Approved	LMPB1, MPRB	uc003pao.4	Q8TEZ7	OTTHUMG00000014846	ENST00000442253.2:c.290C>T	6.37:g.52268301C>T	ENSP00000406197:p.Ala97Val		B2RCF6|Q86WL0|Q8N6D3|Q9HD02	Missense_Mutation	SNP	ENST00000442253.2	37	CCDS4941.1	.	.	.	.	.	.	.	.	.	.	C	3.101	-0.184817	0.06340	.	.	ENSG00000170915	ENST00000512121;ENST00000442253;ENST00000360726	T;T;T	0.44482	0.92;1.67;1.67	5.17	3.33	0.38152	.	0.416266	0.24881	N	0.034847	T	0.07188	0.0182	N	0.11255	0.115	0.09310	N	1	B	0.10296	0.003	B	0.19666	0.026	T	0.38735	-0.9647	10	0.17369	T	0.5	-3.5338	6.4141	0.21708	0.0:0.5804:0.0:0.4196	.	97	Q8TEZ7	MPRB_HUMAN	V	97	ENSP00000427161:A97V;ENSP00000406197:A97V;ENSP00000353953:A97V	ENSP00000353953:A97V	A	+	2	0	PAQR8	52376260	0.011000	0.17503	0.119000	0.21687	0.770000	0.43624	0.560000	0.23500	0.529000	0.28599	0.563000	0.77884	GCC		0.572	PAQR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040903.2	NM_133367		17	71	17	71
SIM1	6492	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	100841631	100841631	+	Silent	SNP	G	G	A			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr6:100841631G>A	ENST00000369208.3	-	11	2084	c.1302C>T	c.(1300-1302)tgC>tgT	p.C434C	SIM1_ENST00000262901.4_Silent_p.C434C			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	434	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.				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)		GTCTGTAGGCGCACGATGCGT	0.617																																																0													74.0	70.0	71.0					6																	100841631		2203	4300	6503	SO:0001819	synonymous_variant	6492			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.1302C>T	6.37:g.100841631G>A			Q5TDP7	Silent	SNP	ENST00000369208.3	37	CCDS5045.1																																																																																				0.617	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068		21	75	21	75
JAK2	3717	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	5090496	5090496	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr9:5090496C>T	ENST00000381652.3	+	21	3306	c.2812C>T	c.(2812-2814)Cga>Tga	p.R938*	JAK2_ENST00000544510.1_Nonsense_Mutation_p.R789*|JAK2_ENST00000539801.1_Nonsense_Mutation_p.R938*	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	938	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)	TGGAAGTTTACGAGACTATCT	0.313		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial																														Dom	yes		9	9p24	3717	Janus kinase 2		L	0													83.0	88.0	87.0					9																	5090496		2201	4295	6496	SO:0001587	stop_gained	3717	Familial Cancer Database			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.2812C>T	9.37:g.5090496C>T	ENSP00000371067:p.Arg938*		O14636|O75297	Nonsense_Mutation	SNP	ENST00000381652.3	37	CCDS6457.1	.	.	.	.	.	.	.	.	.	.	C	44	10.558137	0.99427	.	.	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	.	.	.	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.8476	18.9148	0.92501	0.0:1.0:0.0:0.0	.	.	.	.	X	938;938;789	.	ENSP00000371067:R938X	R	+	1	2	JAK2	5080496	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.952000	0.49097	2.463000	0.83235	0.591000	0.81541	CGA		0.313	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			111	22	111	22
