#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
ITIH2	3698	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	7780699	7780699	+	Silent	SNP	G	G	A			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr10:7780699G>A	ENST00000358415.4	+	16	2239	c.2073G>A	c.(2071-2073)acG>acA	p.T691T	ITIH2_ENST00000379587.4_Silent_p.T680T	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	691					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						TAGAGTCCACGCCACCCCCAC	0.562																																																0													119.0	101.0	107.0					10																	7780699		2203	4300	6503	SO:0001819	synonymous_variant	3698			X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"""inter-alpha (globulin) inhibitor, H2 polypeptide"""			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.2073G>A	10.37:g.7780699G>A			Q14659|Q15484|Q5T986	Silent	SNP	ENST00000358415.4	37	CCDS31141.1																																																																																				0.562	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216		12	44	12	44
RAG1	5896	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	36596675	36596675	+	Silent	SNP	C	C	T	rs183806098		TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr11:36596675C>T	ENST00000299440.5	+	2	1933	c.1821C>T	c.(1819-1821)gaC>gaT	p.D607D		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	607					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				GAATGGGAGACGTGAGTGAGA	0.468									Familial Hemophagocytic Lymphohistiocytosis				C|||	1	0.000199681	0.0	0.0	5008	,	,		22545	0.0		0.001	False		,,,				2504	0.0				Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)											0													109.0	90.0	97.0					11																	36596675		2202	4298	6500	SO:0001819	synonymous_variant	5896	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"""RING-type (C3HC4) zinc fingers"""	9831	protein-coding gene	gene with protein product	"""recombination activating protein 1"", ""RING finger protein 74"", ""V(D)J recombination-activating protein 1"""	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.1821C>T	11.37:g.36596675C>T			E9PPC4|Q8IY72|Q8NER2	Silent	SNP	ENST00000299440.5	37	CCDS7902.1																																																																																				0.468	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448		11	34	11	34
SORL1	6653	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	121421301	121421301	+	Missense_Mutation	SNP	A	A	G			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr11:121421301A>G	ENST00000260197.7	+	16	2317	c.2188A>G	c.(2188-2190)Aag>Gag	p.K730E		NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	730					cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		CAGCTACCGGAAGATTTCTGG	0.557																																																0													99.0	88.0	91.0					11																	121421301		2203	4299	6502	SO:0001583	missense	6653			Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"""Fibronectin type III domain containing"""	11185	protein-coding gene	gene with protein product	"""LDLR relative with 11 ligand-binding repeats"""	602005	"""chromosome 11 open reading frame 32"", ""sortilin-related receptor, L(DLR class) A repeats-containing"""	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.2188A>G	11.37:g.121421301A>G	ENSP00000260197:p.Lys730Glu		B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	37	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.908646	0.92107	.	.	ENSG00000137642	ENST00000260197	D	0.94000	-3.33	5.37	5.37	0.77165	VPS10 (1);	0.000000	0.85682	D	0.000000	D	0.94627	0.8268	M	0.88377	2.95	0.80722	D	1	D	0.53745	0.962	P	0.44394	0.448	D	0.95225	0.8337	10	0.62326	D	0.03	.	15.3709	0.74564	1.0:0.0:0.0:0.0	.	730	Q92673	SORL_HUMAN	E	730	ENSP00000260197:K730E	ENSP00000260197:K730E	K	+	1	0	SORL1	120926511	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.562000	0.90719	2.031000	0.59945	0.533000	0.62120	AAG		0.557	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105		7	65	7	65
KCNMB4	27345	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	70824288	70824288	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr12:70824288G>A	ENST00000258111.4	+	3	947	c.488G>A	c.(487-489)cGc>cAc	p.R163H		NM_014505.5	NP_055320.4	Q86W47	KCMB4_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 4	163					action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of neurotransmitter secretion (GO:0046928)|regulation of vasoconstriction (GO:0019229)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)			kidney(1)|large_intestine(4)|lung(5)	10	Renal(347;0.236)		Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)		Miconazole(DB01110)|Procaine(DB00721)	CTTCTGCATCGCACTCATGAT	0.488																																																0													204.0	188.0	193.0					12																	70824288		2203	4300	6503	SO:0001583	missense	27345			AF207992	CCDS8997.1	12q15	2006-06-10			ENSG00000135643	ENSG00000135643		"""Potassium channels"""	6289	protein-coding gene	gene with protein product		605223				10692449, 10828459	Standard	NM_014505		Approved		uc001svx.3	Q86W47	OTTHUMG00000167586	ENST00000258111.4:c.488G>A	12.37:g.70824288G>A	ENSP00000258111:p.Arg163His		Q8IVR3|Q9NPA4|Q9P0G5	Missense_Mutation	SNP	ENST00000258111.4	37	CCDS8997.1	.	.	.	.	.	.	.	.	.	.	G	33	5.268925	0.95429	.	.	ENSG00000135643	ENST00000258111	T	0.15834	2.39	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.43322	0.1242	M	0.63843	1.955	0.58432	D	0.999997	D	0.89917	1.0	D	0.85130	0.997	T	0.12682	-1.0538	10	0.66056	D	0.02	-23.5357	20.1653	0.98150	0.0:0.0:1.0:0.0	.	163	Q86W47	KCMB4_HUMAN	H	163	ENSP00000258111:R163H	ENSP00000258111:R163H	R	+	2	0	KCNMB4	69110555	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.440000	0.73435	2.768000	0.95171	0.655000	0.94253	CGC		0.488	KCNMB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395208.1	NM_014505		19	152	19	152
HECTD4	283450	hgsc.bcm.edu;broad.mit.edu	37	12	112617095	112617095	+	Silent	SNP	G	G	C			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr12:112617095G>C	ENST00000430131.2	-	62	10973	c.9828C>G	c.(9826-9828)gtC>gtG	p.V3276V	HECTD4_ENST00000550722.1_Silent_p.V3552V|HECTD4_ENST00000377560.5_Silent_p.V3526V			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3276					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										AAATGTCAGAGACTCTGATGG	0.542																																																0													76.0	86.0	83.0					12																	112617095		2038	4206	6244	SO:0001819	synonymous_variant	283450			AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 51"""	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.9828C>G	12.37:g.112617095G>C			L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	37																																																																																					0.542	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		6	14	6	14
SOHLH2	54937	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	36776075	36776075	+	Silent	SNP	A	A	G			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr13:36776075A>G	ENST00000379881.3	-	2	292	c.204T>C	c.(202-204)gtT>gtC	p.V68V	SOHLH2_ENST00000317764.6_Silent_p.V68V|SOHLH2_ENST00000554962.1_Silent_p.V145V|CCDC169-SOHLH2_ENST00000511166.1_Silent_p.V145V	NM_017826.2	NP_060296.2	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 2	68					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;4.63e-08)|Epithelial(112;2.67e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|BRCA - Breast invasive adenocarcinoma(63;0.00685)|GBM - Glioblastoma multiforme(144;0.0273)		CCTTCAAGAGAACCATGTTGA	0.423																																																0													134.0	111.0	119.0					13																	36776075		2203	4300	6503	SO:0001819	synonymous_variant	54937			AK000456	CCDS9355.1, CCDS61309.1	13q13.3	2013-05-21			ENSG00000120669	ENSG00000120669		"""Basic helix-loop-helix proteins"""	26026	protein-coding gene	gene with protein product	"""spermatogenesis associated 28"""					12477932	Standard	NM_017826		Approved	FLJ20449, TEB1, bHLHe81, SPATA28		Q9NX45	OTTHUMG00000016728	ENST00000379881.3:c.204T>C	13.37:g.36776075A>G			B4DX90|Q5EGC3|Q8TC74|Q96QX4	Silent	SNP	ENST00000379881.3	37	CCDS9355.1																																																																																				0.423	SOHLH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044477.2	NM_017826		23	71	23	71
FNDC3A	22862	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	49710555	49710555	+	Missense_Mutation	SNP	G	G	A	rs369583924		TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr13:49710555G>A	ENST00000492622.2	+	6	883	c.578G>A	c.(577-579)cGc>cAc	p.R193H	FNDC3A_ENST00000398316.3_Missense_Mutation_p.R137H|FNDC3A_ENST00000541916.1_Missense_Mutation_p.R193H	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	193					fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		TTGAAGGATCGCCAAGGAACA	0.388																																																0								G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	100.0	97.0	98.0		578,410	5.6	1.0	13		98	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	FNDC3A	NM_001079673.1,NM_014923.3	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	193/1199,137/1143	49710555	1,13005	2203	4300	6503	SO:0001583	missense	22862			AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531		"""Fibronectin type III domain containing"""	20296	protein-coding gene	gene with protein product		615794	"""fibronectin type III domain containing 3"""	FNDC3			Standard	NM_001079673		Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.578G>A	13.37:g.49710555G>A	ENSP00000417257:p.Arg193His		B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Missense_Mutation	SNP	ENST00000492622.2	37	CCDS41886.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.921636	0.92319	0.0	1.16E-4	ENSG00000102531	ENST00000492622;ENST00000337156;ENST00000541916;ENST00000398316	T;T;T	0.37584	1.19;1.19;1.19	5.61	5.61	0.85477	.	0.000000	0.64402	D	0.000005	T	0.60932	0.2307	M	0.68317	2.08	0.49798	D	0.999822	D;D;P	0.89917	1.0;1.0;0.75	D;D;B	0.91635	0.997;0.999;0.126	T	0.61922	-0.6963	10	0.66056	D	0.02	-6.4611	18.6226	0.91326	0.0:0.0:1.0:0.0	.	137;193;193	Q9Y2H6-2;G5E9X3;Q9Y2H6	.;.;FND3A_HUMAN	H	193;129;193;137	ENSP00000417257:R193H;ENSP00000441831:R193H;ENSP00000381362:R137H	ENSP00000338579:R129H	R	+	2	0	FNDC3A	48608556	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.526000	0.81920	2.638000	0.89438	0.563000	0.77884	CGC		0.388	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923		27	26	27	26
NGDN	25983	hgsc.bcm.edu;broad.mit.edu	37	14	23940135	23940135	+	Silent	SNP	A	A	G			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr14:23940135A>G	ENST00000408901.3	+	3	121	c.93A>G	c.(91-93)caA>caG	p.Q31Q	NGDN_ENST00000397154.3_Silent_p.Q31Q	NM_001042635.1|NM_015514.1	NP_001036100.1|NP_056329.1	Q8NEJ9	NGDN_HUMAN	neuroguidin, EIF4E binding protein	31					regulation of translation (GO:0006417)	cell projection (GO:0042995)|chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	12	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00654)		TAACTGCACAAGTGAAATCAC	0.368																																																0													154.0	144.0	147.0					14																	23940135		2203	4300	6503	SO:0001819	synonymous_variant	25983			AK022215	CCDS32051.1, CCDS41926.1	14q11.2	2014-06-13	2006-08-02	2006-08-02	ENSG00000129460	ENSG00000129460			20271	protein-coding gene	gene with protein product		610777	"""chromosome 14 open reading frame 120"""	C14orf120		16705177	Standard	NM_001042635		Approved	DKFZP564O092, LCP5, lpd-2, NGD	uc001wjy.3	Q8NEJ9	OTTHUMG00000171501	ENST00000408901.3:c.93A>G	14.37:g.23940135A>G			A8K760|Q9Y400	Silent	SNP	ENST00000408901.3	37	CCDS41926.1	.	.	.	.	.	.	.	.	.	.	A	4.233	0.042067	0.08196	.	.	ENSG00000129460	ENST00000556483	.	.	.	5.1	-0.211	0.13172	.	.	.	.	.	T	0.42877	0.1222	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.19844	-1.0293	4	.	.	.	-4.6906	3.0437	0.06146	0.4296:0.0:0.2757:0.2947	.	.	.	.	G	25	.	.	S	+	1	0	NGDN	23009975	0.991000	0.36638	0.944000	0.38274	0.469000	0.32828	0.015000	0.13355	-0.296000	0.08947	-0.609000	0.04063	AGT		0.368	NGDN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413782.3	NM_001042635		6	101	6	101
