#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_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_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_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
IGHG3	3502	broad.mit.edu	37	14	106237611	106237611	+	RNA	SNP	C	C	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr14:106237611C>T	ENST00000390551.2	-	0	131							P01860	IGHG3_HUMAN	immunoglobulin heavy constant gamma 3 (G3m marker)						complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)										CTGGTCAGGGCGCCTGAGTTC	0.672																																																	0													33.0	29.0	30.0					14																	106237611		1917	4061	5978			8755			M12958		14q32.33	2012-10-02			ENSG00000211897	ENSG00000211897		"""Immunoglobulins / IGH locus"""	5527	other	immunoglobulin gene		147120				6808505	Standard	NG_001019		Approved			P01860	OTTHUMG00000152539		14.37:g.106237611C>T		Somatic		WXS	Illumina GAIIx	Phase_I	A2NU35	RNA	SNP	ENST00000390551.2	37																																																																																					0.672	IGHG3-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	IG_C_gene	IG_C_gene	OTTHUMT00000326654.1		NG_001019	
ETNPPL	64850	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	109667938	109667938	+	Silent	SNP	T	T	C			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr4:109667938T>C	ENST00000296486.3	-	10	1306	c.1152A>G	c.(1150-1152)gaA>gaG	p.E384E	ETNPPL_ENST00000512646.1_Silent_p.E326E|ETNPPL_ENST00000510706.1_Silent_p.E344E|ETNPPL_ENST00000411864.2_Silent_p.E378E	NM_001146590.1|NM_031279.3	NP_001140062.1|NP_112569.2	Q8TBG4	AT2L1_HUMAN	ethanolamine-phosphate phospho-lyase	384						mitochondrion (GO:0005739)	ethanolamine-phosphate phospho-lyase activity (GO:0050459)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)	p.E384E(1)									TGTGCTGAGCTTCAGCTGTGG	0.488																																																	1	Substitution - coding silent(1)	kidney(1)											239.0	241.0	240.0					4																	109667938		2203	4300	6503	SO:0001819	synonymous_variant	64850			AJ298293	CCDS3682.1, CCDS54792.1, CCDS54793.1	4q25	2013-06-12	2013-06-12	2013-06-12	ENSG00000164089	ENSG00000164089	4.2.3.2		14404	protein-coding gene	gene with protein product		614682	"""alanine-glyoxylate aminotransferase 2-like 1"""	AGXT2L1		7592550, 22241472	Standard	NM_031279		Approved		uc003hzc.3	Q8TBG4	OTTHUMG00000161036	ENST00000296486.3:c.1152A>G	4.37:g.109667938T>C		Somatic		WXS	Illumina HiSeq	Phase_I	B7Z1Y0|E9PBY0|Q9H174	Silent	SNP	ENST00000296486.3	37	CCDS3682.1																																																																																				0.488	ETNPPL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363508.1		NM_031279	
ZFAND4	93550	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	46121526	46121526	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr10:46121526A>G	ENST00000344646.5	-	7	1960	c.1745T>C	c.(1744-1746)tTa>tCa	p.L582S	ZFAND4_ENST00000374371.2_Intron|ZFAND4_ENST00000374370.1_5'UTR|ZFAND4_ENST00000374366.3_Missense_Mutation_p.L508S	NM_001128324.2|NM_174890.2	NP_001121796.1|NP_777550.2	Q86XD8	ZFAN4_HUMAN	zinc finger, AN1-type domain 4	582							zinc ion binding (GO:0008270)	p.L582S(1)									TGTGCTCTGTAATCTATTTCT	0.458																																																	1	Substitution - Missense(1)	kidney(1)											93.0	94.0	94.0					10																	46121526		2203	4300	6503	SO:0001583	missense	0			AF311324	CCDS7214.1, CCDS60520.1	10q11.22	2013-01-09	2011-11-10	2011-11-10	ENSG00000172671	ENSG00000172671		"""Zinc fingers, AN1-type domain containing"""	23504	protein-coding gene	gene with protein product			"""AN1, ubiquitin-like, homolog (Xenopus laevis)"""	ANUBL1			Standard	XM_005271837		Approved	FLJ40185	uc001jcp.4	Q86XD8	OTTHUMG00000018085	ENST00000344646.5:c.1745T>C	10.37:g.46121526A>G	ENSP00000339484:p.Leu582Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A8K8V4|B2RAX2|Q5VVY5	Missense_Mutation	SNP	ENST00000344646.5	37	CCDS7214.1	.	.	.	.	.	.	.	.	.	.	A	5.201	0.222652	0.09863	.	.	ENSG00000172671	ENST00000344646;ENST00000374366;ENST00000374370	T;T	0.25414	1.8;1.8	5.6	1.94	0.25998	.	1.103350	0.06899	N	0.805679	T	0.29158	0.0725	M	0.66939	2.045	0.09310	N	0.999997	B	0.13594	0.008	B	0.06405	0.002	T	0.31223	-0.9951	10	0.51188	T	0.08	-33.4013	8.5544	0.33471	0.763:0.0:0.237:0.0	.	582	Q86XD8	ANUB1_HUMAN	S	582;508;464	ENSP00000339484:L582S;ENSP00000363486:L508S	ENSP00000339484:L582S	L	-	2	0	ANUBL1	45441532	0.028000	0.19301	0.111000	0.21465	0.291000	0.27294	2.134000	0.42102	0.413000	0.25759	0.379000	0.24179	TTA		0.458	ZFAND4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047790.1		NM_174890	
ATG7	10533	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	11389435	11389435	+	Nonsense_Mutation	SNP	G	G	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr3:11389435G>T	ENST00000354449.3	+	12	1235	c.1210G>T	c.(1210-1212)Gaa>Taa	p.E404*	ATG7_ENST00000354956.5_Nonsense_Mutation_p.E404*|ATG7_ENST00000446450.2_Nonsense_Mutation_p.E365*	NM_006395.2	NP_006386.1	O95352	ATG7_HUMAN	autophagy related 7	404					adult walking behavior (GO:0007628)|C-terminal protein lipidation (GO:0006501)|cardiac muscle cell development (GO:0055013)|cellular amino acid metabolic process (GO:0006520)|cellular protein modification process (GO:0006464)|cellular response to hyperoxia (GO:0071455)|cellular response to nitrogen starvation (GO:0006995)|cellular response to starvation (GO:0009267)|central nervous system neuron axonogenesis (GO:0021955)|cerebellar Purkinje cell layer development (GO:0021680)|cerebral cortex development (GO:0021987)|late nucleophagy (GO:0044805)|liver development (GO:0001889)|membrane fusion (GO:0061025)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of apoptotic process (GO:0043066)|negative stranded viral RNA replication (GO:0039689)|neurological system process (GO:0050877)|piecemeal microautophagy of nucleus (GO:0034727)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein modification process (GO:0031401)|post-embryonic development (GO:0009791)|protein catabolic process (GO:0030163)|protein lipidation (GO:0006497)|protein modification by small protein conjugation (GO:0032446)|protein transport (GO:0015031)|pyramidal neuron development (GO:0021860)|regulation of protein ubiquitination (GO:0031396)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)	Atg12 activating enzyme activity (GO:0019778)|Atg8 activating enzyme (GO:0019779)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)|ubiquitin activating enzyme activity (GO:0004839)	p.E404*(2)		central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	34						CTATGAGTTTGAAGATTGCCT	0.522																																																	2	Substitution - Nonsense(2)	lung(1)|kidney(1)											119.0	117.0	118.0					3																	11389435		2203	4300	6503	SO:0001587	stop_gained	10533			AF094516	CCDS2605.1, CCDS46752.1, CCDS46753.1	3p25.3-p25.2	2014-02-18	2012-06-06	2005-09-11	ENSG00000197548	ENSG00000197548		"""Ubiquitin-like modifier activating enzymes"""	16935	protein-coding gene	gene with protein product	"""ubiquitin-activating enzyme E1-like protein"""	608760	"""APG7 autophagy 7-like (S. cerevisiae)"", ""ATG7 autophagy related 7 homolog (S. cerevisiae)"""	APG7L		10233149	Standard	NM_006395		Approved	GSA7, DKFZp434N0735	uc003bwc.3	O95352	OTTHUMG00000129740	ENST00000354449.3:c.1210G>T	3.37:g.11389435G>T	ENSP00000346437:p.Glu404*	Somatic		WXS	Illumina HiSeq	Phase_I	B4E170|E9PB95|Q7L8L0|Q9BWP2|Q9UFH4	Nonsense_Mutation	SNP	ENST00000354449.3	37	CCDS2605.1	.	.	.	.	.	.	.	.	.	.	G	33	5.278909	0.95489	.	.	ENSG00000197548	ENST00000446450;ENST00000354956;ENST00000354449	.	.	.	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-27.1626	15.2218	0.73316	0.0:0.0:0.8595:0.1405	.	.	.	.	X	365;404;404	.	ENSP00000346437:E404X	E	+	1	0	ATG7	11364435	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	9.316000	0.96319	2.840000	0.97914	0.655000	0.94253	GAA		0.522	ATG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251951.3		NM_006395	