CKS2	1164	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	91926227	91926227	+	Missense_Mutation	SNP	A	A	G			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr9:91926227A>G	ENST00000314355.6	+	1	115	c.20A>G	c.(19-21)tAc>tGc	p.Y7C	MIR3153_ENST00000580744.1_RNA	NM_001827.1	NP_001818.1	P33552	CKS2_HUMAN	CDC28 protein kinase regulatory subunit 2	7					cell proliferation (GO:0008283)|meiosis I (GO:0007127)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)		cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			kidney(1)|large_intestine(1)	2						AAGCAGATCTACTACTCGGAC	0.642																																																0													44.0	40.0	41.0					9																	91926227		2202	4300	6502	SO:0001583	missense	1164			X54942	CCDS6682.1	9q22	2008-02-05	2002-10-07		ENSG00000123975	ENSG00000123975			2000	protein-coding gene	gene with protein product		116901	"""CDC28 protein kinase 2"""			2227411, 8697818	Standard	NM_001827		Approved		uc004aqh.3	P33552	OTTHUMG00000020180	ENST00000314355.6:c.20A>G	9.37:g.91926227A>G	ENSP00000364976:p.Tyr7Cys		Q6FGI9|Q6LET5	Missense_Mutation	SNP	ENST00000314355.6	37	CCDS6682.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.816482	0.90790	.	.	ENSG00000123975	ENST00000314355	.	.	.	5.0	5.0	0.66597	.	0.000000	0.64402	D	0.000001	T	0.77089	0.4079	.	.	.	0.80722	D	1	D	0.76494	0.999	D	0.66847	0.947	T	0.78196	-0.2298	8	0.45353	T	0.12	0.9919	15.1544	0.72730	1.0:0.0:0.0:0.0	.	7	P33552	CKS2_HUMAN	C	7	.	ENSP00000364976:Y7C	Y	+	2	0	CKS2	91116047	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.371000	0.90123	2.227000	0.72691	0.459000	0.35465	TAC		0.642	CKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052988.1	NM_001827		16	20	16	20
RPL7A	6130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	136217156	136217156	+	Silent	SNP	C	C	T	rs142456845		TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr9:136217156C>T	ENST00000323345.6	+	5	507	c.477C>T	c.(475-477)caC>caT	p.H159H	SNORD36B_ENST00000363961.1_RNA|RPL7A_ENST00000315731.4_Silent_p.H44H|SURF1_ENST00000495952.1_5'Flank|RPL7A_ENST00000463740.1_3'UTR|MED22_ENST00000476080.1_5'Flank|SNORD24_ENST00000383884.1_RNA|MED22_ENST00000343730.5_5'Flank|MED22_ENST00000491289.1_5'Flank|MED22_ENST00000371999.1_5'Flank|MED22_ENST00000344469.5_5'Flank|SNORD36C_ENST00000516733.1_RNA|MED22_ENST00000471524.1_5'Flank|SNORD36A_ENST00000362874.1_RNA	NM_000972.2	NP_000963.1	P62424	RL7A_HUMAN	ribosomal protein L7a	159					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)		TGATTGCACACGACGTGGATC	0.522													C|||	1	0.000199681	0.0	0.0	5008	,	,		20771	0.0		0.001	False		,,,				2504	0.0															0													75.0	63.0	67.0					9																	136217156		2203	4300	6503	SO:0001819	synonymous_variant	6130			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.477C>T	9.37:g.136217156C>T			P11518|Q5T8U4	Silent	SNP	ENST00000323345.6	37	CCDS6965.1																																																																																				0.522	RPL7A-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054869.1	NM_000972		9	40	9	40
MAGEC1	9947	hgsc.bcm.edu;broad.mit.edu	37	X	140995929	140995929	+	Silent	SNP	C	C	T	rs370841892		TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chrX:140995929C>T	ENST00000285879.4	+	4	3025	c.2739C>T	c.(2737-2739)gaC>gaT	p.D913D	MAGEC1_ENST00000406005.2_5'UTR	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	913	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					AAAAGGTGGACGAGTTGGCGC	0.488										HNSCC(15;0.026)																																						0								C		1,3834		0,1,1631,571	170.0	168.0	169.0		2739	-1.7	0.0	X		169	0,6728		0,0,2428,1872	no	coding-synonymous	MAGEC1	NM_005462.4		0,1,4059,2443	TT,TC,CC,C		0.0,0.0261,0.0095		913/1143	140995929	1,10562	2203	4300	6503	SO:0001819	synonymous_variant	9947			AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.2739C>T	X.37:g.140995929C>T			A0PK03|O75451|Q8TCV4	Silent	SNP	ENST00000285879.4	37	CCDS35417.1																																																																																				0.488	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		12	200	12	200