CTAGE5	4253	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	39784908	39784908	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr14:39784908G>A	ENST00000280083.3	+	16	1692	c.1378G>A	c.(1378-1380)Gca>Aca	p.A460T	CTAGE5_ENST00000396165.4_Missense_Mutation_p.A431T|CTAGE5_ENST00000341749.3_Missense_Mutation_p.A448T|CTAGE5_ENST00000348007.3_Missense_Mutation_p.A460T|CTAGE5_ENST00000396158.2_Missense_Mutation_p.A465T|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.A995T|CTAGE5_ENST00000556148.1_Missense_Mutation_p.A385T|CTAGE5_ENST00000341502.5_Missense_Mutation_p.A460T|CTAGE5_ENST00000557038.1_Missense_Mutation_p.A380T|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.A431T|CTAGE5_ENST00000553352.1_Missense_Mutation_p.A431T			O15320	CTGE5_HUMAN	CTAGE family, member 5	460					positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)		CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		TGAGAAAAAAGCACATGATAA	0.254																																																0													81.0	96.0	90.0					14																	39784908		2201	4297	6498	SO:0001583	missense	0			U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"""meningioma expressed antigen 6 (coiled-coil proline-rich)"""	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.1378G>A	14.37:g.39784908G>A	ENSP00000280083:p.Ala460Thr		B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	37	CCDS9674.1	.	.	.	.	.	.	.	.	.	.	G	32	5.188266	0.94923	.	.	ENSG00000258941;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527	ENST00000553728;ENST00000341749;ENST00000557038;ENST00000382245;ENST00000396165;ENST00000341502;ENST00000396158;ENST00000280083;ENST00000556148;ENST00000348007;ENST00000553352	T;T;T;T;T;T;T;T;T;T	0.77877	0.3;-1.13;-1.13;-1.13;-1.13;-1.13;-1.13;-1.13;-1.13;-1.13	5.68	5.68	0.88126	.	0.000000	0.33144	N	0.005222	D	0.88757	0.6523	M	0.86953	2.85	0.58432	D	0.999995	D;P;P;P;P;P	0.52996	0.957;0.813;0.952;0.813;0.917;0.709	P;P;P;P;P;P	0.60609	0.828;0.67;0.877;0.67;0.839;0.67	D	0.89062	0.3463	9	.	.	.	.	18.32	0.90234	0.0:0.0:1.0:0.0	.	422;465;460;460;431;448	F8W9E1;O15320-5;O15320-2;O15320;O15320-7;G3XAC5	.;.;.;CTGE5_HUMAN;.;.	T	995;448;380;422;431;460;465;460;385;460;431	ENSP00000452252:A995T;ENSP00000343897:A448T;ENSP00000450869:A380T;ENSP00000379468:A431T;ENSP00000339286:A460T;ENSP00000379462:A465T;ENSP00000280083:A460T;ENSP00000452562:A385T;ENSP00000343912:A460T;ENSP00000450449:A431T	.	A	+	1	0	CTAGE5;RP11-407N17.3	38854659	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.918000	0.75788	2.843000	0.97960	0.585000	0.79938	GCA		0.254	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930		26	88	26	88
EIF2AK4	440275	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	40241413	40241413	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr15:40241413C>T	ENST00000263791.5	+	4	500	c.457C>T	c.(457-459)Cgg>Tgg	p.R153W	EIF2AK4_ENST00000382727.2_Missense_Mutation_p.R153W|EIF2AK4_ENST00000559624.1_Missense_Mutation_p.R153W|snoU13_ENST00000459610.1_RNA	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	153					cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		GCTGGAAAGGCGGGCTCAGGA	0.537																																																0													98.0	96.0	97.0					15																	40241413		2011	4182	6193	SO:0001583	missense	440275			AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.457C>T	15.37:g.40241413C>T	ENSP00000263791:p.Arg153Trp		C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Missense_Mutation	SNP	ENST00000263791.5	37	CCDS42016.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.103126	0.76983	.	.	ENSG00000128829	ENST00000263791;ENST00000382727	T;T	0.15718	2.4;2.4	5.8	2.78	0.32641	.	0.679268	0.15405	N	0.264103	T	0.22322	0.0538	L	0.29908	0.895	0.27136	N	0.961776	P;D	0.65815	0.941;0.995	B;P	0.52710	0.38;0.707	T	0.09552	-1.0669	10	0.62326	D	0.03	-0.8572	14.6143	0.68537	0.3817:0.6183:0.0:0.0	.	153;153	Q9P2K8;Q9P2K8-3	E2AK4_HUMAN;.	W	153	ENSP00000263791:R153W;ENSP00000372174:R153W	ENSP00000263791:R153W	R	+	1	2	EIF2AK4	38028705	0.875000	0.30112	0.008000	0.14137	0.842000	0.47809	1.858000	0.39408	0.314000	0.23086	0.555000	0.69702	CGG		0.537	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1			47	79	47	79
BUB1B	701	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	40509802	40509802	+	Silent	SNP	C	C	T	rs139066741	byFrequency	TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr15:40509802C>T	ENST00000287598.6	+	21	2979	c.2784C>T	c.(2782-2784)agC>agT	p.S928S	PAK6_ENST00000441369.1_5'UTR|BUB1B_ENST00000412359.3_Silent_p.S942S|RP11-133K1.2_ENST00000558658.1_Silent_p.S5S|PAK6_ENST00000453867.1_5'UTR	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	928	Protein kinase.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|protein localization to chromosome, centromeric region (GO:0071459)|protein localization to kinetochore (GO:0034501)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|condensed chromosome kinetochore (GO:0000777)|condensed chromosome outer kinetochore (GO:0000940)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|perinuclear region of cytoplasm (GO:0048471)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(1)|stomach(2)|urinary_tract(2)	36		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		TTACCCTCAGCGGCTTTCGGA	0.443			"""Mis, N, F, S"""			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome				C|||	2	0.000399361	0.0	0.0	5008	,	,		18199	0.002		0.0	False		,,,				2504	0.0					yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	0													234.0	237.0	236.0					15																	40509802		2203	4300	6503	SO:0001819	synonymous_variant	701	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	AF107297	CCDS10053.1	15q15	2014-09-17	2013-01-17		ENSG00000156970	ENSG00000156970			1149	protein-coding gene	gene with protein product		602860	"""budding uninhibited by benzimidazoles 1 (yeast homolog), beta"", ""budding uninhibited by benzimidazoles 1 homolog beta (yeast)"""			9889005	Standard	NM_001211		Approved	BUBR1, MAD3L, Bub1A, SSK1	uc001zkx.4	O60566	OTTHUMG00000129877	ENST00000287598.6:c.2784C>T	15.37:g.40509802C>T			B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Silent	SNP	ENST00000287598.6	37	CCDS10053.1																																																																																				0.443	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4			95	305	95	305
TP53	7157	hgsc.bcm.edu;broad.mit.edu	37	17	7577121	7577121	+	Missense_Mutation	SNP	G	G	A	rs121913343		TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr17:7577121G>A	ENST00000269305.4	-	8	1006	c.817C>T	c.(817-819)Cgt>Tgt	p.R273C	TP53_ENST00000359597.4_Missense_Mutation_p.R273C|TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Missense_Mutation_p.R273C|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Missense_Mutation_p.R273C|TP53_ENST00000455263.2_Missense_Mutation_p.R273C	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R273C(481)|p.R273S(16)|p.R273G(9)|p.0?(8)|p.?(2)|p.R273fs*72(2)|p.R273fs*33(2)|p.R273fs*32(2)|p.V272>?(2)|p.F270fs*72(1)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.E258fs*71(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCACAAACACGCACCTCAAAG	0.542	R273C(8MGBA_CENTRAL_NERVOUS_SYSTEM)|R273C(BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(EFO27_OVARY)|R273C(KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(MFE319_ENDOMETRIUM)|R273C(NCIH1048_LUNG)|R273C(PANC0213_PANCREAS)|R273C(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(RDES_BONE)|R273C(RH30_SOFT_TISSUE)|R273C(RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SH10TC_STOMACH)|R273C(SJRH30_SOFT_TISSUE)|R273C(SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SW1710_URINARY_TRACT)|R273C(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273C(TT2609C02_THYROID)	111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	533	Substitution - Missense(506)|Whole gene deletion(8)|Deletion - Frameshift(8)|Deletion - In frame(5)|Insertion - Frameshift(2)|Unknown(2)|Complex(2)	central_nervous_system(117)|large_intestine(108)|ovary(32)|haematopoietic_and_lymphoid_tissue(31)|upper_aerodigestive_tract(30)|stomach(25)|urinary_tract(23)|lung(21)|breast(21)|liver(20)|endometrium(17)|oesophagus(17)|bone(16)|pancreas(15)|prostate(8)|skin(7)|cervix(6)|biliary_tract(6)|kidney(3)|thyroid(3)|vulva(2)|genital_tract(1)|penis(1)|adrenal_gland(1)|salivary_gland(1)|small_intestine(1)	GRCh37	CM010471|CM010473|CM951233	TP53	M	rs121913343						65.0	56.0	59.0					17																	7577121		2203	4300	6503	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.817C>T	17.37:g.7577121G>A	ENSP00000269305:p.Arg273Cys		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.400216	0.62177	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.92	3.95	0.45737	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99851	0.9931	M	0.90759	3.145	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.999;0.996	D	0.96877	0.9643	10	0.87932	D	0	-11.9995	11.2235	0.48869	0.0895:0.0:0.9105:0.0	.	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	C	273;273;273;273;273;262;141	ENSP00000352610:R273C;ENSP00000269305:R273C;ENSP00000398846:R273C;ENSP00000391127:R273C;ENSP00000391478:R273C;ENSP00000425104:R141C	ENSP00000269305:R273C	R	-	1	0	TP53	7517846	1.000000	0.71417	0.066000	0.19879	0.723000	0.41478	4.540000	0.60664	1.299000	0.44798	0.462000	0.41574	CGT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		23	3	23	3
CTC1	80169	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	8132163	8132163	+	Missense_Mutation	SNP	T	T	C	rs368562418		TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr17:8132163T>C	ENST00000315684.8	-	21	3276	c.3269A>G	c.(3268-3270)aAt>aGt	p.N1090S		NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	1090					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						CACATGGTGATTCCTACAGGT	0.567																																																0								T	SER/ASN	0,4064		0,0,2032	41.0	45.0	44.0		3269	5.6	1.0	17		44	1,8345		0,1,4172	no	missense	CTC1	NM_025099.5	46	0,1,6204	CC,CT,TT		0.012,0.0,0.0081	possibly-damaging	1090/1218	8132163	1,12409	2032	4173	6205	SO:0001583	missense	80169			AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"""conserved telomere maintenance component 1"", ""alpha accessory factor 132"", ""conserved telomere capping protein 1"""	613129	"""tmp494178"", ""chromosome 17 open reading frame 68"""	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.3269A>G	17.37:g.8132163T>C	ENSP00000313759:p.Asn1090Ser		B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Missense_Mutation	SNP	ENST00000315684.8	37	CCDS42259.1	.	.	.	.	.	.	.	.	.	.	T	14.94	2.684198	0.47991	0.0	1.2E-4	ENSG00000178971	ENST00000315684	D	0.82984	-1.67	5.56	5.56	0.83823	.	0.367840	0.31358	N	0.007784	T	0.78013	0.4217	L	0.55481	1.735	0.31559	N	0.657736	P	0.44139	0.827	B	0.38500	0.275	T	0.80901	-0.1175	10	0.34782	T	0.22	-3.604	12.1139	0.53854	0.0:0.0:0.0:1.0	.	1090	Q2NKJ3	CTC1_HUMAN	S	1090	ENSP00000313759:N1090S	ENSP00000313759:N1090S	N	-	2	0	CTC1	8072888	0.998000	0.40836	0.991000	0.47740	0.972000	0.66771	4.328000	0.59253	2.133000	0.65898	0.533000	0.62120	AAT		0.567	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099		4	20	4	20