CFAP43	80217	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	105953637	105953637	+	Missense_Mutation	SNP	C	C	T	rs145913363	byFrequency	TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr10:105953637C>T	ENST00000278064.2	-	11	1547	c.1222G>A	c.(1222-1224)Gtg>Atg	p.V408M	WDR96_ENST00000369720.1_Missense_Mutation_p.V408M|WDR96_ENST00000428666.1_Missense_Mutation_p.V478M|WDR96_ENST00000357060.3_Missense_Mutation_p.V477M														p.V477M(1)		NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						ACGTGCTGCACGGACGATTCC	0.517													C|||	2	0.000399361	0.0	0.0029	5008	,	,		18860	0.0		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)											81.0	59.0	66.0					10																	105953637		2203	4300	6503	SO:0001583	missense	0																														ENST00000278064.2:c.1222G>A	10.37:g.105953637C>T	ENSP00000278064:p.Val408Met	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000278064.2	37		2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	C	15.41	2.825653	0.50739	.	.	ENSG00000197748	ENST00000357060;ENST00000428666;ENST00000278064;ENST00000369720	T;T;T;T	0.40756	1.17;1.17;1.17;1.02	5.07	0.744	0.18353	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.772182	0.10654	N	0.649509	T	0.45013	0.1321	M	0.72118	2.19	0.09310	N	1	D;D	0.76494	0.999;0.997	P;D	0.64042	0.882;0.921	T	0.37079	-0.9721	10	0.72032	D	0.01	.	1.6925	0.02855	0.1603:0.4797:0.1743:0.1857	.	478;477	B4DHB6;Q8NDM7	.;WDR96_HUMAN	M	477;478;408;408	ENSP00000349568:V477M;ENSP00000400289:V478M;ENSP00000278064:V408M;ENSP00000358734:V408M	ENSP00000278064:V408M	V	-	1	0	WDR96	105943627	0.014000	0.17966	0.002000	0.10522	0.028000	0.11728	0.284000	0.18864	0.349000	0.23975	0.650000	0.86243	GTG		0.517	WDR96-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050200.1			
C1orf112	55732	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	169822055	169822055	+	Nonsense_Mutation	SNP	G	G	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr1:169822055G>A	ENST00000286031.6	+	24	3189	c.2489G>A	c.(2488-2490)tGg>tAg	p.W830*	SCYL3_ENST00000367771.6_3'UTR|C1orf112_ENST00000498289.1_3'UTR|C1orf112_ENST00000359326.4_Nonsense_Mutation_p.W830*|SCYL3_ENST00000367772.4_3'UTR	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	830								p.W830*(1)		breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					GCTCCAGCCTGGCTTTCAATG	0.483																																																	1	Substitution - Nonsense(1)	kidney(1)											110.0	115.0	113.0					1																	169822055		2203	4300	6503	SO:0001587	stop_gained	55732			AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.2489G>A	1.37:g.169822055G>A	ENSP00000286031:p.Trp830*	Somatic		WXS	Illumina HiSeq	Phase_I	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Nonsense_Mutation	SNP	ENST00000286031.6	37	CCDS1285.1	.	.	.	.	.	.	.	.	.	.	G	41	8.772778	0.98948	.	.	ENSG00000000460	ENST00000359326;ENST00000286031	.	.	.	5.5	4.59	0.56863	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.615	11.2482	0.49008	0.0854:0.0:0.9146:0.0	.	.	.	.	X	830	.	ENSP00000286031:W830X	W	+	2	0	C1orf112	168088679	1.000000	0.71417	0.849000	0.33467	0.014000	0.08584	6.063000	0.71162	1.319000	0.45190	-0.218000	0.12543	TGG		0.483	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3		NM_018186	
CA7	766	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	66887326	66887326	+	Silent	SNP	G	G	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr16:66887326G>A	ENST00000338437.2	+	7	829	c.720G>A	c.(718-720)agG>agA	p.R240R	CA7_ENST00000394069.3_Silent_p.R184R|RP11-61A14.1_ENST00000551187.1_RNA	NM_005182.2	NP_005173.1	P43166	CAH7_HUMAN	carbonic anhydrase VII	240					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|positive regulation of cellular pH reduction (GO:0032849)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of chloride transport (GO:2001225)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)	p.R240R(1)		kidney(1)|large_intestine(1)|lung(4)	6		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.088)|Epithelial(162;0.204)	Acetazolamide(DB00819)|Diclofenamide(DB01144)|Methazolamide(DB00703)|Zonisamide(DB00909)	ACGATGAGAGGATCCACATGG	0.602																																																	1	Substitution - coding silent(1)	kidney(1)											71.0	63.0	66.0					16																	66887326		2200	4300	6500	SO:0001819	synonymous_variant	766				CCDS10821.1, CCDS42173.1	16q22.1	2008-02-05			ENSG00000168748	ENSG00000168748	4.2.1.1	"""Carbonic anhydrases"""	1381	protein-coding gene	gene with protein product		114770				1783392	Standard	XM_005256135		Approved		uc002eqi.3	P43166	OTTHUMG00000137524	ENST00000338437.2:c.720G>A	16.37:g.66887326G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q541F0|Q86YU0	Silent	SNP	ENST00000338437.2	37	CCDS10821.1																																																																																				0.602	CA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268847.1			
CHD5	26038	broad.mit.edu;ucsc.edu	37	1	6208965	6208965	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr1:6208965G>T	ENST00000262450.3	-	9	1431	c.1332C>A	c.(1330-1332)aaC>aaA	p.N444K	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.N444K(1)		breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		GCAGCGGCGGGTTGAGGCAAT	0.692																																																	1	Substitution - Missense(1)	kidney(1)											50.0	55.0	53.0					1																	6208965		2199	4297	6496	SO:0001583	missense	26038			AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"""Zinc fingers, PHD-type"""	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.1332C>A	1.37:g.6208965G>T	ENSP00000262450:p.Asn444Lys	Somatic		WXS	Illumina GAIIx	Phase_I	A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	37	CCDS57.1	.	.	.	.	.	.	.	.	.	.	G	18.31	3.594963	0.66219	.	.	ENSG00000116254	ENST00000262450	T	0.21734	1.99	3.56	3.56	0.40772	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, RING-type (1);Zinc finger, PHD-type (1);Chromo domain-like (1);	0.000000	0.64402	U	0.000001	T	0.37571	0.1008	L	0.43701	1.375	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	T	0.23048	-1.0199	10	0.54805	T	0.06	-32.8825	15.1444	0.72637	0.0:0.0:1.0:0.0	.	444	Q8TDI0	CHD5_HUMAN	K	444	ENSP00000262450:N444K	ENSP00000262450:N444K	N	-	3	2	CHD5	6131552	1.000000	0.71417	1.000000	0.80357	0.676000	0.39594	3.348000	0.52209	1.725000	0.51514	0.313000	0.20887	AAC		0.692	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2		NM_015557	