SART1	9092	broad.mit.edu;ucsc.edu	37	11	65733982	65733982	+	Silent	SNP	A	A	G			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr11:65733982A>G	ENST00000312397.5	+	9	1235	c.1143A>G	c.(1141-1143)acA>acG	p.T381T		NM_005146.4	NP_005137.1	O43290	SNUT1_HUMAN	squamous cell carcinoma antigen recognized by T cells	381					cell cycle arrest (GO:0007050)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of cytotoxic T cell differentiation (GO:0045585)|spliceosomal snRNP assembly (GO:0000387)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						CCCTGAGCACAGTGGGGCCCC	0.677																																																0													16.0	17.0	17.0					11																	65733982		2199	4294	6493	SO:0001819	synonymous_variant	9092			AB006198	CCDS31611.1	11q13.1	2009-01-06	2006-12-07		ENSG00000175467	ENSG00000175467			10538	protein-coding gene	gene with protein product	"""small nuclear ribonucleoprotein 110kDa (U4/U6.U5)"""	605941	"""squamous cell carcinoma antigen recognised by T cells"""			9449708	Standard	NM_005146		Approved	Ara1, Snu66, SNRNP110	uc001ogl.3	O43290	OTTHUMG00000166771	ENST00000312397.5:c.1143A>G	11.37:g.65733982A>G			A6NDN1|Q53GB5	Silent	SNP	ENST00000312397.5	37	CCDS31611.1																																																																																				0.677	SART1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391409.1			5	15	5	15
TPST2	8459	broad.mit.edu;ucsc.edu	37	22	26937282	26937282	+	Silent	SNP	G	G	A	rs146078388	byFrequency	TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr22:26937282G>A	ENST00000338754.4	-	3	585	c.315C>T	c.(313-315)cgC>cgT	p.R105R	TPST2_ENST00000403880.1_Silent_p.R105R|TPST2_ENST00000398110.2_Silent_p.R105R	NM_003595.3	NP_003586.3	O60704	TPST2_HUMAN	tyrosylprotein sulfotransferase 2	105					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						TGGCCAGCACGCGCGGGATGA	0.706																																																0								G	,	0,4398		0,0,2199	27.0	24.0	25.0		315,315	0.1	1.0	22	dbSNP_134	25	7,8587		0,7,4290	no	coding-synonymous,coding-synonymous	TPST2	NM_001008566.1,NM_003595.3	,	0,7,6489	AA,AG,GG		0.0815,0.0,0.0539	,	105/378,105/378	26937282	7,12985	2199	4297	6496	SO:0001819	synonymous_variant	8459			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.315C>T	22.37:g.26937282G>A			B3KQA7|Q6FI98|Q9H0V4	Silent	SNP	ENST00000338754.4	37	CCDS13839.1																																																																																				0.706	TPST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320820.3	NM_003595		7	25	7	25