PSMD3	5709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	38151212	38151212	+	Missense_Mutation	SNP	C	C	G			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr17:38151212C>G	ENST00000264639.4	+	7	1161	c.987C>G	c.(985-987)caC>caG	p.H329Q	PSMD3_ENST00000541736.1_Missense_Mutation_p.H191Q	NM_002809.3	NP_002800.2	O43242	PSMD3_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	329					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Colorectal(19;0.000442)					TCCAGGTGCACAAGCTTCTCA	0.572																																					Ovarian(186;531 2051 6385 19668 48409)											0													63.0	63.0	63.0					17																	38151212		2203	4300	6503	SO:0001583	missense	5709			D67025	CCDS11356.1	17q21.2	2010-07-23			ENSG00000108344	ENSG00000108344		"""Proteasome (prosome, macropain) subunits"""	9560	protein-coding gene	gene with protein product			"""tissue specific transplantation antigen 2"""	TSTA2		9017604	Standard	NM_002809		Approved	S3, P58, Rpn3	uc002htn.2	O43242	OTTHUMG00000133251	ENST00000264639.4:c.987C>G	17.37:g.38151212C>G	ENSP00000264639:p.His329Gln		B3KMW9|B4DT72|Q96EI2|Q9BQA4	Missense_Mutation	SNP	ENST00000264639.4	37	CCDS11356.1	.	.	.	.	.	.	.	.	.	.	C	14.50	2.555430	0.45487	.	.	ENSG00000108344	ENST00000264639;ENST00000415039;ENST00000541736	T;T	0.75260	-0.92;-0.92	5.22	5.22	0.72569	Tetratricopeptide-like helical (1);PCI/PINT associated module (1);	0.044211	0.85682	D	0.000000	T	0.48607	0.1509	N	0.03029	-0.43	0.80722	D	1	B	0.21688	0.059	B	0.15484	0.013	T	0.49204	-0.8964	10	0.15952	T	0.53	-36.6542	12.9395	0.58335	0.0:0.9216:0.0:0.0784	.	329	O43242	PSMD3_HUMAN	Q	329;316;191	ENSP00000264639:H329Q;ENSP00000442508:H191Q	ENSP00000264639:H329Q	H	+	3	2	PSMD3	35404738	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.625000	0.54238	2.720000	0.93068	0.655000	0.94253	CAC		0.572	PSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257018.1	NM_002809		19	45	19	45
CCR7	1236	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	38711759	38711759	+	Silent	SNP	G	G	A	rs371166143		TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr17:38711759G>A	ENST00000246657.2	-	3	434	c.372C>T	c.(370-372)ttC>ttT	p.F124F	CCR7_ENST00000579344.1_Silent_p.F118F	NM_001838.3	NP_001829.1	P32248	CCR7_HUMAN	chemokine (C-C motif) receptor 7	124					activation of Rho GTPase activity (GO:0032862)|cellular response to cytokine stimulus (GO:0071345)|chemokine (C-C motif) ligand 19 signaling pathway (GO:0038115)|chemokine (C-C motif) ligand 21 signaling pathway (GO:0038116)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|establishment of T cell polarity (GO:0001768)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-12 secretion (GO:0072610)|lymphocyte migration into lymph node (GO:0097022)|mature dendritic cell differentiation (GO:0097029)|myeloid dendritic cell chemotaxis (GO:0002408)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative thymic T cell selection (GO:0045060)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell motility (GO:2000147)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of glycoprotein biosynthetic process involved in immunological synapse formation (GO:2000526)|positive regulation of humoral immune response (GO:0002922)|positive regulation of hypersensitivity (GO:0002885)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immunological synapse formation (GO:2000522)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of T cell costimulation (GO:2000525)|positive regulation of T cell receptor signaling pathway (GO:0050862)|regulation of dendritic cell dendrite assembly (GO:2000547)|regulation of interferon-gamma production (GO:0032649)|regulation of interleukin-1 beta secretion (GO:0050706)|release of sequestered calcium ion into cytosol (GO:0051209)|response to lipopolysaccharide (GO:0032496)|response to nitric oxide (GO:0071731)|response to prostaglandin E (GO:0034695)|ruffle organization (GO:0031529)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-C motif chemokine 19 receptor activity (GO:0038117)|C-C motif chemokine 21 receptor activity (GO:0038121)|chemokine (C-C motif) ligand 19 binding (GO:0035757)|chemokine (C-C motif) ligand 21 binding (GO:0035758)|G-protein coupled receptor activity (GO:0004930)			breast(1)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		Breast(137;0.000496)				AGTGGACACCGAAGACCCAGG	0.552																																																0								G		0,4406		0,0,2203	51.0	51.0	51.0		372	-5.8	0.1	17		51	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CCR7	NM_001838.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		124/379	38711759	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1236				CCDS11369.1	17q12-q21.2	2012-08-08			ENSG00000126353	ENSG00000126353		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1608	protein-coding gene	gene with protein product		600242		CMKBR7, EBI1		8383238	Standard	NM_001838		Approved	BLR2, CDw197, CD197	uc002huw.3	P32248	OTTHUMG00000133375	ENST00000246657.2:c.372C>T	17.37:g.38711759G>A				Silent	SNP	ENST00000246657.2	37	CCDS11369.1																																																																																				0.552	CCR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257222.1			19	20	19	20
HDAC5	10014	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	42169818	42169818	+	Missense_Mutation	SNP	G	G	A	rs138137922		TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr17:42169818G>A	ENST00000393622.2	-	8	1181	c.850C>T	c.(850-852)Cgc>Tgc	p.R284C	HDAC5_ENST00000586802.1_Missense_Mutation_p.R284C|HDAC5_ENST00000225983.6_Missense_Mutation_p.R285C|HDAC5_ENST00000336057.5_Missense_Mutation_p.R284C	NM_001015053.1|NM_005474.4	NP_001015053.1|NP_005465.2	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5	284					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|inflammatory response (GO:0006954)|multicellular organismal response to stress (GO:0033555)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression, epigenetic (GO:0040029)|regulation of myotube differentiation (GO:0010830)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|histone deacetylase complex (GO:0000118)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.R284S(1)		central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	21		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		CCATCCTTGCGACGCAGGAGG	0.537																																																1	Substitution - Missense(1)	prostate(1)						G	CYS/ARG,CYS/ARG	0,4406		0,0,2203	45.0	47.0	47.0		853,850	4.2	1.0	17	dbSNP_134	47	1,8599		0,1,4299	no	missense,missense	HDAC5	NM_001015053.1,NM_005474.4	180,180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	285/1124,284/1123	42169818	1,13005	2203	4300	6503	SO:0001583	missense	10014			AF249731	CCDS32663.1, CCDS45696.1	17q21	2008-07-18					3.5.1.98		14068	protein-coding gene	gene with protein product		605315				10220385, 9610721	Standard	XM_005256905		Approved	KIAA0600, NY-CO-9, FLJ90614	uc002iff.1	Q9UQL6		ENST00000393622.2:c.850C>T	17.37:g.42169818G>A	ENSP00000377244:p.Arg284Cys		C9JFV9|O60340|O60528|Q96DY4	Missense_Mutation	SNP	ENST00000393622.2	37	CCDS45696.1	.	.	.	.	.	.	.	.	.	.	G	17.81	3.481687	0.63849	0.0	1.16E-4	ENSG00000108840	ENST00000225983;ENST00000393622;ENST00000336057	T;T;T	0.68765	-0.22;-0.22;-0.35	5.21	4.18	0.49190	.	0.077678	0.46145	D	0.000301	T	0.79627	0.4478	M	0.78049	2.395	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.99;0.994;0.985	T	0.81391	-0.0954	10	0.87932	D	0	-17.0907	10.1323	0.42687	0.0:0.0:0.6066:0.3934	.	284;284;285;284	Q9UQL6-2;B4DGT4;Q9UQL6-3;Q9UQL6	.;.;.;HDAC5_HUMAN	C	285;284;284	ENSP00000225983:R285C;ENSP00000377244:R284C;ENSP00000337290:R284C	ENSP00000225983:R285C	R	-	1	0	HDAC5	39525344	0.984000	0.35163	1.000000	0.80357	0.997000	0.91878	1.773000	0.38563	2.434000	0.82447	0.462000	0.41574	CGC		0.537	HDAC5-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457686.1	NM_001015053		10	13	10	13
KLHL14	57565	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	30349844	30349844	+	Silent	SNP	C	C	T	rs377506830		TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr18:30349844C>T	ENST00000359358.4	-	2	1149	c.711G>A	c.(709-711)gcG>gcA	p.A237A	AC012123.1_ENST00000426194.1_Silent_p.S24S|KLHL14_ENST00000358095.4_Silent_p.A237A	NM_020805.1	NP_065856.1	Q9P2G3	KLH14_HUMAN	kelch-like family member 14	237	BACK.					endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(20)|ovary(2)	31						TCTGGAAGAGCGCCAGCTCCG	0.657																																																0													40.0	35.0	37.0					18																	30349844		2203	4299	6502	SO:0001819	synonymous_variant	57565			AB037805	CCDS32813.1	18q12.1	2013-10-15	2013-01-30		ENSG00000197705	ENSG00000197705		"""Kelch-like"", ""BTB/POZ domain containing"""	29266	protein-coding gene	gene with protein product	"""printor"""	613772	"""kelch-like 14 (Drosophila)"""			10718198, 19535332	Standard	NM_020805		Approved	KIAA1384	uc002kxm.1	Q9P2G3	OTTHUMG00000179819	ENST00000359358.4:c.711G>A	18.37:g.30349844C>T			A6NNW1|B4DHA0|Q8WU41	Silent	SNP	ENST00000359358.4	37	CCDS32813.1																																																																																				0.657	KLHL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448376.1			10	30	10	30
FCGBP	8857	hgsc.bcm.edu;broad.mit.edu	37	19	40408740	40408740	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr19:40408740C>T	ENST00000221347.6	-	8	4106	c.4099G>A	c.(4099-4101)Gcc>Acc	p.A1367T		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1367	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AGGTCGTAGGCCACACGCAGG	0.587																																																0													77.0	66.0	70.0					19																	40408740		2203	4300	6503	SO:0001583	missense	8857			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.4099G>A	19.37:g.40408740C>T	ENSP00000221347:p.Ala1367Thr		O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	7.433	0.639102	0.14386	.	.	ENSG00000090920	ENST00000221347	T	0.59224	0.28	4.91	1.61	0.23674	von Willebrand factor, type D domain (3);	0.355301	0.24178	N	0.040835	T	0.20700	0.0498	N	0.00894	-1.105	0.26437	N	0.975843	B	0.17268	0.021	B	0.16289	0.015	T	0.24048	-1.0171	10	0.13853	T	0.58	.	6.2565	0.20877	0.0:0.571:0.0:0.429	.	1367	Q9Y6R7	FCGBP_HUMAN	T	1367	ENSP00000221347:A1367T	ENSP00000221347:A1367T	A	-	1	0	FCGBP	45100580	0.000000	0.05858	0.984000	0.44739	0.175000	0.22909	-0.537000	0.06128	1.076000	0.40961	0.644000	0.83932	GCC		0.587	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		16	32	16	32
MST1L	11223	hgsc.bcm.edu;broad.mit.edu	37	1	17084292	17084293	+	RNA	DNP	AG	AG	GT			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr1:17084292_17084293AG>GT	ENST00000455405.2	-	0	515_516							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										TGGTCCCTGGAGGCACCACATA	0.589																																																0																																												11223			U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578	Exception_encountered	1.37:g.17084292_17084293delinsGT			B7WPB1|Q13209	RNA	SNP	ENST00000455405.2	37																																																																																					0.589	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733		27|26	181|179	26	179
SCMH1	22955	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	41579187	41579187	+	Silent	SNP	C	C	T			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr1:41579187C>T	ENST00000326197.7	-	7	782	c.483G>A	c.(481-483)tcG>tcA	p.S161S	SCMH1_ENST00000397174.2_Silent_p.S141S|SCMH1_ENST00000402904.2_Silent_p.S161S|SCMH1_ENST00000361705.3_Silent_p.S114S|SCMH1_ENST00000372597.1_Silent_p.S114S|SCMH1_ENST00000372595.1_Silent_p.S100S|SCMH1_ENST00000456518.2_Intron|SCMH1_ENST00000361191.5_Silent_p.S100S|SCMH1_ENST00000372596.1_Silent_p.S100S|SCMH1_ENST00000337495.5_Silent_p.S171S|SCMH1_ENST00000397171.2_Silent_p.S100S					sex comb on midleg homolog 1 (Drosophila)											breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(2)|pancreas(2)|upper_aerodigestive_tract(1)	15	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				TGTGGGAAGGCGATGGTGGCT	0.443																																																0													58.0	60.0	59.0					1																	41579187		2203	4300	6503	SO:0001819	synonymous_variant	22955			AF149045	CCDS461.1, CCDS30688.1, CCDS53301.1, CCDS53302.1, CCDS53303.1, CCDS53304.1	1p34	2013-01-10			ENSG00000010803	ENSG00000010803		"""Sterile alpha motif (SAM) domain containing"""	19003	protein-coding gene	gene with protein product						10524249	Standard	NM_012236		Approved	Scml3	uc001cgs.3	Q96GD3	OTTHUMG00000005720	ENST00000326197.7:c.483G>A	1.37:g.41579187C>T				Silent	SNP	ENST00000326197.7	37	CCDS30688.1																																																																																				0.443	SCMH1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015656.1			14	24	14	24