CHRNB2	1141	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	154543879	154543879	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr1:154543879C>A	ENST00000368476.3	+	5	844	c.580C>A	c.(580-582)Ctg>Atg	p.L194M		NM_000748.2	NP_000739.1	P17787	ACHB2_HUMAN	cholinergic receptor, nicotinic, beta 2 (neuronal)	194					action potential (GO:0001508)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|central nervous system projection neuron axonogenesis (GO:0021952)|cognition (GO:0050890)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|lateral geniculate nucleus development (GO:0021771)|learning (GO:0007612)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|neurological system process (GO:0050877)|optic nerve morphogenesis (GO:0021631)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|protein heterooligomerization (GO:0051291)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of circadian sleep/wake cycle, REM sleep (GO:0042320)|regulation of dendrite morphogenesis (GO:0048814)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine secretion (GO:0014059)|regulation of synapse assembly (GO:0051963)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|sensory perception of pain (GO:0019233)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)|vestibulocochlear nerve development (GO:0021562)|visual learning (GO:0008542)|visual perception (GO:0007601)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)|ligand-gated ion channel activity (GO:0015276)	p.L194M(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|skin(1)|urinary_tract(3)	28	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)		Dextromethorphan(DB00514)|Galantamine(DB00674)|Nicotine(DB00184)	GGTGGCCAGCCTGGACGACTT	0.587																																																	1	Substitution - Missense(1)	kidney(1)											159.0	118.0	132.0					1																	154543879		2203	4300	6503	SO:0001583	missense	1141			U62437	CCDS1070.1	1q21.3	2012-02-11	2006-02-01		ENSG00000160716	ENSG00000160716		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1962	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, beta 2 (neuronal)"""	118507	"""cholinergic receptor, nicotinic, beta polypeptide 2 (neuronal)"""			1505988	Standard	NM_000748		Approved		uc001ffg.3	P17787	OTTHUMG00000037262	ENST00000368476.3:c.580C>A	1.37:g.154543879C>A	ENSP00000357461:p.Leu194Met	Somatic		WXS	Illumina HiSeq	Phase_I	Q9UEH9	Missense_Mutation	SNP	ENST00000368476.3	37	CCDS1070.1	.	.	.	.	.	.	.	.	.	.	C	10.04	1.240653	0.22711	.	.	ENSG00000160716	ENST00000368476	D	0.82619	-1.63	4.25	2.14	0.27477	Neurotransmitter-gated ion-channel ligand-binding (3);	0.059842	0.64402	D	0.000004	T	0.53965	0.1829	N	0.17838	0.53	0.35339	D	0.786337	B	0.13594	0.008	B	0.24006	0.05	T	0.45498	-0.9257	10	0.33141	T	0.24	.	8.7953	0.34876	0.1543:0.7508:0.0:0.0949	.	194	P17787	ACHB2_HUMAN	M	194	ENSP00000357461:L194M	ENSP00000357461:L194M	L	+	1	2	CHRNB2	152810503	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	1.474000	0.35398	0.940000	0.37473	0.467000	0.42956	CTG		0.587	CHRNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090697.1		NM_000748	
CD5L	922	broad.mit.edu	37	1	157805891	157805891	+	Missense_Mutation	SNP	A	A	C			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr1:157805891A>C	ENST00000368174.4	-	3	206	c.110T>G	c.(109-111)gTg>gGg	p.V37G	CD5L_ENST00000484609.1_5'UTR	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	37	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	scavenger receptor activity (GO:0005044)	p.V37G(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			TTCCACCTCCACCCGCCCTTC	0.632																																																	1	Substitution - Missense(1)	kidney(1)											67.0	67.0	67.0					1																	157805891		2203	4300	6503	SO:0001583	missense	922			U82812	CCDS1171.1	1q21-q23	2008-02-05	2006-03-28		ENSG00000073754	ENSG00000073754			1690	protein-coding gene	gene with protein product		602592	"""apoptosis inhibitor 6"", ""CD5 antigen-like (scavenger receptor cysteine rich family)"""	API6		9045627	Standard	NM_005894		Approved	Spalpha	uc001frk.4	O43866	OTTHUMG00000022440	ENST00000368174.4:c.110T>G	1.37:g.157805891A>C	ENSP00000357156:p.Val37Gly	Somatic		WXS	Illumina GAIIx	Phase_I	A8K7M5|Q6UX63	Missense_Mutation	SNP	ENST00000368174.4	37	CCDS1171.1	.	.	.	.	.	.	.	.	.	.	A	18.03	3.531821	0.64972	.	.	ENSG00000073754	ENST00000368174	T	0.56275	0.47	4.85	4.85	0.62838	Speract/scavenger receptor (4);Speract/scavenger receptor-related (2);	0.342835	0.20929	N	0.083135	T	0.78672	0.4320	H	0.97874	4.095	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.85860	0.1409	10	0.87932	D	0	.	12.4384	0.55612	1.0:0.0:0.0:0.0	.	37	O43866	CD5L_HUMAN	G	37	ENSP00000357156:V37G	ENSP00000357156:V37G	V	-	2	0	CD5L	156072515	1.000000	0.71417	0.928000	0.36995	0.245000	0.25701	6.867000	0.75511	2.025000	0.59659	0.460000	0.39030	GTG		0.632	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1		NM_005894	
CRYGS	1427	broad.mit.edu;ucsc.edu	37	3	186262113	186262113	+	Start_Codon_SNP	SNP	C	C	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr3:186262113C>T	ENST00000392499.2	-	2	342	c.3G>A	c.(1-3)atG>atA	p.M1I	CRYGS_ENST00000307944.5_Start_Codon_SNP_p.M1I	NM_017541.2	NP_060011.1	P22914	CRBS_HUMAN	crystallin, gamma S	1					lens development in camera-type eye (GO:0002088)|morphogenesis of an epithelium (GO:0002009)		structural constituent of eye lens (GO:0005212)	p.M1I(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)	11	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.5e-22)	GBM - Glioblastoma multiforme(93;0.0906)		CAGTTTTAGACATTTTTGGTG	0.398																																																	1	Substitution - Missense(1)	kidney(1)											145.0	133.0	137.0					3																	186262113		2203	4300	6503	SO:0001582	initiator_codon_variant	1427				CCDS3275.1	3q27.3	2013-02-14			ENSG00000213139	ENSG00000213139			2417	protein-coding gene	gene with protein product	"""crystallin, gamma 8"""	123730		CRYG8			Standard	NM_017541		Approved		uc003fqe.3	P22914	OTTHUMG00000156615	ENST00000392499.2:c.3G>A	3.37:g.186262113C>T	ENSP00000376287:p.Met1Ile	Somatic		WXS	Illumina GAIIx	Phase_I	B2RAF8	Missense_Mutation	SNP	ENST00000392499.2	37	CCDS3275.1	.	.	.	.	.	.	.	.	.	.	C	15.66	2.899291	0.52227	.	.	ENSG00000213139	ENST00000392499;ENST00000307944	T;T	0.73575	-0.76;-0.76	5.85	5.85	0.93711	.	0.813810	0.10541	U	0.662673	T	0.70055	0.3180	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.59979	-0.7352	9	0.52906	T	0.07	.	15.6654	0.77225	0.0:1.0:0.0:0.0	.	1	P22914	CRBS_HUMAN	I	1	ENSP00000376287:M1I;ENSP00000312099:M1I	ENSP00000312099:M1I	M	-	3	0	CRYGS	187744807	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.848000	0.55903	2.768000	0.95171	0.655000	0.94253	ATG		0.398	CRYGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344784.1		NM_017541	Missense_Mutation