SNHG14	104472715	broad.mit.edu;ucsc.edu	37	15	25444675	25444675	+	RNA	SNP	C	C	A			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr15:25444675C>A	ENST00000424208.1	+	0	1811				SNORD115-16_ENST00000363887.1_RNA|SNHG14_ENST00000456576.1_RNA|SNORD115-15_ENST00000364809.1_RNA|SNHG14_ENST00000424333.1_RNA|SNORD115-17_ENST00000364612.1_RNA	NR_003305.1				small nucleolar RNA host gene 14 (non-protein coding)																		ACGCTGAGGCCCAGCCTAGGT	0.493																																																0													344.0	357.0	353.0					15																	25444675		876	1991	2867			104472715					15q11.2	2014-01-17	2011-08-22	2011-08-22	ENSG00000224078	ENSG00000224078		"""Long non-coding RNAs"""	37462	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 214"""		"""UBE3A antisense RNA 1 (non-protein coding)"""	UBE3A-AS1		23771028	Standard			Approved	NCRNA00214, UBE3A-AS			OTTHUMG00000056661		15.37:g.25444675C>A				RNA	SNP	ENST00000424208.1	37																																																																																					0.493	SNHG14-002	KNOWN	basic	antisense	processed_transcript	OTTHUMT00000126729.2			75	231	75	231
GPX6	257202	broad.mit.edu;ucsc.edu	37	6	28472105	28472105	+	Missense_Mutation	SNP	G	G	A			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr6:28472105G>A	ENST00000474923.1	-	4	573	c.530C>T	c.(529-531)aCa>aTa	p.T177I	GPX6_ENST00000483058.1_5'Flank|GPX6_ENST00000361902.1_Silent_p.D210D			P59796	GPX6_HUMAN	glutathione peroxidase 6 (olfactory)	0					response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)	glutathione peroxidase activity (GO:0004602)			NS(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19					Glutathione(DB00143)	ACTCCAGGATGTCTGACTTGA	0.502																																																0													151.0	146.0	148.0					6																	28472105		2051	4229	6280	SO:0001583	missense	257202				CCDS43432.1	6p22.1	2012-03-01			ENSG00000198704	ENSG00000198704	1.11.1.9		4558	protein-coding gene	gene with protein product		607913	"""glutathione peroxidase pseudogene 3"""	GPXP3			Standard	NM_182701		Approved		uc021yrx.1	P59796	OTTHUMG00000044828	ENST00000474923.1:c.530C>T	6.37:g.28472105G>A	ENSP00000417364:p.Thr177Ile		Q4PJ17	Missense_Mutation	SNP	ENST00000474923.1	37		.	.	.	.	.	.	.	.	.	.	G	10.62	1.402376	0.25291	.	.	ENSG00000198704	ENST00000474923	T	0.12255	2.7	4.5	2.73	0.32206	.	.	.	.	.	T	0.01489	0.0048	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38628	-0.9652	6	0.02654	T	1	.	4.8641	0.13600	0.1893:0.1758:0.6349:0.0	.	.	.	.	I	177	ENSP00000417364:T177I	ENSP00000417364:T177I	T	-	2	0	GPX6	28580084	1.000000	0.71417	0.982000	0.44146	0.113000	0.19764	3.441000	0.52893	0.817000	0.34445	0.655000	0.94253	ACA		0.502	GPX6-002	PUTATIVE	basic|exp_conf|seleno	protein_coding	protein_coding	OTTHUMT00000356246.5			60	74	60	74
ENSA	2029	broad.mit.edu;ucsc.edu	37	1	150599964	150599964	+	Silent	SNP	G	G	A			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr1:150599964G>A	ENST00000369014.5	-	2	287	c.162C>T	c.(160-162)ctC>ctT	p.L54L	ENSA_ENST00000361631.5_Silent_p.L50L|ENSA_ENST00000354702.3_5'UTR|ENSA_ENST00000271690.8_Silent_p.L54L|ENSA_ENST00000361532.5_Silent_p.L50L|ENSA_ENST00000339643.5_Silent_p.L54L|ENSA_ENST00000503345.1_Silent_p.L54L|ENSA_ENST00000369009.3_Silent_p.L54L|ENSA_ENST00000362052.7_Silent_p.L54L|ENSA_ENST00000356527.5_Silent_p.L54L|ENSA_ENST00000369016.4_Silent_p.L54L|ENSA_ENST00000513281.1_Silent_p.L50L|ENSA_ENST00000503241.1_Silent_p.L54L			O43768	ENSA_HUMAN	endosulfine alpha	54					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)			GTCTCTTCATGAGGAAGTCGG	0.493																																					Esophageal Squamous(188;763 2078 3002 3411 26027)											0													71.0	71.0	71.0					1																	150599964		2203	4300	6503	SO:0001819	synonymous_variant	2029			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.162C>T	1.37:g.150599964G>A			A8K1Z9|E9PB69|Q5T5H2|Q68D48|Q6FHW0|Q6IAM4|Q6NUL2|Q6VUC6|Q6VUC7|Q6VUC8|Q6VUC9|Q6VUD0|Q6VUD1|Q9NRZ0	Silent	SNP	ENST00000369014.5	37	CCDS958.1																																																																																				0.493	ENSA-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000084720.2	NM_207042		90	83	90	83