CFHR5	81494	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	196973949	196973949	+	Missense_Mutation	SNP	T	T	C			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr1:196973949T>C	ENST00000256785.4	+	9	1598	c.1489T>C	c.(1489-1491)Tgg>Cgg	p.W497R	CFHR5_ENST00000367414.5_Missense_Mutation_p.W521R			Q9BXR6	FHR5_HUMAN	complement factor H-related 5	497	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, alternative pathway (GO:0006957)	extracellular region (GO:0005576)				NS(2)|breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(23)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	49						AAATAAACAGTGGTCAGAACC	0.378																																																0													87.0	84.0	85.0					1																	196973949		2203	4300	6503	SO:0001583	missense	81494			AF295327	CCDS1387.1	1q31.3	2014-09-17		2006-02-28	ENSG00000134389	ENSG00000134389		"""Complement system"""	24668	protein-coding gene	gene with protein product	"""factor H related protein 5"""	608593		CFHL5		11058592, 12041828	Standard	NM_030787		Approved	FHR5, FHR-5	uc001gts.4	Q9BXR6	OTTHUMG00000036517	ENST00000256785.4:c.1489T>C	1.37:g.196973949T>C	ENSP00000256785:p.Trp497Arg		Q2NKK2	Missense_Mutation	SNP	ENST00000256785.4	37	CCDS1387.1	.	.	.	.	.	.	.	.	.	.	T	13.18	2.159482	0.38119	.	.	ENSG00000134389	ENST00000367414;ENST00000256785	D;D	0.91068	-2.78;-2.78	3.79	3.79	0.43588	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	D	0.97607	0.9216	H	0.99949	5.025	0.29766	N	0.835175	D	0.89917	1.0	D	0.97110	1.0	D	0.92836	0.6284	9	0.87932	D	0	.	9.1856	0.37168	0.0:0.0:0.0:1.0	.	497	Q9BXR6	FHR5_HUMAN	R	521;497	ENSP00000356384:W521R;ENSP00000256785:W497R	ENSP00000256785:W497R	W	+	1	0	CFHR5	195240572	0.988000	0.35896	0.948000	0.38648	0.356000	0.29392	2.403000	0.44530	1.468000	0.48064	0.397000	0.26171	TGG		0.378	CFHR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088814.2	NM_030787		25	58	25	58
HHIPL2	79802	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	222717481	222717481	+	Silent	SNP	C	C	T			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr1:222717481C>T	ENST00000343410.6	-	2	430	c.372G>A	c.(370-372)acG>acA	p.T124T		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	124					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)			NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		TCCGGAGAGGCGTCTGGGTGT	0.597																																																0													87.0	100.0	96.0					1																	222717481		1956	4138	6094	SO:0001819	synonymous_variant	79802			BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"""KIAA1822-like"""	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.372G>A	1.37:g.222717481C>T			Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Silent	SNP	ENST00000343410.6	37	CCDS1530.2																																																																																				0.597	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746		40	159	40	159
PRND	23627	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	20	4705632	4705632	+	Silent	SNP	C	C	T			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr20:4705632C>T	ENST00000305817.2	+	2	506	c.435C>T	c.(433-435)tgC>tgT	p.C145C		NM_012409.2	NP_036541.2	Q9UKY0	PRND_HUMAN	prion protein 2 (dublet)	145	Globular.				protein homooligomerization (GO:0051260)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	13						TCAAGCATTGCGAGTTTTGGT	0.602																																																0													41.0	41.0	41.0					20																	4705632		2203	4300	6503	SO:0001819	synonymous_variant	23627			AF106918	CCDS13081.1	20p13	2013-09-19			ENSG00000171864	ENSG00000171864			15748	protein-coding gene	gene with protein product	"""prion-like protein doppel"""	604263				10525406, 10577243	Standard	NM_012409		Approved	DPL, dJ1068H6.4, DOPPEL, PrPLP	uc002wkz.3	Q9UKY0	OTTHUMG00000031789	ENST00000305817.2:c.435C>T	20.37:g.4705632C>T			A7U7M5|Q9H311|Q9H312|Q9NTM4	Silent	SNP	ENST00000305817.2	37	CCDS13081.1																																																																																				0.602	PRND-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077827.2	NM_012409		8	38	8	38
PLCG1	5335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	20	39795459	39795459	+	Missense_Mutation	SNP	A	A	G			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr20:39795459A>G	ENST00000373271.1	+	19	2666	c.2261A>G	c.(2260-2262)tAt>tGt	p.Y754C	PLCG1_ENST00000244007.3_Missense_Mutation_p.Y754C|PLCG1_ENST00000373272.2_Missense_Mutation_p.Y754C	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	754	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				AAGCTGCGCTATCCCATCAAC	0.562																																																0													118.0	108.0	111.0					20																	39795459		2203	4300	6503	SO:0001583	missense	5335			M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"", ""SH2 domain containing"""	9065	protein-coding gene	gene with protein product		172420	"""phospholipase C, gamma 1 (formerly subtype 148)"""	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.2261A>G	20.37:g.39795459A>G	ENSP00000362368:p.Tyr754Cys		B7ZLY7|B9EGH4|E1P5W4|Q2V575	Missense_Mutation	SNP	ENST00000373271.1	37	CCDS13314.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.347540	0.82022	.	.	ENSG00000124181	ENST00000244007;ENST00000373271;ENST00000373272	T;T;T	0.66638	-0.22;-0.22;-0.22	5.63	5.63	0.86233	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);SH2 motif (2);	0.000000	0.85682	D	0.000000	T	0.82006	0.4943	M	0.79475	2.455	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.76575	0.988;0.976;0.973;0.973	D	0.84408	0.0564	10	0.72032	D	0.01	.	15.8331	0.78773	1.0:0.0:0.0:0.0	.	754;330;754;754	P19174-2;B4DMA3;P19174;A2A284	.;.;PLCG1_HUMAN;.	C	754	ENSP00000244007:Y754C;ENSP00000362368:Y754C;ENSP00000362369:Y754C	ENSP00000244007:Y754C	Y	+	2	0	PLCG1	39228873	1.000000	0.71417	0.974000	0.42286	0.855000	0.48748	9.339000	0.96797	2.132000	0.65825	0.528000	0.53228	TAT		0.562	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811		33	55	33	55
MAP3K19	80122	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	135744754	135744754	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr2:135744754G>A	ENST00000375845.3	-	7	1718	c.1688C>T	c.(1687-1689)aCc>aTc	p.T563I	MAP3K19_ENST00000392915.1_Missense_Mutation_p.T580I|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000358371.4_Missense_Mutation_p.T450I|MAP3K19_ENST00000392918.3_Intron	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	563							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										TTTATGCATGGTAGGCTTAAT	0.423																																																0													107.0	108.0	107.0					2																	135744754		2203	4300	6503	SO:0001583	missense	80122			AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	26249	protein-coding gene	gene with protein product			"""Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)"", ""yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)"", ""YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"""	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.1688C>T	2.37:g.135744754G>A	ENSP00000365005:p.Thr563Ile		B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	37	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	G	8.716	0.913226	0.17907	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000392915	T;T;T	0.71934	-0.61;-0.6;1.75	5.81	2.91	0.33838	.	0.547159	0.16607	N	0.207057	T	0.69663	0.3136	L	0.42245	1.32	0.09310	N	0.999998	P;D;P	0.59357	0.919;0.985;0.868	P;P;B	0.55391	0.483;0.775;0.289	T	0.59941	-0.7359	10	0.87932	D	0	.	5.0485	0.14496	0.0731:0.1032:0.2968:0.5269	.	450;580;563	Q56UN5-3;A8MWG7;Q56UN5	.;.;YSK4_HUMAN	I	563;450;580	ENSP00000365005:T563I;ENSP00000351140:T450I;ENSP00000376647:T580I	ENSP00000351140:T450I	T	-	2	0	YSK4	135461224	0.000000	0.05858	0.001000	0.08648	0.032000	0.12392	0.201000	0.17276	0.297000	0.22615	0.655000	0.94253	ACC		0.423	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		16	98	16	98
IFIH1	64135	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	163134056	163134056	+	Missense_Mutation	SNP	A	A	C			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr2:163134056A>C	ENST00000263642.2	-	10	2308	c.1913T>G	c.(1912-1914)tTt>tGt	p.F638C		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	638					cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|protein sumoylation (GO:0016925)|regulation of apoptotic process (GO:0042981)|regulation of type III interferon production (GO:0034344)|response to virus (GO:0009615)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|ribonucleoprotein complex binding (GO:0043021)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	39						TATGACTGCAAACTTCTTATC	0.353																																																0													124.0	106.0	112.0					2																	163134056		2202	4300	6502	SO:0001583	missense	64135			AF095844	CCDS2217.1	2q24.2	2010-02-09			ENSG00000115267	ENSG00000115267			18873	protein-coding gene	gene with protein product	"""helicard"""	606951					Standard	NM_022168		Approved	MDA-5, Hlcd, MDA5, IDDM19	uc002uce.4	Q9BYX4	OTTHUMG00000132055	ENST00000263642.2:c.1913T>G	2.37:g.163134056A>C	ENSP00000263642:p.Phe638Cys		Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Missense_Mutation	SNP	ENST00000263642.2	37	CCDS2217.1	.	.	.	.	.	.	.	.	.	.	A	15.16	2.749635	0.49257	.	.	ENSG00000115267	ENST00000263642;ENST00000543192	T	0.05580	3.42	5.66	3.21	0.36854	.	0.641961	0.16974	N	0.191998	T	0.07234	0.0183	L	0.51422	1.61	0.09310	N	1	P	0.47604	0.898	B	0.39876	0.312	T	0.21690	-1.0238	10	0.49607	T	0.09	0.0	9.4599	0.38778	0.7197:0.0:0.0:0.2803	.	638	Q9BYX4	IFIH1_HUMAN	C	638	ENSP00000263642:F638C	ENSP00000263642:F638C	F	-	2	0	IFIH1	162842302	0.006000	0.16342	0.543000	0.28128	0.563000	0.35712	0.285000	0.18883	0.386000	0.24997	0.460000	0.39030	TTT		0.353	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168		17	19	17	19
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_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			24	52	24	52
FLNB	2317	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	58094210	58094210	+	Missense_Mutation	SNP	A	A	G			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr3:58094210A>G	ENST00000295956.4	+	13	2132	c.1967A>G	c.(1966-1968)gAg>gGg	p.E656G	FLNB_ENST00000429972.2_Missense_Mutation_p.E656G|FLNB_ENST00000493452.1_Missense_Mutation_p.E487G|FLNB_ENST00000358537.3_Missense_Mutation_p.E656G|FLNB_ENST00000419752.2_Missense_Mutation_p.E487G|FLNB_ENST00000348383.5_Missense_Mutation_p.E656G|FLNB_ENST00000357272.4_Missense_Mutation_p.E656G|FLNB_ENST00000490882.1_Missense_Mutation_p.E656G	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	656					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		CCAGGTTTGGAGAAATCTGGA	0.448																																																0													76.0	72.0	74.0					3																	58094210		2203	4300	6503	SO:0001583	missense	2317			AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.1967A>G	3.37:g.58094210A>G	ENSP00000295956:p.Glu656Gly		B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	37	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.210665	0.79240	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.86562	-2.14;-2.14;-2.14;-2.14;-2.14;-2.14;-2.14;-2.14	5.56	5.56	0.83823	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.043726	0.85682	D	0.000000	D	0.93562	0.7945	M	0.84846	2.72	0.53005	D	0.999963	P;D;D;B;D;D	0.60575	0.951;0.988;0.961;0.037;0.961;0.961	P;D;D;B;D;D	0.64877	0.864;0.93;0.917;0.139;0.917;0.917	D	0.94511	0.7718	10	0.87932	D	0	.	16.002	0.80301	1.0:0.0:0.0:0.0	.	656;656;487;487;656;656	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	G	656;656;656;656;656;656;487;487	ENSP00000295956:E656G;ENSP00000420213:E656G;ENSP00000351339:E656G;ENSP00000415599:E656G;ENSP00000232447:E656G;ENSP00000349819:E656G;ENSP00000418510:E487G;ENSP00000414532:E487G	ENSP00000295956:E656G	E	+	2	0	FLNB	58069250	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	9.287000	0.95975	2.241000	0.73720	0.533000	0.62120	GAG		0.448	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		12	21	12	21