ELFN2	114794	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	37769171	37769171	+	Nonsense_Mutation	SNP	C	C	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr22:37769171C>A	ENST00000402918.2	-	3	3189	c.2404G>T	c.(2404-2406)Gag>Tag	p.E802*	RP1-63G5.5_ENST00000430883.1_RNA|RP1-63G5.8_ENST00000609322.1_RNA|ELFN2_ENST00000435824.1_5'Flank	NM_052906.3	NP_443138.2	Q5R3F8	PPR29_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 2	802					negative regulation of phosphatase activity (GO:0010923)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)	p.E802*(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	35	Melanoma(58;0.0574)					TGCAGATCCTCGTCCTTGGCG	0.637																																																	1	Substitution - Nonsense(1)	kidney(1)											96.0	86.0	89.0					22																	37769171		2203	4300	6503	SO:0001587	stop_gained	114794			BC041596	CCDS33642.1	22q13.1	2013-02-11	2011-10-27	2011-10-27	ENSG00000166897	ENSG00000166897		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"""	29396	protein-coding gene	gene with protein product			"""leucine rich repeat containing 62"", ""extracellular leucine-rich repeat and fibronectin type III containing 2"", ""extracellular leucine-rich repeat and fibronectin type III domain containing 2"", ""protein phosphatase 1, regulatory subunit 29"""	LRRC62, PPP1R29		17868438	Standard	XR_244427		Approved	dJ63G5.3, KIAA1904	uc003asq.4	Q5R3F8	OTTHUMG00000150558	ENST00000402918.2:c.2404G>T	22.37:g.37769171C>A	ENSP00000385277:p.Glu802*	Somatic		WXS	Illumina HiSeq	Phase_I	Q96PY3	Nonsense_Mutation	SNP	ENST00000402918.2	37	CCDS33642.1	.	.	.	.	.	.	.	.	.	.	C	39	7.911634	0.98557	.	.	ENSG00000166897	ENST00000349653;ENST00000402918	.	.	.	4.63	4.63	0.57726	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-20.5699	17.8461	0.88730	0.0:1.0:0.0:0.0	.	.	.	.	X	802	.	ENSP00000300147:E802X	E	-	1	0	ELFN2	36099117	1.000000	0.71417	0.996000	0.52242	0.858000	0.48976	7.292000	0.78731	2.265000	0.75225	0.561000	0.74099	GAG		0.637	ELFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318900.2		NM_052906	
FAM179B	23116	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	45432114	45432114	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr14:45432114C>T	ENST00000361577.3	+	1	704	c.490C>T	c.(490-492)Cgg>Tgg	p.R164W	KLHL28_ENST00000396128.4_5'Flank|KLHL28_ENST00000355081.2_5'Flank|FAM179B_ENST00000361462.2_Missense_Mutation_p.R164W|FAM179B_ENST00000382233.2_Missense_Mutation_p.R164W|KLHL28_ENST00000553817.1_5'Flank	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	164								p.R164W(1)		endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						GGACGTTCTCCGGGGTCAGGG	0.567																																																	1	Substitution - Missense(1)	kidney(1)											73.0	81.0	78.0					14																	45432114		2203	4300	6503	SO:0001583	missense	23116			AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"""KIAA0423"""	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.490C>T	14.37:g.45432114C>T	ENSP00000355045:p.Arg164Trp	Somatic		WXS	Illumina HiSeq	Phase_I	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	37	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.393303	0.62066	.	.	ENSG00000198718	ENST00000429476;ENST00000361577;ENST00000361462;ENST00000382233	T;T;T	0.58358	0.34;0.34;0.34	4.54	4.54	0.55810	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.38381	N	0.001705	T	0.57681	0.2070	N	0.24115	0.695	0.43667	D	0.996093	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.978;0.995;0.989;0.978	T	0.62034	-0.6939	10	0.72032	D	0.01	-6.6038	12.6429	0.56718	0.0:1.0:0.0:0.0	.	164;164;164;164	Q9Y4F4-3;G3XAE9;Q9Y4F4;Q9Y4F4-2	.;.;F179B_HUMAN;.	W	164	ENSP00000355045:R164W;ENSP00000354917:R164W;ENSP00000371668:R164W	ENSP00000354917:R164W	R	+	1	2	FAM179B	44501864	0.992000	0.36948	1.000000	0.80357	0.997000	0.91878	2.245000	0.43133	2.352000	0.79861	0.655000	0.94253	CGG		0.567	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1		XM_113781	
FBXO42	54455	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	16583146	16583146	+	Missense_Mutation	SNP	T	T	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr1:16583146T>G	ENST00000375592.3	-	5	827	c.611A>C	c.(610-612)gAg>gCg	p.E204A		NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	204								p.E204A(1)		autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		AAAGAATCTCTCTGGCTGGTG	0.463																																																	1	Substitution - Missense(1)	kidney(1)											95.0	90.0	92.0					1																	16583146		2203	4300	6503	SO:0001583	missense	54455			BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637		"""F-boxes /  ""other"""""	29249	protein-coding gene	gene with protein product		609109				10718198	Standard	XM_006710698		Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.611A>C	1.37:g.16583146T>G	ENSP00000364742:p.Glu204Ala	Somatic		WXS	Illumina HiSeq	Phase_I	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Missense_Mutation	SNP	ENST00000375592.3	37	CCDS30613.1	.	.	.	.	.	.	.	.	.	.	T	19.09	3.759407	0.69763	.	.	ENSG00000037637	ENST00000375592	T	0.66460	-0.21	5.94	5.94	0.96194	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.49133	0.1539	N	0.14661	0.345	0.80722	D	1	B	0.24882	0.113	B	0.25291	0.059	T	0.47368	-0.9123	10	0.10902	T	0.67	-22.9282	15.5763	0.76392	0.0:0.0:0.0:1.0	.	204	Q6P3S6	FBX42_HUMAN	A	204	ENSP00000364742:E204A	ENSP00000364742:E204A	E	-	2	0	FBXO42	16455733	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.449000	0.80643	2.272000	0.75746	0.460000	0.39030	GAG		0.463	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1			
STRIP1	85369	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	110582061	110582061	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr1:110582061A>T	ENST00000369795.3	+	5	527	c.505A>T	c.(505-507)Atg>Ttg	p.M169L	STRIP1_ENST00000369794.2_Missense_Mutation_p.M169L|STRIP1_ENST00000369796.1_Missense_Mutation_p.M74L	NM_033088.3	NP_149079.2	Q5VSL9	STRP1_HUMAN	striatin interacting protein 1	169					cortical actin cytoskeleton organization (GO:0030866)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.M169L(1)									GCAGTCCTGGATGCGCTACAA	0.547																																																	1	Substitution - Missense(1)	kidney(1)											116.0	92.0	100.0					1																	110582061		2203	4300	6503	SO:0001583	missense	0			AK027649	CCDS30798.1, CCDS59197.1	1p13.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000143093	ENSG00000143093			25916	protein-coding gene	gene with protein product	"""FAR11 factor arrest 11 homolog A (yeast)"""		"""family with sequence similarity 40, member A"""	FAM40A		11214970, 12588993, 22782902, 22298706, 18782753	Standard	NM_033088		Approved	FLJ14743, KIAA1761, FAR11A	uc001dza.2	Q5VSL9	OTTHUMG00000170607	ENST00000369795.3:c.505A>T	1.37:g.110582061A>T	ENSP00000358810:p.Met169Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q0V925|Q5VSL8|Q658K2|Q6ZV31|Q8N598|Q96SN2|Q9C0A2	Missense_Mutation	SNP	ENST00000369795.3	37	CCDS30798.1	.	.	.	.	.	.	.	.	.	.	A	10.14	1.267770	0.23136	.	.	ENSG00000143093	ENST00000369796;ENST00000369795;ENST00000369794	T;T	0.41400	1.03;1.0	5.99	4.77	0.60923	.	0.109693	0.85682	D	0.000000	T	0.10465	0.0256	N	0.12182	0.205	0.48830	D	0.999717	B	0.02656	0.0	B	0.09377	0.004	T	0.12734	-1.0536	10	0.18276	T	0.48	-32.8279	9.4993	0.39008	0.7618:0.1146:0.0:0.1237	.	169	Q5VSL9	FA40A_HUMAN	L	74;169;169	ENSP00000358811:M74L;ENSP00000358810:M169L	ENSP00000358809:M169L	M	+	1	0	FAM40A	110383584	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.985000	0.40668	2.310000	0.77875	0.449000	0.29647	ATG		0.547	STRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032213.1		NM_033088	