FSIP1	161835	broad.mit.edu;ucsc.edu	37	15	39910063	39910063	+	Silent	SNP	C	C	T	rs144527032	byFrequency	TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr15:39910063C>T	ENST00000350221.3	-	11	1781	c.1572G>A	c.(1570-1572)tcG>tcA	p.S524S		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	524										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)		CAAGAGTCTTCGACATAAAAT	0.398													C|||	2	0.000399361	0.0	0.0014	5008	,	,		21218	0.0		0.0	False		,,,				2504	0.001															0								C		1,4399	2.1+/-5.4	0,1,2199	107.0	101.0	103.0		1572	-9.7	0.0	15	dbSNP_134	103	22,8572	16.0+/-53.3	0,22,4275	no	coding-synonymous	FSIP1	NM_152597.4		0,23,6474	TT,TC,CC		0.256,0.0227,0.177		524/582	39910063	23,12971	2200	4297	6497	SO:0001819	synonymous_variant	161835			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.1572G>A	15.37:g.39910063C>T			Q6X2C8|Q86Y89	Silent	SNP	ENST00000350221.3	37	CCDS10050.1																																																																																				0.398	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597		86	52	86	52
NEGR1	257194	broad.mit.edu;ucsc.edu	37	1	72748110	72748110	+	Missense_Mutation	SNP	C	C	T			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr1:72748110C>T	ENST00000357731.5	-	1	307	c.68G>A	c.(67-69)aGc>aAc	p.S23N	NEGR1_ENST00000434200.1_Missense_Mutation_p.S21N	NM_173808.2	NP_776169.2	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1	23					feeding behavior (GO:0007631)|locomotory behavior (GO:0007626)|positive regulation of neuron projection development (GO:0010976)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.S23N(1)		endometrium(1)|kidney(4)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)		GCAGCACAGGCTGAGGAGCAC	0.627																																																1	Substitution - Missense(1)	kidney(1)											83.0	69.0	74.0					1																	72748110		2203	4300	6503	SO:0001583	missense	257194			AK092307	CCDS661.1	1p31.1	2013-01-11			ENSG00000172260	ENSG00000172260		"""Immunoglobulin superfamily / I-set domain containing"""	17302	protein-coding gene	gene with protein product	"""a kindred of IgLON"", ""neurotractin"", ""IgLON family member 4"""	613173				10075727	Standard	NM_173808		Approved	KILON, MGC46680, Ntra, IGLON4	uc001dfw.3	Q7Z3B1	OTTHUMG00000009698	ENST00000357731.5:c.68G>A	1.37:g.72748110C>T	ENSP00000350364:p.Ser23Asn		Q5VT21|Q6UY06|Q8N440|Q8NAQ3	Missense_Mutation	SNP	ENST00000357731.5	37	CCDS661.1	.	.	.	.	.	.	.	.	.	.	C	16.94	3.260309	0.59431	.	.	ENSG00000172260	ENST00000357731;ENST00000434200	T;T	0.72725	0.59;-0.68	5.25	4.33	0.51752	.	0.000000	0.85682	D	0.000000	T	0.37598	0.1009	N	0.19112	0.55	0.38063	D	0.936135	B;B	0.30482	0.221;0.281	B;B	0.27076	0.027;0.076	T	0.28170	-1.0052	10	0.25751	T	0.34	-6.3905	13.6553	0.62336	0.0:0.8436:0.1564:0.0	.	21;23	B4DI94;Q7Z3B1	.;NEGR1_HUMAN	N	23;21	ENSP00000350364:S23N;ENSP00000413294:S21N	ENSP00000350364:S23N	S	-	2	0	NEGR1	72520698	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.916000	0.56416	1.192000	0.43071	0.561000	0.74099	AGC		0.627	NEGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026722.4	NM_173808		5	17	5	17