LEKR1	389170	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	156763496	156763496	+	Missense_Mutation	SNP	A	A	G	rs202202030		TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr3:156763496A>G	ENST00000470811.1	+	14	2459	c.1124A>G	c.(1123-1125)cAg>cGg	p.Q375R	LEKR1_ENST00000356539.4_Missense_Mutation_p.Q679R			Q6ZMV7	LEKR1_HUMAN	leucine, glutamate and lysine rich 1	375										breast(1)|large_intestine(5)|lung(3)|ovary(1)|skin(1)	11			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			GAGACTAGACAGAGACTGGCT	0.547																																																0													69.0	75.0	73.0					3																	156763496		2203	4300	6503	SO:0001583	missense	389170			AK131473	CCDS54660.1	3q25.31	2014-02-12	2008-02-21		ENSG00000197980	ENSG00000197980			33765	protein-coding gene	gene with protein product		613536					Standard	NM_001004316		Approved	FLJ16641	uc021xgh.1	Q6ZMV7	OTTHUMG00000160130	ENST00000470811.1:c.1124A>G	3.37:g.156763496A>G	ENSP00000418214:p.Gln375Arg			Missense_Mutation	SNP	ENST00000470811.1	37		.	.	.	.	.	.	.	.	.	.	A	8.875	0.950273	0.18431	.	.	ENSG00000178110	ENST00000470811;ENST00000356539	T;T	0.46451	0.88;0.87	5.06	-0.124	0.13523	.	0.335679	0.21883	N	0.067713	T	0.23171	0.0560	L	0.43152	1.355	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.30238	-0.9985	10	0.02654	T	1	-0.3495	4.2338	0.10616	0.5945:0.0:0.2637:0.1418	.	375	Q6ZMV7	LEKR1_HUMAN	R	375;679	ENSP00000418214:Q375R;ENSP00000348936:Q679R	ENSP00000348936:Q679R	Q	+	2	0	LEKR1	158246190	0.194000	0.23325	0.153000	0.22517	0.446000	0.32137	0.686000	0.25392	-0.034000	0.13713	-0.333000	0.08304	CAG		0.547	LEKR1-010	KNOWN	upstream_ATG|basic	protein_coding	protein_coding	OTTHUMT00000351625.3	NM_001004316		31	58	31	58
IGF2BP2	10644	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	185393095	185393095	+	Silent	SNP	G	G	A			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr3:185393095G>A	ENST00000382199.2	-	9	1155	c.1060C>T	c.(1060-1062)Ctg>Ttg	p.L354L	IGF2BP2_ENST00000457616.2_Silent_p.L360L|IGF2BP2_ENST00000494906.1_5'UTR|IGF2BP2_ENST00000421047.2_Silent_p.L297L|IGF2BP2_ENST00000346192.3_Silent_p.L354L	NM_006548.4	NP_006539.3	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding protein 2	354					anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	20	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			TTAACAGCCAGCATATCATTT	0.463																																																0													130.0	121.0	124.0					3																	185393095		2203	4300	6503	SO:0001819	synonymous_variant	10644			BC021290	CCDS3273.2, CCDS33903.1	3q27.2	2013-02-12			ENSG00000073792	ENSG00000073792		"""RNA binding motif (RRM) containing"""	28867	protein-coding gene	gene with protein product	"""IGF II mRNA binding protein 2"""	608289				10190901, 9891060	Standard	NM_001007225		Approved	IMP-2	uc003fpo.3	Q9Y6M1	OTTHUMG00000074025	ENST00000382199.2:c.1060C>T	3.37:g.185393095G>A			A0A4Z0|B3FTN2|B3FTN3|B3FTN4	Silent	SNP	ENST00000382199.2	37	CCDS3273.2																																																																																				0.463	IGF2BP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157087.2	NM_006548		17	134	17	134
ANK2	287	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	114280346	114280346	+	Silent	SNP	C	C	T			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr4:114280346C>T	ENST00000357077.4	+	38	10625	c.10572C>T	c.(10570-10572)acC>acT	p.T3524T	ANK2_ENST00000509550.1_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000264366.6_Silent_p.T3491T|ANK2_ENST00000510275.2_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	3524					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		CTGTTGAGACCGAGCACTCAG	0.473																																																0													111.0	111.0	111.0					4																	114280346		2203	4300	6503	SO:0001819	synonymous_variant	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.10572C>T	4.37:g.114280346C>T			Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	37	CCDS3702.1																																																																																				0.473	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		17	77	17	77
SEC24D	9871	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	119649799	119649799	+	Silent	SNP	G	G	A			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr4:119649799G>A	ENST00000280551.6	-	22	3113	c.2875C>T	c.(2875-2877)Ctg>Ttg	p.L959L	SEC24D_ENST00000379735.5_Silent_p.L960L|SEC24D_ENST00000511481.1_Silent_p.L590L|SEC24D_ENST00000429811.2_3'UTR|SEC24D_ENST00000505134.1_5'UTR			O94855	SC24D_HUMAN	SEC24 family member D	959					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						ACTTCAGGCAGCAATGTCTTA	0.303																																																0													120.0	114.0	116.0					4																	119649799		2203	4298	6501	SO:0001819	synonymous_variant	9871			AB018298	CCDS3710.1	4q26	2013-10-21	2013-10-21		ENSG00000150961	ENSG00000150961			10706	protein-coding gene	gene with protein product		607186	"""SEC24 (S. cerevisiae) related gene family, member D"", ""SEC24 family, member D (S. cerevisiae)"""			9872452, 10075675	Standard	NM_014822		Approved	KIAA0755	uc003ici.4	O94855	OTTHUMG00000132957	ENST00000280551.6:c.2875C>T	4.37:g.119649799G>A			Q8IYI7	Silent	SNP	ENST00000280551.6	37	CCDS3710.1																																																																																				0.303	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4			9	51	9	51
GFM2	84340	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	74034187	74034187	+	Missense_Mutation	SNP	A	A	C			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr5:74034187A>C	ENST00000296805.3	-	14	1733	c.1276T>G	c.(1276-1278)Tca>Gca	p.S426A	GFM2_ENST00000509430.1_Missense_Mutation_p.S426A|GFM2_ENST00000427854.2_Missense_Mutation_p.S426A|GFM2_ENST00000515125.1_5'Flank|GFM2_ENST00000345239.2_Missense_Mutation_p.S379A	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		GCAGTCAATGAAGGGATTTCT	0.333																																																0													134.0	133.0	133.0					5																	74034187		2203	4300	6503	SO:0001583	missense	84340			AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.1276T>G	5.37:g.74034187A>C	ENSP00000296805:p.Ser426Ala			Missense_Mutation	SNP	ENST00000296805.3	37	CCDS4023.1	.	.	.	.	.	.	.	.	.	.	A	17.29	3.352659	0.61293	.	.	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000546082;ENST00000509430;ENST00000427854	T;T;T;T	0.62364	0.03;1.55;0.03;0.03	5.91	4.71	0.59529	Translation elongation factor EFTu/EF1A, domain 2 (1);Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.113551	0.64402	N	0.000007	T	0.61185	0.2327	L	0.54863	1.705	0.54753	D	0.999989	B;B;P;B	0.35107	0.024;0.345;0.484;0.03	B;B;B;B	0.40285	0.037;0.204;0.325;0.063	T	0.57883	-0.7734	10	0.34782	T	0.22	-6.4332	13.0613	0.59008	0.8657:0.1343:0.0:0.0	.	426;426;379;426	Q969S9-3;Q969S9-5;Q969S9-2;Q969S9	.;.;.;RRF2M_HUMAN	A	426;379;426;426;426	ENSP00000296805:S426A;ENSP00000296804:S379A;ENSP00000427004:S426A;ENSP00000405808:S426A	ENSP00000296805:S426A	S	-	1	0	GFM2	74069943	1.000000	0.71417	0.985000	0.45067	0.868000	0.49771	7.454000	0.80714	1.016000	0.39470	0.533000	0.62120	TCA		0.333	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380		88	83	88	83
PCDHAC1	56135	hgsc.bcm.edu;broad.mit.edu	37	5	140308171	140308171	+	Missense_Mutation	SNP	T	T	C			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr5:140308171T>C	ENST00000253807.2	+	1	1694	c.1694T>C	c.(1693-1695)gTc>gCc	p.V565A	PCDHA6_ENST00000529310.1_Intron|PCDHAC1_ENST00000409700.3_Missense_Mutation_p.V565A|PCDHA1_ENST00000394633.3_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA9_ENST00000532602.1_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	565					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AATGGTTCTGTCCCAGTGGAA	0.473																																																0													123.0	127.0	125.0					5																	140308171		2203	4300	6503	SO:0001583	missense	56135			AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"""Cadherins / Protocadherins : Clustered"""	8676	other	complex locus constituent	"""PCDH-ALPHA-C1"""	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.1694T>C	5.37:g.140308171T>C	ENSP00000253807:p.Val565Ala		Q9Y5F5|Q9Y5I5	Missense_Mutation	SNP	ENST00000253807.2	37	CCDS4241.1	.	.	.	.	.	.	.	.	.	.	T	0.012	-1.670602	0.00758	.	.	ENSG00000248383	ENST00000409700;ENST00000253807	T;T	0.59906	0.23;0.23	5.95	3.47	0.39725	Cadherin-like (1);	.	.	.	.	T	0.32224	0.0822	N	0.12746	0.255	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.16722	0.016;0.007	T	0.26677	-1.0096	9	0.02654	T	1	.	7.6444	0.28312	0.0:0.0711:0.1404:0.7885	.	565;565	Q9H158;Q9H158-2	PCDC1_HUMAN;.	A	565	ENSP00000386356:V565A;ENSP00000253807:V565A	ENSP00000253807:V565A	V	+	2	0	PCDHAC1	140288355	0.000000	0.05858	0.869000	0.34112	0.477000	0.33069	0.345000	0.19979	1.078000	0.41014	0.460000	0.39030	GTC		0.473	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898		7	108	7	108
STK10	6793	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	171520604	171520604	+	Missense_Mutation	SNP	C	C	T	rs563239491		TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr5:171520604C>T	ENST00000176763.5	-	9	1709	c.1366G>A	c.(1366-1368)Gcc>Acc	p.A456T	STK10_ENST00000517775.1_5'Flank	NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	456					cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			GTCTCCAGGGCGCTGCTGTTG	0.647																																																0													41.0	46.0	44.0					5																	171520604		2203	4300	6503	SO:0001583	missense	6793			AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.1366G>A	5.37:g.171520604C>T	ENSP00000176763:p.Ala456Thr		A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Missense_Mutation	SNP	ENST00000176763.5	37	CCDS34290.1	.	.	.	.	.	.	.	.	.	.	C	13.06	2.124587	0.37533	.	.	ENSG00000072786	ENST00000176763;ENST00000545839	T	0.54866	0.55	4.95	3.03	0.35002	.	0.763150	0.12411	N	0.471270	T	0.33644	0.0870	L	0.51422	1.61	0.38772	D	0.954573	P	0.40794	0.729	B	0.25140	0.058	T	0.23904	-1.0175	10	0.15952	T	0.53	.	5.6758	0.17747	0.0:0.693:0.2018:0.1052	.	456	O94804	STK10_HUMAN	T	456	ENSP00000176763:A456T	ENSP00000176763:A456T	A	-	1	0	STK10	171453209	0.626000	0.27120	0.982000	0.44146	0.995000	0.86356	0.824000	0.27379	2.450000	0.82876	0.650000	0.86243	GCC		0.647	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990		10	56	10	56