FGFR1	2260	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	38282176	38282176	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr8:38282176C>A	ENST00000447712.2	-	7	1728	c.787G>T	c.(787-789)Gcc>Tcc	p.A263S	FGFR1_ENST00000335922.5_Missense_Mutation_p.A255S|FGFR1_ENST00000326324.6_Missense_Mutation_p.A172S|FGFR1_ENST00000397103.1_Missense_Mutation_p.A172S|FGFR1_ENST00000532791.1_Missense_Mutation_p.A263S|FGFR1_ENST00000397108.4_Missense_Mutation_p.A261S|FGFR1_ENST00000425967.3_Missense_Mutation_p.A294S|FGFR1_ENST00000341462.5_Missense_Mutation_p.A264S|RP11-350N15.4_ENST00000528407.1_RNA|FGFR1_ENST00000397113.2_Missense_Mutation_p.A261S|FGFR1_ENST00000397091.5_Missense_Mutation_p.A261S|FGFR1_ENST00000356207.5_Missense_Mutation_p.A174S	NM_001174063.1|NM_015850.3|NM_023110.2	NP_001167534.1|NP_056934.2|NP_075598.2	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1	263	Ig-like C2-type 3.				angiogenesis (GO:0001525)|auditory receptor cell development (GO:0060117)|axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell maturation (GO:0048469)|cell migration (GO:0016477)|chondrocyte differentiation (GO:0002062)|chordate embryonic development (GO:0043009)|embryonic limb morphogenesis (GO:0030326)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|MAPK cascade (GO:0000165)|mesenchymal cell differentiation (GO:0048762)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|outer ear morphogenesis (GO:0042473)|paraxial mesoderm development (GO:0048339)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of cell differentiation (GO:0045595)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of lateral mesodermal cell fate specification (GO:0048378)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ventricular zone neuroblast division (GO:0021847)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.A263S(3)|p.A174S(1)|p.A255S(1)	FGFR1/ZNF703(2)	breast(2)|central_nervous_system(7)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	50	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	GTTTTGTTGGCGGGCAACCCT	0.587		1	T	"""BCR, FOP, ZNF198, CEP1"""	"""MPD, NHL"""		"""Pfeiffer syndrome, Kallman syndrome"""																														Melanoma(146;1153 1840 21453 21841 43625)			Dom	yes		8	8p11.2-p11.1	2260	fibroblast growth factor receptor 1	yes	L	5	Substitution - Missense(5)	kidney(5)											89.0	96.0	94.0					8																	38282176		2109	4233	6342	SO:0001583	missense	2260			M34185	CCDS6107.2, CCDS43730.1, CCDS43731.1, CCDS43732.1, CCDS55221.1, CCDS55222.1, CCDS55223.1	8p11.23-p11.22	2014-04-03	2008-08-01		ENSG00000077782	ENSG00000077782	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3688	protein-coding gene	gene with protein product	"""Pfeiffer syndrome"""	136350	"""fms-related tyrosine kinase 2"""	FLT2, KAL2		2162671	Standard	NM_015850		Approved	H2, H3, H4, H5, CEK, FLG, BFGFR, N-SAM, CD331	uc011lbu.2	P11362	OTTHUMG00000147366	ENST00000447712.2:c.787G>T	8.37:g.38282176C>A	ENSP00000400162:p.Ala263Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A8K6T9|A8K8V5|C1KBH8|P17049|Q02063|Q02065|Q14306|Q14307|Q53H63|Q59H40|Q5BJG2|Q8N685|Q9UD50|Q9UDF0|Q9UDF1|Q9UDF2	Missense_Mutation	SNP	ENST00000447712.2	37	CCDS6107.2	.	.	.	.	.	.	.	.	.	.	C	36	5.695958	0.96802	.	.	ENSG00000077782	ENST00000397091;ENST00000425967;ENST00000447712;ENST00000341462;ENST00000310729;ENST00000532791;ENST00000397113;ENST00000356207;ENST00000335922;ENST00000326324;ENST00000397103;ENST00000397108;ENST00000326296;ENST00000533668;ENST00000525001	T;T;T;T;T;T;T;T;T;T;T;T;T	0.75589	-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;2.8;-0.95	6.08	6.08	0.98989	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.093568	0.64402	D	0.000001	T	0.74245	0.3691	N	0.04116	-0.275	0.80722	D	1	P;D;D;D;D;D;D;D;D;D;D;D	0.63880	0.947;0.988;0.988;0.993;0.987;0.968;0.968;0.991;0.988;0.979;0.979;0.988	P;P;P;D;D;P;P;D;P;D;D;D	0.68353	0.825;0.907;0.886;0.928;0.943;0.857;0.857;0.957;0.907;0.953;0.936;0.928	T	0.80398	-0.1399	10	0.62326	D	0.03	.	20.2738	0.98482	0.0:1.0:0.0:0.0	.	174;174;261;294;172;172;174;263;255;174;172;263	B5A959;P11362-3;P11362-7;P11362-21;B5A958;P11362-14;P11362-4;P11362;P11362-20;P11362-16;P11362-18;P11362-2	.;.;.;.;.;.;.;FGFR1_HUMAN;.;.;.;.	S	261;294;263;264;263;263;261;174;255;172;172;261;264;103;263	ENSP00000380280:A261S;ENSP00000393312:A294S;ENSP00000400162:A263S;ENSP00000340636:A264S;ENSP00000432972:A263S;ENSP00000380302:A261S;ENSP00000348537:A174S;ENSP00000337247:A255S;ENSP00000327229:A172S;ENSP00000380292:A172S;ENSP00000380297:A261S;ENSP00000434869:A103S;ENSP00000434712:A263S	ENSP00000311337:A263S	A	-	1	0	FGFR1	38401333	1.000000	0.71417	0.994000	0.49952	0.932000	0.56968	7.818000	0.86416	2.894000	0.99253	0.655000	0.94253	GCC		0.587	FGFR1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				
FER1L6	654463	broad.mit.edu;hgsc.bcm.edu	37	8	125035809	125035809	+	Silent	SNP	C	C	T	rs559137171		TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr8:125035809C>T	ENST00000522917.1	+	18	2465	c.2259C>T	c.(2257-2259)tgC>tgT	p.C753C	FER1L6_ENST00000399018.1_Silent_p.C753C|FER1L6-AS1_ENST00000518567.1_RNA	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	753						integral component of membrane (GO:0016021)		p.C753C(2)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			GCAAACACTGCGGCAAGATCA	0.493													C|||	1	0.000199681	0.0	0.0	5008	,	,		18874	0.0		0.0	False		,,,				2504	0.001																2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(1)|kidney(1)											67.0	70.0	69.0					8																	125035809		1948	4140	6088	SO:0001819	synonymous_variant	654463			AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"""fer-1-like 6 (C. elegans)"""				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.2259C>T	8.37:g.125035809C>T		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000522917.1	37	CCDS43767.1																																																																																				0.493	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1		NM_001039112	
FGFR2	2263	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	123298145	123298145	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr10:123298145A>G	ENST00000358487.5	-	6	981	c.709T>C	c.(709-711)Tac>Cac	p.Y237H	FGFR2_ENST00000357555.5_Missense_Mutation_p.Y148H|FGFR2_ENST00000356226.4_Missense_Mutation_p.Y122H|FGFR2_ENST00000369060.4_Missense_Mutation_p.Y237H|FGFR2_ENST00000346997.2_Missense_Mutation_p.Y237H|FGFR2_ENST00000369059.1_Missense_Mutation_p.Y122H|FGFR2_ENST00000360144.3_Missense_Mutation_p.Y148H|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000369061.4_Missense_Mutation_p.Y237H|FGFR2_ENST00000369056.1_Missense_Mutation_p.Y237H|FGFR2_ENST00000457416.2_Missense_Mutation_p.Y237H|FGFR2_ENST00000351936.6_Missense_Mutation_p.Y237H|FGFR2_ENST00000359354.2_Missense_Mutation_p.Y237H	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	237	Ig-like C2-type 2.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.Y237H(3)|p.Y148H(1)		breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	ATGGACCCGTATTCATTCTCC	0.493		5	Mis		"""gastric. NSCLC, endometrial"""		"""Crouzon, Pfeiffer, and Apert syndromes"""		Saethre-Chotzen syndrome;Apert syndrome																															Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	4	Substitution - Missense(4)	kidney(4)											179.0	146.0	157.0					10																	123298145		2203	4300	6503	SO:0001583	missense	2263	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3689	protein-coding gene	gene with protein product	"""Crouzon syndrome"", ""Pfeiffer syndrome"""	176943	"""bacteria-expressed kinase"", ""keratinocyte growth factor receptor"", ""craniofacial dysostosis 1"", ""Jackson-Weiss syndrome"""	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.709T>C	10.37:g.123298145A>G	ENSP00000351276:p.Tyr237His	Somatic		WXS	Illumina HiSeq	Phase_I	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Missense_Mutation	SNP	ENST00000358487.5	37	CCDS31298.1	.	