SLA	6503	broad.mit.edu;ucsc.edu	37	8	134050855	134050855	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr8:134050855G>A	ENST00000338087.5	-	9	1564	c.745C>T	c.(745-747)Cga>Tga	p.R249*	TG_ENST00000542445.1_Intron|SLA_ENST00000517648.1_Nonsense_Mutation_p.R222*|SLA_ENST00000524345.1_Nonsense_Mutation_p.R141*|TG_ENST00000220616.4_Intron|SLA_ENST00000427060.2_Nonsense_Mutation_p.R289*|TG_ENST00000377869.1_Intron|SLA_ENST00000395352.3_Nonsense_Mutation_p.R266*|TG_ENST00000519543.1_Intron	NM_001045556.2	NP_001039021.1	Q13239	SLAP1_HUMAN	Src-like-adaptor	249	SLA C-terminal.				positive regulation of signal transduction (GO:0009967)	endosome (GO:0005768)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(1)|lung(6)|prostate(1)|skin(1)	17	all_epithelial(106;3.51e-21)|Lung NSC(106;4.24e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0279)|Breast(495;0.037)	BRCA - Breast invasive adenocarcinoma(115;0.000701)			TTCTTCTTTCGATCAAAGGAG	0.498																																																0													216.0	186.0	196.0					8																	134050855		2203	4300	6503	SO:0001587	stop_gained	6503				CCDS6370.1, CCDS47922.1, CCDS47923.1, CCDS64977.1, CCDS64978.1	8q24.22	2013-09-19	2001-11-28		ENSG00000155926	ENSG00000155926		"""SH2 domain containing"""	10902	protein-coding gene	gene with protein product		601099	"""Src-like-adapter"""			8825655, 11179692	Standard	NM_001045556		Approved	SLA1	uc011ljd.2	Q13239	OTTHUMG00000164439	ENST00000338087.5:c.745C>T	8.37:g.134050855G>A	ENSP00000337548:p.Arg249*		B7Z4J2|B7Z4L6|Q6FI01|Q9UMQ8	Nonsense_Mutation	SNP	ENST00000338087.5	37	CCDS6370.1	.	.	.	.	.	.	.	.	.	.	G	40	7.942645	0.98574	.	.	ENSG00000155926	ENST00000338087;ENST00000427060;ENST00000395352;ENST00000524345;ENST00000517648	.	.	.	5.92	3.04	0.35103	.	0.108147	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-24.2154	14.2325	0.65903	0.0:0.0:0.4917:0.5083	.	.	.	.	X	249;289;266;141;222	.	ENSP00000337548:R249X	R	-	1	2	SLA	134120037	0.201000	0.23410	0.168000	0.22838	0.025000	0.11179	1.051000	0.30417	0.341000	0.23771	-0.181000	0.13052	CGA		0.498	SLA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378771.1			67	210	67	210
ZCCHC9	84240	broad.mit.edu;hgsc.bcm.edu	37	5	80607067	80607070	+	Frame_Shift_Del	DEL	AAAG	AAAG	-			TCGA-DB-5279-01A-01D-1468-08	TCGA-DB-5279-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277aa1d8-ce6a-4e32-a267-73c33665ab97	1761720c-3e2f-4ce7-8551-b859117e150f	g.chr5:80607067_80607070delAAAG	ENST00000254037.2	+	4	3821_3824	c.666_669delAAAG	c.(664-669)ttaaagfs	p.LK222fs	ZCCHC9_ENST00000380199.5_Frame_Shift_Del_p.LK222fs|ZCCHC9_ENST00000506458.1_3'UTR|ZCCHC9_ENST00000407610.3_Frame_Shift_Del_p.LK222fs|ZCCHC9_ENST00000438268.2_Frame_Shift_Del_p.LK222fs			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	222					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)		TGGAACATTTAAAGAAAGATTGCC	0.417																																																0																																										SO:0001589	frameshift_variant	84240			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.666_669delAAAG	5.37:g.80607071_80607074delAAAG	ENSP00000254037:p.Leu222fs		B2RAE7|Q9H027	Frame_Shift_Del	DEL	ENST00000254037.2	37	CCDS4054.1																																																																																				0.417	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239213.1	NM_032280		190	348	190	348