NPC1L1	29881	hgsc.bcm.edu;ucsc.edu	37	7	44579068	44579068	+	Missense_Mutation	SNP	C	C	T	rs79803700	byFrequency	TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr7:44579068C>T	ENST00000289547.4	-	2	983	c.928G>A	c.(928-930)Gcc>Acc	p.A310T	NPC1L1_ENST00000423141.1_Missense_Mutation_p.A310T|NPC1L1_ENST00000381160.3_Missense_Mutation_p.A310T|NPC1L1_ENST00000546276.1_Missense_Mutation_p.A310T	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	310					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	TTGTCCCTGGCGGGGGCCACA	0.602																																																0													88.0	92.0	91.0					7																	44579068		2203	4300	6503	SO:0001583	missense	29881				CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"""NPC1 (Niemann-Pick disease, type C1, gene)-like 1"""			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.928G>A	7.37:g.44579068C>T	ENSP00000289547:p.Ala310Thr		A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Missense_Mutation	SNP	ENST00000289547.4	37	CCDS5491.1	.	.	.	.	.	.	.	.	.	.	N	1.266	-0.614521	0.03663	.	.	ENSG00000015520	ENST00000289547;ENST00000381160;ENST00000546276;ENST00000423141	D;D;D;D	0.90385	-2.66;-2.66;-2.66;-2.66	4.98	-8.08	0.01094	.	2.577080	0.01629	N	0.023437	T	0.81302	0.4794	L	0.47716	1.5	0.09310	N	1	B;B;B;B	0.31680	0.002;0.335;0.005;0.0	B;B;B;B	0.25614	0.005;0.062;0.005;0.0	T	0.70791	-0.4776	10	0.10636	T	0.68	-0.5623	4.2652	0.10759	0.1579:0.4765:0.0845:0.281	.	310;310;310;310	B7ZLE6;Q9UHC9-3;Q17RV5;D3DVK9	.;.;.;.	T	310	ENSP00000289547:A310T;ENSP00000370552:A310T;ENSP00000438033:A310T;ENSP00000404670:A310T	ENSP00000289547:A310T	A	-	1	0	NPC1L1	44545593	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-3.419000	0.00477	-1.200000	0.02662	-1.632000	0.00781	GCC		0.602	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389		19	98	19	98
LMTK2	22853	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	97823142	97823142	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr7:97823142G>A	ENST00000297293.5	+	11	3658	c.3365G>A	c.(3364-3366)gGa>gAa	p.G1122E		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	1122					early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					GAGGTCCCGGGAACCTCCCCA	0.607																																																0													65.0	64.0	64.0					7																	97823142		2203	4300	6503	SO:0001583	missense	22853			AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 100"""	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.3365G>A	7.37:g.97823142G>A	ENSP00000297293:p.Gly1122Glu		A4D272|Q75MG7|Q9UPS3	Missense_Mutation	SNP	ENST00000297293.5	37	CCDS5654.1	.	.	.	.	.	.	.	.	.	.	G	16.66	3.184097	0.57800	.	.	ENSG00000164715	ENST00000297293	T	0.77620	-1.11	5.37	3.45	0.39498	.	0.408600	0.29383	N	0.012304	T	0.70937	0.3281	M	0.69823	2.125	0.09310	N	0.999995	B	0.25390	0.125	B	0.22753	0.041	T	0.57562	-0.7790	10	0.25751	T	0.34	.	6.5638	0.22501	0.1577:0.149:0.6933:0.0	.	1122	Q8IWU2	LMTK2_HUMAN	E	1122	ENSP00000297293:G1122E	ENSP00000297293:G1122E	G	+	2	0	LMTK2	97661078	0.675000	0.27558	0.057000	0.19452	0.059000	0.15707	0.436000	0.21526	1.407000	0.46875	0.650000	0.86243	GGA		0.607	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916		29	39	29	39
COG5	10466	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	107204267	107204267	+	Silent	SNP	G	G	C			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr7:107204267G>C	ENST00000347053.3	-	1	218	c.168C>G	c.(166-168)gtC>gtG	p.V56V	COG5_ENST00000297135.3_Silent_p.V56V|DUS4L_ENST00000265720.3_5'Flank|DUS4L_ENST00000498786.1_Intron|DUS4L_ENST00000402620.1_5'Flank|COG5_ENST00000393603.2_Silent_p.V56V	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	56					intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						GAAGTTCCCGGACTGTAGCTG	0.667																																																0													43.0	41.0	42.0					7																	107204267		2202	4298	6500	SO:0001819	synonymous_variant	10466			AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"""Components of oligomeric golgi complex"""	14857	protein-coding gene	gene with protein product		606821	"""golgi transport complex 1 (90 kDa subunit)"""	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.168C>G	7.37:g.107204267G>C			A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Silent	SNP	ENST00000347053.3	37	CCDS5743.1																																																																																				0.667	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4			11	24	11	24
PLXNA4	91584	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	131848964	131848964	+	Silent	SNP	G	G	A			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr7:131848964G>A	ENST00000359827.3	-	24	5399	c.4437C>T	c.(4435-4437)ggC>ggT	p.G1479G	PLXNA4_ENST00000321063.4_Silent_p.G1479G			Q9HCM2	PLXA4_HUMAN	plexin A4	1479					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						AGCGGGCCTCGCCCGTGATGG	0.592																																																0													75.0	78.0	77.0					7																	131848964		2203	4300	6503	SO:0001819	synonymous_variant	91584			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.4437C>T	7.37:g.131848964G>A			A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																				0.592	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		8	32	8	32
SHH	6469	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	155599004	155599004	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr7:155599004C>T	ENST00000297261.2	-	2	698	c.548G>A	c.(547-549)tGc>tAc	p.C183Y	SHH_ENST00000472308.1_5'Flank	NM_000193.2	NP_000184.1	Q15465	SHH_HUMAN	sonic hedgehog	183			C -> F (in HPE3). {ECO:0000269|PubMed:11479728, ECO:0000269|PubMed:19603532}.|C -> R (in HPE3). {ECO:0000269|PubMed:19603532}.|C -> Y (in HPE3). {ECO:0000269|PubMed:19603532}.		androgen metabolic process (GO:0008209)|apoptotic signaling pathway (GO:0097190)|artery development (GO:0060840)|axon guidance (GO:0007411)|Bergmann glial cell differentiation (GO:0060020)|blood coagulation (GO:0007596)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|branching morphogenesis of an epithelial tube (GO:0048754)|bud outgrowth involved in lung branching (GO:0060447)|camera-type eye development (GO:0043010)|canonical Wnt signaling pathway (GO:0060070)|CD4-positive or CD8-positive, alpha-beta T cell lineage commitment (GO:0043369)|cell development (GO:0048468)|cell fate specification (GO:0001708)|cell-cell signaling (GO:0007267)|cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|cerebellar granule cell precursor proliferation (GO:0021930)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|dorsal/ventral neural tube patterning (GO:0021904)|dorsal/ventral pattern formation (GO:0009953)|ectoderm development (GO:0007398)|embryo development (GO:0009790)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic skeletal system development (GO:0048706)|endocytosis (GO:0006897)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial-mesenchymal signaling involved in prostate gland development (GO:0060738)|establishment of cell polarity (GO:0030010)|forebrain development (GO:0030900)|formation of anatomical boundary (GO:0048859)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|hindgut morphogenesis (GO:0007442)|inner ear development (GO:0048839)|intein-mediated protein splicing (GO:0016539)|intermediate filament organization (GO:0045109)|left lung development (GO:0060459)|limb bud formation (GO:0060174)|lung development (GO:0030324)|lung epithelium development (GO:0060428)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|lymphoid progenitor cell differentiation (GO:0002320)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal smoothened signaling pathway involved in prostate gland development (GO:0060783)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|metanephros development (GO:0001656)|midbrain development (GO:0030901)|multicellular structure septum development (GO:0080125)|myoblast differentiation (GO:0045445)|myotube differentiation (GO:0014902)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell migration (GO:0030336)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of kidney smooth muscle cell differentiation (GO:2000357)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of ureter smooth muscle cell differentiation (GO:2000062)|negative thymic T cell selection (GO:0045060)|neural crest cell migration (GO:0001755)|neuroblast proliferation (GO:0007405)|neuron fate commitment (GO:0048663)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|organ formation (GO:0048645)|osteoblast development (GO:0002076)|palate development (GO:0060021)|pancreas development (GO:0031016)|pattern specification process (GO:0007389)|patterning of blood vessels (GO:0001569)|polarity specification of anterior/posterior axis (GO:0009949)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of immature T cell proliferation in thymus (GO:0033092)|positive regulation of kidney smooth muscle cell differentiation (GO:2000358)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of sclerotome development (GO:0061189)|positive regulation of skeletal muscle cell proliferation (GO:0014858)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of striated muscle cell differentiation (GO:0051155)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureter smooth muscle cell differentiation (GO:2000063)|positive regulation of Wnt signaling pathway (GO:0030177)|positive thymic T cell selection (GO:0045059)|primary prostatic bud elongation (GO:0060516)|prostate epithelial cord elongation (GO:0060523)|prostate gland development (GO:0030850)|protein localization to nucleus (GO:0034504)|regulation of cell proliferation (GO:0042127)|regulation of mesenchymal cell proliferation involved in prostate gland development (GO:0060782)|regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900175)|regulation of odontogenesis (GO:0042481)|regulation of prostatic bud formation (GO:0060685)|regulation of protein localization to nucleus (GO:1900180)|regulation of proteolysis (GO:0030162)|renal system development (GO:0072001)|right lung development (GO:0060458)|salivary gland cavitation (GO:0060662)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|somite development (GO:0061053)|spinal cord dorsal/ventral patterning (GO:0021513)|spinal cord motor neuron differentiation (GO:0021522)|stem cell development (GO:0048864)|striated muscle tissue development (GO:0014706)|T cell differentiation in thymus (GO:0033077)|telencephalon regionalization (GO:0021978)|thalamus development (GO:0021794)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|trachea morphogenesis (GO:0060439)|vasculogenesis (GO:0001570)|ventral midline development (GO:0007418)	cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|laminin-1 binding (GO:0043237)|morphogen activity (GO:0016015)|patched binding (GO:0005113)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)			central_nervous_system(3)|kidney(1)|large_intestine(1)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	14	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00882)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TTTCACCGAGCAGTGGATATG	0.622																																																0			GRCh37	CM012473	SHH	M							64.0	61.0	62.0					7																	155599004		2203	4298	6501	SO:0001583	missense	6469				CCDS5942.1	7q36	2010-06-25	2010-06-25		ENSG00000164690	ENSG00000164690			10848	protein-coding gene	gene with protein product		600725	"""sonic hedgehog (Drosophila) homolog"", ""sonic hedgehog homolog (Drosophila)"""	HPE3, HLP3		7590746	Standard	NM_000193		Approved	HHG1, SMMCI, TPT, TPTPS, MCOPCB5	uc003wmk.1	Q15465	OTTHUMG00000151349	ENST00000297261.2:c.548G>A	7.37:g.155599004C>T	ENSP00000297261:p.Cys183Tyr		A4D247|Q75MC9	Missense_Mutation	SNP	ENST00000297261.2	37	CCDS5942.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.339053	0.81911	.	.	ENSG00000164690	ENST00000297261;ENST00000430104	D;D	0.99422	-5.88;-5.88	3.35	3.35	0.38373	Hedgehog/DD-peptidase (2);Hedgehog, N-terminal signaling domain (1);	0.000000	0.85682	D	0.000000	D	0.99609	0.9858	M	0.93763	3.455	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.998;0.998	D	0.97529	1.0078	10	0.87932	D	0	.	15.2317	0.73395	0.0:1.0:0.0:0.0	.	183;186;96	Q15465;D9ZGF9;C9JC48	SHH_HUMAN;.;.	Y	183;96	ENSP00000297261:C183Y;ENSP00000396621:C96Y	ENSP00000297261:C183Y	C	-	2	0	SHH	155291765	1.000000	0.71417	0.989000	0.46669	0.960000	0.62799	3.739000	0.55075	1.858000	0.53909	0.561000	0.74099	TGC		0.622	SHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322327.1	NM_000193		25	88	25	88