.	.	.	.	.	.	.	.	.	A	12.44	1.938381	0.34189	.	.	ENSG00000066468	ENST00000357555;ENST00000369062;ENST00000369061;ENST00000358487;ENST00000356226;ENST00000369060;ENST00000369059;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000360144;ENST00000369056;ENST00000369058;ENST00000336553;ENST00000359354	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26;-0.26	6.17	6.17	0.99709	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.218522	0.49305	D	0.000155	T	0.61974	0.2390	L	0.33245	0.995	0.22171	N	0.999316	B;B;B;B;B;B;B;B;B;B;B;B	0.28801	0.048;0.025;0.01;0.223;0.015;0.045;0.01;0.005;0.033;0.087;0.004;0.131	B;B;B;B;B;B;B;B;B;B;B;B	0.42214	0.236;0.082;0.084;0.38;0.072;0.105;0.096;0.025;0.365;0.273;0.02;0.354	T	0.57353	-0.7826	10	0.33141	T	0.24	.	8.9722	0.35912	0.8635:0.0:0.1365:0.0	.	256;256;122;237;256;237;148;122;237;256;148;237	D3DRD9;D3DRD4;B5A963;B5A960;D3DRD5;P21802-18;P21802-21;P21802-20;P21802;D3DRE0;P21802-22;P21802-17	.;.;.;.;.;.;.;.;FGFR2_HUMAN;.;.;.	H	148;237;237;237;122;237;122;237;237;237;148;237;237;148;237	ENSP00000350166:Y148H;ENSP00000358057:Y237H;ENSP00000351276:Y237H;ENSP00000348559:Y122H;ENSP00000358056:Y237H;ENSP00000358055:Y122H;ENSP00000263451:Y237H;ENSP00000410294:Y237H;ENSP00000309878:Y237H;ENSP00000353262:Y148H;ENSP00000358052:Y237H;ENSP00000358054:Y237H;ENSP00000337665:Y148H;ENSP00000352309:Y237H	ENSP00000337665:Y148H	Y	-	1	0	FGFR2	123288135	0.914000	0.31030	0.045000	0.18777	0.879000	0.50718	4.565000	0.60836	2.371000	0.80710	0.533000	0.62120	TAC		0.493	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1		NM_022976, NM_000141	
FGFR2	2263	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	123298147	123298147	+	Missense_Mutation	SNP	T	T	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr10:123298147T>G	ENST00000358487.5	-	6	979	c.707A>C	c.(706-708)gAa>gCa	p.E236A	FGFR2_ENST00000357555.5_Missense_Mutation_p.E147A|FGFR2_ENST00000356226.4_Missense_Mutation_p.E121A|FGFR2_ENST00000369060.4_Missense_Mutation_p.E236A|FGFR2_ENST00000346997.2_Missense_Mutation_p.E236A|FGFR2_ENST00000369059.1_Missense_Mutation_p.E121A|FGFR2_ENST00000360144.3_Missense_Mutation_p.E147A|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000369061.4_Missense_Mutation_p.E236A|FGFR2_ENST00000369056.1_Missense_Mutation_p.E236A|FGFR2_ENST00000457416.2_Missense_Mutation_p.E236A|FGFR2_ENST00000351936.6_Missense_Mutation_p.E236A|FGFR2_ENST00000359354.2_Missense_Mutation_p.E236A	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	236	Ig-like C2-type 2.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.E236A(3)|p.E147A(1)		breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	GGACCCGTATTCATTCTCCAC	0.488		5	Mis		"""gastric. NSCLC, endometrial"""		"""Crouzon, Pfeiffer, and Apert syndromes"""		Saethre-Chotzen syndrome;Apert syndrome																															Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	4	Substitution - Missense(4)	kidney(4)											179.0	147.0	158.0					10																	123298147		2203	4300	6503	SO:0001583	missense	2263	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3689	protein-coding gene	gene with protein product	"""Crouzon syndrome"", ""Pfeiffer syndrome"""	176943	"""bacteria-expressed kinase"", ""keratinocyte growth factor receptor"", ""craniofacial dysostosis 1"", ""Jackson-Weiss syndrome"""	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.707A>C	10.37:g.123298147T>G	ENSP00000351276:p.Glu236Ala	Somatic		WXS	Illumina HiSeq	Phase_I	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Missense_Mutation	SNP	ENST00000358487.5	37	CCDS31298.1	.	.	.	.	.	.	.	.	.	.	T	12.82	2.051539	0.36181	.	.	ENSG00000066468	ENST00000357555;ENST00000369062;ENST00000369061;ENST00000358487;ENST00000356226;ENST00000369060;ENST00000369059;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000360144;ENST00000369056;ENST00000369058;ENST00000336553;ENST00000359354	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35;-0.35;-0.35;-0.35;-0.35;-0.35;-0.35;-0.35;-0.35;-0.35;-0.35	6.17	5.01	0.66863	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.186804	0.56097	D	0.000031	T	0.53578	0.1805	L	0.35249	1.045	0.26128	N	0.980458	B;B;B;B;B;B;B;B;B;B;B;B	0.29232	0.009;0.238;0.031;0.04;0.004;0.005;0.025;0.057;0.001;0.005;0.026;0.003	B;B;B;B;B;B;B;B;B;B;B;B	0.31946	0.095;0.101;0.095;0.047;0.01;0.009;0.068;0.138;0.033;0.017;0.025;0.026	T	0.49293	-0.8955	10	0.41790	T	0.15	.	7.2975	0.26401	0.1268:0.073:0.0:0.8002	.	255;255;121;236;255;236;147;121;236;255;147;236	D3DRD9;D3DRD4;B5A963;B5A960;D3DRD5;P21802-18;P21802-21;P21802-20;P21802;D3DRE0;P21802-22;P21802-17	.;.;.;.;.;.;.;.;FGFR2_HUMAN;.;.;.	A	147;236;236;236;121;236;121;236;236;236;147;236;236;147;236	ENSP00000350166:E147A;ENSP00000358057:E236A;ENSP00000351276:E236A;ENSP00000348559:E121A;ENSP00000358056:E236A;ENSP00000358055:E121A;ENSP00000263451:E236A;ENSP00000410294:E236A;ENSP00000309878:E236A;ENSP00000353262:E147A;ENSP00000358052:E236A;ENSP00000358054:E236A;ENSP00000337665:E147A;ENSP00000352309:E236A	ENSP00000337665:E147A	E	-	2	0	FGFR2	123288137	0.030000	0.19436	0.111000	0.21465	0.850000	0.48378	2.230000	0.42999	1.114000	0.41781	-0.408000	0.06270	GAA		0.488	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1		NM_022976, NM_000141	
FRMPD4	9758	hgsc.bcm.edu;ucsc.edu	37	X	12736252	12736253	+	Frame_Shift_Ins	INS	-	-	A	rs35659462		TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chrX:12736252_12736253insA	ENST00000380682.1	+	16	3813_3814	c.3307_3308insA	c.(3307-3309)gaafs	p.E1103fs		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	1103					positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						TGGGATGGCTGAAAAAAGTGGA	0.5																																																	0																																										SO:0001589	frameshift_variant	9758			AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"""PDZ domain containing 10"""	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.3313dupA	X.37:g.12736258_12736258dupA	ENSP00000370057:p.Glu1103fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8K0X9|O15032	Frame_Shift_Ins	INS	ENST00000380682.1	37	CCDS35201.1																																																																																				0.500	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1		XM_045712	
FZD3	7976	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	28385020	28385020	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr8:28385020T>C	ENST00000240093.3	+	5	1221	c.743T>C	c.(742-744)gTa>gCa	p.V248A	FZD3_ENST00000537916.1_Missense_Mutation_p.V248A|RNA5SP259_ENST00000365541.1_RNA	NM_017412.3	NP_059108.1	Q9NPG1	FZD3_HUMAN	frizzled class receptor 3	248					canonical Wnt signaling pathway (GO:0060070)|cell proliferation in midbrain (GO:0033278)|commissural neuron axon guidance (GO:0071679)|establishment of planar polarity (GO:0001736)|facial nucleus development (GO:0021754)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|post-anal tail morphogenesis (GO:0036342)|vasculature development (GO:0001944)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|neuron projection membrane (GO:0032589)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.V248A(1)		central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(15)|ovary(1)|prostate(1)|skin(1)	41		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)		TACATGATGGTATCCTTAATT	0.378																																																	1	Substitution - Missense(1)	kidney(1)											94.0	97.0	96.0					8																	28385020		2203	4300	6503	SO:0001583	missense	7976			AJ272427	CCDS6069.1	8p21	2014-06-27	2014-01-29		ENSG00000104290	ENSG00000104290		"""GPCR / Class F : Frizzled receptors"""	4041	protein-coding gene	gene with protein product		606143	"""frizzled (Drosophila) homolog 3"", ""frizzled homolog 3 (Drosophila)"", ""frizzled 3, seven transmembrane spanning receptor"", ""frizzled family receptor 3"""			10777673, 10873558	Standard	NM_145866		Approved		uc010lvb.3	Q9NPG1	OTTHUMG00000102145	ENST00000240093.3:c.743T>C	8.37:g.28385020T>C	ENSP00000240093:p.Val248Ala	Somatic		WXS	Illumina HiSeq	Phase_I	A8K615	Missense_Mutation	SNP	ENST00000240093.3	37	CCDS6069.1	.	.	.	.	.	.	.	.	.	.	T	19.57	3.852652	0.71719	.	.	ENSG00000104290	ENST00000537916;ENST00000240093	D;D	0.82893	-1.66;-1.66	5.24	5.24	0.73138	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	D	0.92011	0.7469	M	0.88377	2.95	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.93478	0.6825	10	0.87932	D	0	.	14.3288	0.66537	0.0:0.0:0.0:1.0	.	248	Q9NPG1	FZD3_HUMAN	A	248	ENSP00000437489:V248A;ENSP00000240093:V248A	ENSP00000240093:V248A	V	+	2	0	FZD3	28440939	1.000000	0.71417	0.985000	0.45067	0.973000	0.67179	8.040000	0.89188	1.974000	0.57490	0.533000	0.62120	GTA		0.378	FZD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219986.2		NM_145866	
HDAC4	9759	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	240111615	240111615	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr2:240111615G>C	ENST00000345617.3	-	4	1044	c.253C>G	c.(253-255)Cag>Gag	p.Q85E	HDAC4_ENST00000541256.1_Missense_Mutation_p.Q54E	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	85					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.Q85E(1)		NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		ATCTGCCTCTGGATCTGCTGC	0.662																																																	1	Substitution - Missense(1)	kidney(1)											38.0	34.0	35.0					2																	240111615		2203	4300	6503	SO:0001583	missense	9759			AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"""brachydactyly-mental retardation syndrome"""	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.253C>G	2.37:g.240111615G>C	ENSP00000264606:p.Gln85Glu	Somatic		WXS	Illumina HiSeq	Phase_I	Q9UND6	Missense_Mutation	SNP	ENST00000345617.3	37	CCDS2529.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.600624	0.87055	.	.	ENSG00000068024	ENST00000345617;ENST00000541256;ENST00000454542;ENST00000446876	D;D;T;T	0.83755	-1.76;-1.76;0.4;0.55	4.42	4.42	0.53409	Histone deacetylase, glutamine rich N-terminal domain (1);	0.000000	0.85682	D	0.000000	D	0.90157	0.6924	M	0.72353	2.195	0.80722	D	1	D;D;D;P;D	0.63046	0.985;0.992;0.992;0.906;0.992	D;P;D;P;D	0.76071	0.981;0.851;0.987;0.551;0.987	D	0.90300	0.4329	9	.	.	.	.	17.4181	0.87506	0.0:0.0:1.0:0.0	.	80;54;54;53;85	B7Z8G5;F5H5W4;B7Z8I2;Q53SM2;P56524	.;.;.;.;HDAC4_HUMAN	E	85;54;54;58	ENSP00000264606:Q85E;ENSP00000443057:Q54E;ENSP00000405226:Q54E;ENSP00000392912:Q58E	.	Q	-	1	0	HDAC4	239776552	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	9.273000	0.95719	2.207000	0.71202	0.655000	0.94253	CAG		0.662	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2		NM_006037	
HYAL4	23553	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	123517205	123517206	+	Missense_Mutation	DNP	TG	TG	CT			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr7:123517205_123517206TG>CT	ENST00000223026.4	+	5	2080_2081	c.1442_1443TG>CT	c.(1441-1443)tTG>tCT	p.L481S	HYAL4_ENST00000476325.1_Missense_Mutation_p.L481S	NM_012269.2	NP_036401.2	Q2M3T9	HYAL4_HUMAN	hyaluronoglucosaminidase 4	481					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|glycosaminoglycan catabolic process (GO:0006027)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)	hyalurononglucosaminidase activity (GO:0004415)	p.L481S(1)|p.L481F(1)|p.L481>?(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	23						AGCATTCAGTTGTGAGATAATT	0.376																																																	3	Substitution - Missense(2)|Complex(1)	kidney(3)																																								SO:0001583	missense	23553			AF009010	CCDS5789.1	7q31.3	2010-01-14			ENSG00000106302	ENSG00000106302			5323	protein-coding gene	gene with protein product	"""hyaluronidase 4"""	604510				10493834	Standard	NM_012269		Approved		uc003vlc.3	Q2M3T9	OTTHUMG00000157349	Exception_encountered	7.37:g.123517205_123517206delinsCT	ENSP00000223026:p.Leu481Ser	Somatic		WXS	Illumina HiSeq	Phase_I	D0VXG1|Q9UL99|Q9Y6T9	Missense_Mutation	SNP	ENST00000223026.4	37	CCDS5789.1																																																																																				0.376	HYAL4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348545.1		NM_012269	
IBTK	25998	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	82950105	82950105	+	Silent	SNP	A	A	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr6:82950105A>T	ENST00000306270.7	-	2	648	c.99T>A	c.(97-99)atT>atA	p.I33I	IBTK_ENST00000510291.1_Silent_p.I33I|IBTK_ENST00000503631.1_Silent_p.I33I	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	33					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)	p.I33I(1)		central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		GAAAGGCCTTAATCTGGTTTT	0.473																																																	1	Substitution - coding silent(1)	kidney(1)											142.0	136.0	138.0					6																	82950105		2203	4300	6503	SO:0001819	synonymous_variant	25998			AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	17853	protein-coding gene	gene with protein product		606457	"""Bruton agammaglobulinemia tyrosine kinase inhibitor"""	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.99T>A	6.37:g.82950105A>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Silent	SNP	ENST00000306270.7	37	CCDS34490.1																																																																																				0.473	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2		NM_015525	
IBTK	25998	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	82950107	82950107	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr6:82950107T>C	ENST00000306270.7	-	2	646	c.97A>G	c.(97-99)Att>Gtt	p.I33V	IBTK_ENST00000510291.1_Missense_Mutation_p.I33V|IBTK_ENST00000503631.1_Missense_Mutation_p.I33V	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	33					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)	p.I33V(1)		central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		AAGGCCTTAATCTGGTTTTCG	0.468																																																	1	Substitution - Missense(1)	kidney(1)											143.0	137.0	139.0					6																	82950107		2203	4300	6503	SO:0001583	missense	25998			AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	17853	protein-coding gene	gene with protein product		606457	"""Bruton agammaglobulinemia tyrosine kinase inhibitor"""	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.97A>G	6.37:g.82950107T>C	ENSP00000305721:p.Ile33Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Missense_Mutation	SNP	ENST00000306270.7	37	CCDS34490.1	.	.	.	.	.	.	.	.	.	.	T	14.65	2.597918	0.46318	.	.	ENSG00000005700	ENST00000306270;ENST00000503631;ENST00000510291	T;T;T	0.57436	0.4;0.4;0.4	5.78	5.78	0.91487	Ankyrin repeat-containing domain (2);	0.055383	0.64402	D	0.000001	T	0.24236	0.0587	N	0.12471	0.22	0.48632	D	0.999682	P;P;P;P	0.43788	0.817;0.738;0.68;0.738	P;P;B;P	0.47744	0.556;0.507;0.136;0.507	T	0.19257	-1.0311	10	0.05620	T	0.96	-20.8027	16.0962	0.81127	0.0:0.0:0.0:1.0	.	33;33;33;33	E9PDR5;E7EPI0;Q9P2D0-2;Q9P2D0	.;.;.;IBTK_HUMAN	V	33	ENSP00000305721:I33V;ENSP00000422762:I33V;ENSP00000426405:I33V	ENSP00000305721:I33V	I	-	1	0	IBTK	83006826	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.125000	0.64715	2.207000	0.71202	0.459000	0.35465	ATT		0.468	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2		NM_015525	