EPPK1	83481	hgsc.bcm.edu;broad.mit.edu	37	8	144942235	144942235	+	Silent	SNP	G	G	A			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr8:144942235G>A	ENST00000525985.1	-	2	5258	c.5187C>T	c.(5185-5187)ttC>ttT	p.F1729F				P58107	EPIPL_HUMAN	epiplakin 1	1729						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TGTTGGGGTCGAAGAAGCCCT	0.622																																																0													97.0	103.0	101.0					8																	144942235		2091	4192	6283	SO:0001819	synonymous_variant	83481			AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.5187C>T	8.37:g.144942235G>A			Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																					0.622	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		35	58	35	58
SVEP1	79987	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	113139596	113139596	+	Missense_Mutation	SNP	C	C	A			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr9:113139596C>A	ENST00000401783.2	-	45	10795	c.10459G>T	c.(10459-10461)Gct>Tct	p.A3487S	SVEP1_ENST00000297826.5_Missense_Mutation_p.A1413S|SVEP1_ENST00000374469.1_Missense_Mutation_p.A3464S	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	3487					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						CAGGAACAAGCATTTGGGCGT	0.507																																																0													69.0	68.0	68.0					9																	113139596		1912	4118	6030	SO:0001583	missense	79987			AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.10459G>T	9.37:g.113139596C>A	ENSP00000384917:p.Ala3487Ser		Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	C	15.07	2.723258	0.48728	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.66280	1.9;1.9;-0.2	5.43	5.43	0.79202	Epidermal growth factor-like (1);	0.216465	0.47852	D	0.000216	T	0.35335	0.0928	N	0.01742	-0.745	0.80722	D	1	B	0.22346	0.068	B	0.15484	0.013	T	0.40590	-0.9555	10	0.07482	T	0.82	.	19.258	0.93955	0.0:1.0:0.0:0.0	.	3487	Q4LDE5	SVEP1_HUMAN	S	3487;3464;1413	ENSP00000384917:A3487S;ENSP00000363593:A3464S;ENSP00000297826:A1413S	ENSP00000297826:A1413S	A	-	1	0	SVEP1	112179417	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.541000	0.53618	2.554000	0.86153	0.655000	0.94253	GCT		0.507	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				20	45	20	45
MAGEB10	139422	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	27840125	27840125	+	Silent	SNP	C	C	T			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chrX:27840125C>T	ENST00000356790.2	+	3	947	c.702C>T	c.(700-702)gaC>gaT	p.D234D		NM_182506.3	NP_872312.2	Q96LZ2	MAGBA_HUMAN	melanoma antigen family B, 10	234	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	26						GGTTATATGACGGAATTGAGC	0.468																																																0													55.0	49.0	51.0					X																	27840125		2202	4300	6502	SO:0001819	synonymous_variant	139422				CCDS35221.1	Xp21.3	2008-02-05			ENSG00000177689	ENSG00000177689			25377	protein-coding gene	gene with protein product		300761				11454705	Standard	NM_182506		Approved	FLJ32965	uc004dbw.3	Q96LZ2	OTTHUMG00000046084	ENST00000356790.2:c.702C>T	X.37:g.27840125C>T			Q494Y6|Q494Y7|Q9BZ78	Silent	SNP	ENST00000356790.2	37	CCDS35221.1																																																																																				0.468	MAGEB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106216.1	NM_182506		8	44	8	44
ARHGEF6	9459	hgsc.bcm.edu;broad.mit.edu	37	X	135825810	135825810	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chrX:135825810C>A	ENST00000250617.6	-	5	1800	c.595G>T	c.(595-597)Gaa>Taa	p.E199*	ARHGEF6_ENST00000535227.1_Nonsense_Mutation_p.E45*|ARHGEF6_ENST00000370620.1_Nonsense_Mutation_p.E45*|ARHGEF6_ENST00000370622.1_Nonsense_Mutation_p.E45*	NM_004840.2	NP_004831.1	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	199	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.			E -> G (in Ref. 2; CAD97632). {ECO:0000305}.	apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell junction assembly (GO:0034329)|JNK cascade (GO:0007254)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|intracellular (GO:0005622)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(1)|lung(14)|prostate(1)	38	Acute lymphoblastic leukemia(192;0.000127)					AATGTGCCTTCCCACCAGCCT	0.408																																																0													219.0	184.0	196.0					X																	135825810		2203	4300	6503	SO:0001587	stop_gained	9459			D13631	CCDS14660.1	Xq26	2013-01-10	2002-05-23		ENSG00000129675	ENSG00000129675		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	685	protein-coding gene	gene with protein product	"""Rac/Cdc42 guanine exchange factor (GEF) 6"", ""PAK-interacting exchange factor, alpha"", ""rho guanine nucleotide exchange factor 6"""	300267	"""mental retardation, X-linked 46"""	MRX46		7584048, 9659915	Standard	NM_004840		Approved	alphaPIX, Cool-2, KIAA0006, alpha-PIX, Cool2	uc004fab.3	Q15052	OTTHUMG00000022518	ENST00000250617.6:c.595G>T	X.37:g.135825810C>A	ENSP00000250617:p.Glu199*		A6NMW9|A8K6S7|B1AL37|Q15396|Q5JQ66|Q7Z3W1|Q86XH0	Nonsense_Mutation	SNP	ENST00000250617.6	37	CCDS14660.1	.	.	.	.	.	.	.	.	.	.	C	42	9.264713	0.99118	.	.	ENSG00000129675	ENST00000250617;ENST00000370620;ENST00000370622;ENST00000535736;ENST00000535227	.	.	.	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	19.057	0.93069	0.0:1.0:0.0:0.0	.	.	.	.	X	199;45;45;45;45	.	ENSP00000250617:E199X	E	-	1	0	ARHGEF6	135653476	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.449000	0.82847	0.600000	0.82982	GAA		0.408	ARHGEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058511.2	NM_004840		13	222	13	222
MAGEC3	139081	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	140969496	140969496	+	Missense_Mutation	SNP	C	C	A			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chrX:140969496C>A	ENST00000298296.1	+	4	823	c.823C>A	c.(823-825)Ctc>Atc	p.L275I	MAGEC3_ENST00000443323.2_Intron|MAGEC3_ENST00000448920.1_Intron|MAGEC3_ENST00000536088.1_Intron	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	275	MAGE 1. {ECO:0000255|PROSITE- ProRule:PRU00127}.									NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					CCAGAACCGCCTCCTGATTCT	0.502																																																0													134.0	127.0	129.0					X																	140969496		2202	4300	6502	SO:0001583	missense	139081			AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 2"""	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.823C>A	X.37:g.140969496C>A	ENSP00000298296:p.Leu275Ile		Q3SYA7|Q5JZ43|Q9BZ80	Missense_Mutation	SNP	ENST00000298296.1	37	CCDS14676.1	.	.	.	.	.	.	.	.	.	.	C	11.38	1.622832	0.28889	.	.	ENSG00000165509	ENST00000298296	T	0.06608	3.28	2.26	1.34	0.21922	.	.	.	.	.	T	0.11836	0.0288	M	0.77103	2.36	0.09310	N	1	D	0.59767	0.986	P	0.49683	0.619	T	0.17806	-1.0357	9	0.32370	T	0.25	.	4.8006	0.13294	0.0:0.8025:0.0:0.1975	.	275	Q8TD91	MAGC3_HUMAN	I	275	ENSP00000298296:L275I	ENSP00000298296:L275I	L	+	1	0	MAGEC3	140797162	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	-0.155000	0.10115	0.359000	0.24239	0.525000	0.51046	CTC		0.502	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702		32	215	32	215
TMEM9	252839	broad.mit.edu;ucsc.edu	37	1	201112999	201112999	+	Missense_Mutation	SNP	G	G	C			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr1:201112999G>C	ENST00000367330.1	-	4	864	c.348C>G	c.(346-348)atC>atG	p.I116M	TMEM9_ENST00000472411.1_5'UTR|TMEM9_ENST00000485839.2_Missense_Mutation_p.I116M|TMEM9_ENST00000367332.1_Missense_Mutation_p.I119M|TMEM9_ENST00000367334.5_Missense_Mutation_p.I116M|TMEM9_ENST00000367333.2_Missense_Mutation_p.I116M			Q9P0T7	TMEM9_HUMAN	transmembrane protein 9	116					transport (GO:0006810)	integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)				liver(1)|lung(1)|stomach(1)	3		Breast(1374;0.000301)				CCGGCTTTCGGATCAGAGGGT	0.572																																																0													120.0	106.0	111.0					1																	201112999		2203	4300	6503	SO:0001583	missense	252839				CCDS1408.1, CCDS73001.1	1q41	2008-02-05			ENSG00000116857	ENSG00000116857			18823	protein-coding gene	gene with protein product							Standard	NM_001288565		Approved	TMEM9A	uc001gvy.3	Q9P0T7	OTTHUMG00000035831	ENST00000367330.1:c.348C>G	1.37:g.201112999G>C	ENSP00000356299:p.Ile116Met		B1ALM6|Q96NQ9|Q9BQF5	Missense_Mutation	SNP	ENST00000367330.1	37	CCDS1408.1	.	.	.	.	.	.	.	.	.	.	G	15.51	2.854117	0.51270	.	.	ENSG00000116857	ENST00000367334;ENST00000367332;ENST00000367330;ENST00000367329;ENST00000367333;ENST00000455367;ENST00000435310	.	.	.	4.97	-4.53	0.03462	.	0.000000	0.85682	D	0.000000	T	0.70859	0.3272	M	0.64997	1.995	0.48452	D	0.999654	P;D;D	0.69078	0.919;0.997;0.997	P;D;D	0.83275	0.581;0.996;0.996	T	0.70292	-0.4912	9	0.46703	T	0.11	-20.2507	13.9059	0.63836	0.1109:0.0:0.8891:0.0	.	141;119;116	B4E1H4;B1ALM5;Q9P0T7	.;.;TMEM9_HUMAN	M	116;119;116;116;119;123;116	.	ENSP00000356298:I116M	I	-	3	3	TMEM9	199379622	0.994000	0.37717	0.499000	0.27577	0.714000	0.41099	0.324000	0.19610	-1.184000	0.02720	-0.768000	0.03414	ATC		0.572	TMEM9-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000087160.1	NM_016456		4	42	4	42
FOSB	2354	broad.mit.edu;ucsc.edu	37	19	45974181	45974181	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr19:45974181C>T	ENST00000353609.3	+	2	1013	c.421C>T	c.(421-423)Cgg>Tgg	p.R141W	FOSB_ENST00000586615.1_Missense_Mutation_p.R92W|FOSB_ENST00000443841.2_Intron|FOSB_ENST00000585836.1_Missense_Mutation_p.R102W|FOSB_ENST00000592436.1_Missense_Mutation_p.R141W|FOSB_ENST00000592811.1_Missense_Mutation_p.R92W|ERCC1_ENST00000423698.2_Intron|FOSB_ENST00000591858.1_Missense_Mutation_p.R102W|FOSB_ENST00000590335.1_Missense_Mutation_p.R141W|FOSB_ENST00000417353.2_Missense_Mutation_p.R141W	NM_006732.2	NP_006723.2	P53539	FOSB_HUMAN	FBJ murine osteosarcoma viral oncogene homolog B	141					cellular response to calcium ion (GO:0071277)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to progesterone (GO:0032570)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)	13		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00814)|Epithelial(262;0.18)|GBM - Glioblastoma multiforme(486;0.242)		AGCCCGAGCCCGGCCTAGGAG	0.632																																																0													29.0	37.0	34.0					19																	45974181		2203	4297	6500	SO:0001583	missense	2354				CCDS12664.1, CCDS46113.1	19q13.3	2013-01-10						"""basic leucine zipper proteins"""	3797	protein-coding gene	gene with protein product	"""oncogene FOS-B"", ""activator protein 1"""	164772				1301997	Standard	NM_006732		Approved	G0S3, GOSB, GOS3, AP-1, MGC42291, DKFZp686C0818	uc002pbx.4	P53539		ENST00000353609.3:c.421C>T	19.37:g.45974181C>T	ENSP00000245919:p.Arg141Trp		A8K9K5|A8VJE1|A8VJE6|A8VJF0|A8VJF3|A8VJF7|A8VJG1|A8VJG5|A8VJG9|E7EPR6|E9PHJ3|K7EMJ6|Q49AD7	Missense_Mutation	SNP	ENST00000353609.3	37	CCDS12664.1	.	.	.	.	.	.	.	.	.	.	C	17.76	3.469301	0.63625	.	.	ENSG00000125740	ENST00000353609;ENST00000417353;ENST00000455928	T;D	0.85411	-0.64;-1.98	4.33	0.544	0.17185	.	0.000000	0.85682	D	0.000000	D	0.87281	0.6138	L	0.47716	1.5	0.46725	D	0.99917	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.79108	0.924;0.987;0.981;0.924;0.992	D	0.84195	0.0447	10	0.38643	T	0.18	-1.6163	11.0857	0.48086	0.4935:0.5064:0.0:0.0	.	102;102;141;141;141	A8VJF0;A8VJF3;E9PHJ3;P53539;A8VJE1	.;.;.;FOSB_HUMAN;.	W	141	ENSP00000245919:R141W;ENSP00000407207:R141W	ENSP00000245919:R141W	R	+	1	2	FOSB	50666021	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	2.410000	0.44592	0.403000	0.25479	-0.314000	0.08810	CGG		0.632	FOSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459561.1	NM_006732		15	28	15	28
MDM4	4194	broad.mit.edu;ucsc.edu	37	1	204518349	204518349	+	Missense_Mutation	SNP	A	A	C			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr1:204518349A>C	ENST00000367182.3	+	11	1174	c.1012A>C	c.(1012-1014)Acc>Ccc	p.T338P	MDM4_ENST00000367183.3_Intron|MDM4_ENST00000463049.1_3'UTR|MDM4_ENST00000454264.2_Missense_Mutation_p.T288P|MDM4_ENST00000391947.2_3'UTR|MDM4_ENST00000507825.2_Intron	NM_001204171.1|NM_001278516.1|NM_001278517.1|NM_001278518.1|NM_001278519.1|NM_002393.4	NP_001191100.1|NP_001265445.1|NP_001265446.1|NP_001265447.1|NP_001265448.1|NP_002384.2	O15151	MDM4_HUMAN	MDM4, p53 regulator	338					cell proliferation (GO:0008283)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|G0 to G1 transition (GO:0045023)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)	nucleus (GO:0005634)	enzyme binding (GO:0019899)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	16	all_cancers(21;0.00146)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.112)|all_epithelial(62;0.118)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;3.15e-47)|all cancers(3;3.56e-32)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|Epithelial(59;0.143)|BRCA - Breast invasive adenocarcinoma(75;0.143)			TTCAAAGTTAACCCATTCTCT	0.428			A		"""GBM, bladder, retinoblastoma"""																																		Dom	yes		1	1q32	4194	Mdm4 p53 binding protein homolog		M	0													145.0	137.0	140.0					1																	204518349		2203	4300	6503	SO:0001583	missense	4194			AF007111	CCDS1447.1, CCDS55674.1, CCDS55675.1, CCDS60396.1, CCDS73007.1, CCDS73008.1, CCDS73009.1	1q32	2014-03-03	2014-03-03		ENSG00000198625	ENSG00000198625			6974	protein-coding gene	gene with protein product		602704	"""mouse double minute 4, human homolog of; p53-binding protein"", ""Mdm4, transformed 3T3 cell double minute 4, p53 binding protein (mouse)"", ""Mdm4 p53 binding protein homolog (mouse)"""			9226370, 14660608	Standard	NM_002393		Approved	MDMX, HDMX	uc001hba.3	O15151	OTTHUMG00000035877	ENST00000367182.3:c.1012A>C	1.37:g.204518349A>C	ENSP00000356150:p.Thr338Pro		Q2M2Y2|Q32SL2|Q6GS18|Q8IV83	Missense_Mutation	SNP	ENST00000367182.3	37	CCDS1447.1	.	.	.	.	.	.	.	.	.	.	A	11.82	1.751441	0.31046	.	.	ENSG00000198625	ENST00000367182;ENST00000454264;ENST00000444261	T;T;T	0.10382	2.88;2.88;2.88	6.17	5.01	0.66863	.	0.299430	0.42420	D	0.000714	T	0.06142	0.0159	N	0.08118	0	0.80722	D	1	B;B	0.10296	0.001;0.003	B;B	0.09377	0.004;0.004	T	0.39563	-0.9608	10	0.27785	T	0.31	-9.1919	12.9562	0.58430	0.8552:0.0:0.0:0.1448	.	338;288	O15151;Q2M2Y2	MDM4_HUMAN;.	P	338;288;116	ENSP00000356150:T338P;ENSP00000396840:T288P;ENSP00000395254:T116P	ENSP00000356150:T338P	T	+	1	0	MDM4	202784972	0.854000	0.29725	1.000000	0.80357	0.990000	0.78478	2.249000	0.43169	2.371000	0.80710	0.533000	0.62120	ACC		0.428	MDM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087415.2	NM_002393		15	121	15	121
KRT73	319101	broad.mit.edu;ucsc.edu	37	12	53008406	53008406	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr12:53008406G>A	ENST00000305748.3	-	4	810	c.776C>T	c.(775-777)gCc>gTc	p.A259V	RP11-641A6.2_ENST00000549180.1_RNA|RP11-641A6.2_ENST00000551089.1_RNA|RP11-641A6.2_ENST00000552364.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	259	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.189)		TCCATCCAGGGCATCCACCTT	0.542																																																0													138.0	114.0	122.0					12																	53008406		2203	4300	6503	SO:0001583	missense	319101			AJ508776	CCDS8834.1	12q13.13	2013-06-25			ENSG00000186049	ENSG00000186049		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28928	protein-coding gene	gene with protein product		608247				12648212, 16831889	Standard	NM_175068		Approved	KRT6IRS3, K6IRS3	uc001sas.3	Q86Y46	OTTHUMG00000169746	ENST00000305748.3:c.776C>T	12.37:g.53008406G>A	ENSP00000307014:p.Ala259Val		Q32MB2	Missense_Mutation	SNP	ENST00000305748.3	37	CCDS8834.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.741580	0.69304	.	.	ENSG00000186049	ENST00000305748	T	0.75367	-0.93	4.99	4.99	0.66335	Filament (1);	0.259831	0.27424	N	0.019437	T	0.76162	0.3949	M	0.68728	2.09	0.09310	N	1	P	0.38535	0.635	B	0.43155	0.41	T	0.73183	-0.4063	10	0.87932	D	0	.	13.602	0.62024	0.0795:0.0:0.9205:0.0	.	259	Q86Y46	K2C73_HUMAN	V	259	ENSP00000307014:A259V	ENSP00000307014:A259V	A	-	2	0	KRT73	51294673	0.000000	0.05858	0.733000	0.30861	0.906000	0.53458	0.803000	0.27083	2.710000	0.92621	0.555000	0.69702	GCC		0.542	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068		5	47	5	47
ASB9	140462	broad.mit.edu;ucsc.edu	37	X	15272893	15272893	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chrX:15272893G>A	ENST00000380488.4	-	3	521	c.248C>T	c.(247-249)tCt>tTt	p.S83F	ASB9_ENST00000380485.3_Missense_Mutation_p.S83F|ASB9_ENST00000546332.1_Missense_Mutation_p.S83F|ASB9_ENST00000473862.1_5'UTR|ASB9_ENST00000380483.3_Missense_Mutation_p.S83F	NM_001031739.2	NP_001026909.1	Q96DX5	ASB9_HUMAN	ankyrin repeat and SOCS box containing 9	83					intracellular signal transduction (GO:0035556)|positive regulation of protein catabolic process (GO:0045732)|protein ubiquitination (GO:0016567)	mitochondrion (GO:0005739)				breast(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(10)	15	Hepatocellular(33;0.183)					CTTCACACAAGAGAGATGACC	0.443																																																0													154.0	150.0	151.0					X																	15272893		2203	4300	6503	SO:0001583	missense	140462			AK000643	CCDS14163.1, CCDS35208.1, CCDS55372.1	Xp22.2	2013-01-10	2011-01-25		ENSG00000102048	ENSG00000102048		"""Ankyrin repeat domain containing"""	17184	protein-coding gene	gene with protein product		300890	"""ankyrin repeat and SOCS box-containing 9"""			12076535	Standard	NM_001031739		Approved	DKFZP564L0862, MGC4954, FLJ20636	uc004cwl.3	Q96DX5	OTTHUMG00000021172	ENST00000380488.4:c.248C>T	X.37:g.15272893G>A	ENSP00000369855:p.Ser83Phe		A8K8A5|Q9BVF5|Q9NWS5|Q9Y4T3	Missense_Mutation	SNP	ENST00000380488.4	37	CCDS35208.1	.	.	.	.	.	.	.	.	.	.	G	18.65	3.670309	0.67814	.	.	ENSG00000102048	ENST00000380483;ENST00000380485;ENST00000380488;ENST00000546332	T;T;T;T	0.65364	0.56;-0.15;-0.15;-0.15	5.93	5.04	0.67666	Ankyrin repeat-containing domain (3);	0.228496	0.44688	D	0.000440	T	0.71558	0.3354	L	0.58925	1.835	0.09310	N	1	P;P;D;D	0.59357	0.947;0.919;0.985;0.97	P;P;P;P	0.60473	0.536;0.464;0.875;0.643	T	0.64571	-0.6376	9	.	.	.	-11.6036	12.0956	0.53752	0.0877:0.0:0.9123:0.0	.	83;83;83;83	Q7Z4A2;Q9BVF5;Q96DX5;Q96DX5-2	.;.;ASB9_HUMAN;.	F	83	ENSP00000369850:S83F;ENSP00000369852:S83F;ENSP00000369855:S83F;ENSP00000438943:S83F	.	S	-	2	0	ASB9	15182814	0.902000	0.30710	0.004000	0.12327	0.317000	0.28152	3.706000	0.54830	1.184000	0.42957	0.600000	0.82982	TCT		0.443	ASB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055844.1			25	205	25	205
ATRX	546	broad.mit.edu;ucsc.edu	37	X	76909629	76909629	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chrX:76909629G>A	ENST00000373344.5	-	14	4490	c.4276C>T	c.(4276-4278)Cga>Tga	p.R1426*	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Nonsense_Mutation_p.R1388*	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1426					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.R1426*(1)|p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						TTAATACGTCGCCTTTTCTTT	0.328			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																																Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	2	Substitution - Nonsense(1)|Unknown(1)	central_nervous_system(1)|bone(1)											236.0	201.0	213.0					X																	76909629		2203	4295	6498	SO:0001587	stop_gained	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.4276C>T	X.37:g.76909629G>A	ENSP00000362441:p.Arg1426*		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Nonsense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	g	44	11.200502	0.99530	.	.	ENSG00000085224	ENST00000373344;ENST00000395603	.	.	.	5.41	3.6	0.41247	.	0.079753	0.50627	D	0.000111	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.8333	13.0038	0.58692	0.0:0.0:0.397:0.603	.	.	.	.	X	1426;1388	.	ENSP00000362441:R1426X	R	-	1	2	ATRX	76796285	0.991000	0.36638	0.982000	0.44146	0.683000	0.39861	1.747000	0.38298	0.544000	0.28883	0.502000	0.49764	CGA		0.328	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		41	102	41	102
PTPRF	5792	broad.mit.edu;ucsc.edu	37	1	44079328	44079328	+	Missense_Mutation	SNP	C	C	T	rs371752134		TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr1:44079328C>T	ENST00000359947.4	+	23	4353	c.4013C>T	c.(4012-4014)gCg>gTg	p.A1338V	PTPRF_ENST00000372414.3_Missense_Mutation_p.A1338V|PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000422171.2_Missense_Mutation_p.A697V|PTPRF_ENST00000438120.1_Missense_Mutation_p.A1329V|PTPRF_ENST00000372413.3_Missense_Mutation_p.A1329V	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1338					cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				ACCGACCTGGCGGACAACATC	0.597																																																0								C	VAL/ALA,VAL/ALA	0,4406		0,0,2203	285.0	228.0	247.0		4013,3986	5.2	0.9	1		247	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	PTPRF	NM_002840.3,NM_130440.2	64,64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	1338/1908,1329/1899	44079328	1,13005	2203	4300	6503	SO:0001583	missense	5792			Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.4013C>T	1.37:g.44079328C>T	ENSP00000353030:p.Ala1338Val		D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Missense_Mutation	SNP	ENST00000359947.4	37	CCDS489.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.10|18.10	3.547975|3.547975	0.65311|0.65311	0.0|0.0	1.16E-4|1.16E-4	ENSG00000142949|ENSG00000142949	ENST00000359947;ENST00000438120;ENST00000372414;ENST00000372413;ENST00000422171;ENST00000372407|ENST00000429895	T;T;T;T;T;T|.	0.29142|.	1.58;1.58;1.58;1.58;1.58;1.58|.	5.24|5.24	5.24|5.24	0.73138|0.73138	.|.	0.000000|.	0.34133|.	N|.	0.004221|.	T|T	0.75162|0.75162	0.3812|0.3812	M|M	0.69248|0.69248	2.105|2.105	0.80722|0.80722	D|D	1|1	B;B;P;P;P|.	0.47302|.	0.073;0.283;0.701;0.668;0.893|.	B;B;B;B;B|.	0.19391|.	0.001;0.004;0.009;0.023;0.025|.	T|T	0.73616|0.73616	-0.3926|-0.3926	10|5	0.54805|.	T|.	0.06|.	.|.	19.2146|19.2146	0.93770|0.93770	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	983;697;915;1329;1338|.	Q59FI2;F2Z3B8;Q5W9G3;P10586-2;P10586|.	.;.;.;.;PTPRF_HUMAN|.	V|W	1338;1329;1338;1329;697;410|984	ENSP00000353030:A1338V;ENSP00000398822:A1329V;ENSP00000361491:A1338V;ENSP00000361490:A1329V;ENSP00000387885:A697V;ENSP00000361484:A410V|.	ENSP00000353030:A1338V|.	A|R	+|+	2|1	0|2	PTPRF|PTPRF	43851915|43851915	1.000000|1.000000	0.71417|0.71417	0.950000|0.950000	0.38849|0.38849	0.423000|0.423000	0.31445|0.31445	7.770000|7.770000	0.85390|0.85390	2.619000|2.619000	0.88677|0.88677	0.561000|0.561000	0.74099|0.74099	GCG|CGG		0.597	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1			19	45	19	45
ARID2	196528	broad.mit.edu;hgsc.bcm.edu	37	12	46245951	46245960	+	Frame_Shift_Del	DEL	ATCAAAAGTG	ATCAAAAGTG	-			TCGA-DU-5855-01A-11D-1705-08	TCGA-DU-5855-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d77baeae-05d1-4edc-ba95-7292fcc375fb	603f649f-20bf-409c-88f4-ba1b89933074	g.chr12:46245951_46245960delATCAAAAGTG	ENST00000334344.6	+	15	4217_4226	c.4045_4054delATCAAAAGTG	c.(4045-4056)atcaaaagtgatfs	p.IKSD1349fs	ARID2_ENST00000422737.1_Frame_Shift_Del_p.IKSD1200fs|ARID2_ENST00000444670.1_Frame_Shift_Del_p.IKSD959fs|ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000479608.1_3'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1349					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		CATGCAAGATATCAAAAGTGATTTGAGAAA	0.357			"""N, S, F"""		hepatocellular carcinoma																																		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	0																																										SO:0001589	frameshift_variant	196528				CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"""-"""	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.4045_4054delATCAAAAGTG	12.37:g.46245951_46245960delATCAAAAGTG	ENSP00000335044:p.Ile1349fs		Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Frame_Shift_Del	DEL	ENST00000334344.6	37	CCDS31783.1																																																																																				0.357	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		19	41	19	41