INPP5D	3635	broad.mit.edu	37	2	234113207	234113207	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr2:234113207delG	ENST00000359570.5	+	28	3375	c.3375delG	c.(3373-3375)ccgfs	p.P1125fs	INPP5D_ENST00000450745.1_Frame_Shift_Del_p.P889fs|RN7SL32P_ENST00000580514.1_RNA|INPP5D_ENST00000455936.2_Frame_Shift_Del_p.P889fs			Q92835	SHIP1_HUMAN	inositol polyphosphate-5-phosphatase, 145kDa	1137	Pro-rich.				apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|determination of adult lifespan (GO:0008340)|immunoglobulin mediated immune response (GO:0016064)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of bone resorption (GO:0045779)|negative regulation of immune response (GO:0050777)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of neutrophil differentiation (GO:0045659)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of signal transduction (GO:0009968)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of erythrocyte differentiation (GO:0045648)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|membrane (GO:0016020)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)			central_nervous_system(1)|ovary(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)		CGCCCACCCCGACGCCGCGGC	0.701																																					NSCLC(82;1215 1426 16163 20348 41018)												0													2.0	3.0	3.0					2																	234113207		1487	3460	4947	SO:0001589	frameshift_variant	3635			U57650	CCDS74672.1	2q37.1	2013-02-14	2002-08-29		ENSG00000168918	ENSG00000168918		"""SH2 domain containing"""	6079	protein-coding gene	gene with protein product		601582	"""inositol polyphosphate-5-phosphatase, 145kD"""			8643691, 8874179	Standard	NM_001017915		Approved	SHIP, hp51CN	uc010zmp.2	Q92835	OTTHUMG00000133688	ENST00000359570.5:c.3375delG	2.37:g.234113207delG	ENSP00000352575:p.Pro1125fs	Somatic		WXS	Illumina GAIIx	Phase_I	O00145|Q13544|Q13545|Q6P5A4|Q92656|Q9UE80	Frame_Shift_Del	DEL	ENST00000359570.5	37																																																																																					0.701	INPP5D-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			NM_001017915	
KCNH8	131096	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	19436689	19436689	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr3:19436689G>A	ENST00000328405.2	+	7	1329	c.1063G>A	c.(1063-1065)Gtc>Atc	p.V355I	KCNH8_ENST00000537696.1_5'UTR|KCNH8_ENST00000475063.1_3'UTR	NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	355					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.V355I(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						CAGTACTATCGTCCTGACTCT	0.498																																					NSCLC(124;1625 1765 8018 24930 42026)												1	Substitution - Missense(1)	kidney(1)											223.0	179.0	194.0					3																	19436689		2203	4300	6503	SO:0001583	missense	131096			AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.1063G>A	3.37:g.19436689G>A	ENSP00000328813:p.Val355Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z2I7|Q59GQ6	Missense_Mutation	SNP	ENST00000328405.2	37	CCDS2632.1	.	.	.	.	.	.	.	.	.	.	G	33	5.267140	0.95399	.	.	ENSG00000183960	ENST00000328405	D	0.97404	-4.37	5.92	5.92	0.95590	Ion transport (1);	0.000000	0.28958	U	0.013596	D	0.97390	0.9146	L	0.41492	1.28	0.80722	D	1	D;D	0.76494	0.971;0.999	P;D	0.64595	0.591;0.927	D	0.96636	0.9470	9	.	.	.	.	20.3172	0.98658	0.0:0.0:1.0:0.0	.	355;355	B7Z398;Q96L42	.;KCNH8_HUMAN	I	355	ENSP00000328813:V355I	.	V	+	1	0	KCNH8	19411693	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.869000	0.99810	2.801000	0.96364	0.650000	0.86243	GTC		0.498	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2		NM_144633	
GSE1	23199	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	85701801	85701801	+	Silent	SNP	C	C	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr16:85701801C>T	ENST00000253458.7	+	14	3362	c.3186C>T	c.(3184-3186)caC>caT	p.H1062H	GSE1_ENST00000405402.2_Silent_p.H958H|GSE1_ENST00000393243.1_Silent_p.H989H	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	1062								p.H1062H(1)									CGTCCGTCCACTACAACATTC	0.642																																																	1	Substitution - coding silent(1)	kidney(1)											137.0	133.0	134.0					16																	85701801		2198	4300	6498	SO:0001819	synonymous_variant	0			D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"""genetic suppressor element 1"""		"""KIAA0182"", ""Gse1 coiled-coil protein homolog (mouse)"""	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.3186C>T	16.37:g.85701801C>T		Somatic		WXS	Illumina HiSeq	Phase_I	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Silent	SNP	ENST00000253458.7	37	CCDS10952.1	.	.	.	.	.	.	.	.	.	.	C	2.608	-0.291481	0.05568	.	.	ENSG00000131149	ENST00000412692;ENST00000438180	.	.	.	5.53	4.52	0.55395	.	.	.	.	.	T	0.56366	0.1980	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53450	-0.8437	4	.	.	.	-33.2119	6.7534	0.23499	0.0:0.7003:0.1514:0.1483	.	.	.	.	I	831;264	.	.	T	+	2	0	KIAA0182	84259302	1.000000	0.71417	1.000000	0.80357	0.276000	0.26787	1.416000	0.34759	2.608000	0.88229	0.561000	0.74099	ACT		0.642	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1		NM_014615	
FOCAD	54914	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	20874780	20874780	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr9:20874780C>T	ENST00000380249.1	+	21	2655	c.2291C>T	c.(2290-2292)tCa>tTa	p.S764L	FOCAD_ENST00000605086.1_Missense_Mutation_p.S200L|FOCAD_ENST00000338382.6_Missense_Mutation_p.S764L|FOCAD_ENST00000604828.1_3'UTR	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	764						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)		p.S764L(1)									AAACTGTTGTCACTCACTCCC	0.403																																																	1	Substitution - Missense(1)	kidney(1)											253.0	229.0	237.0					9																	20874780		2203	4300	6503	SO:0001583	missense	0			AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"""KIAA1797"""	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.2291C>T	9.37:g.20874780C>T	ENSP00000369599:p.Ser764Leu	Somatic		WXS	Illumina HiSeq	Phase_I	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	37	CCDS34993.1	.	.	.	.	.	.	.	.	.	.	C	12.04	1.817849	0.32145	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.66099	-0.19;-0.19	5.6	5.6	0.85130	Armadillo-type fold (1);	0.485335	0.22755	N	0.056022	T	0.53254	0.1785	L	0.48642	1.525	0.34088	D	0.660366	B	0.06786	0.001	B	0.06405	0.002	T	0.55879	-0.8071	10	0.12766	T	0.61	-27.2634	14.2003	0.65699	0.0:0.9284:0.0:0.0716	.	764	Q5VW36	K1797_HUMAN	L	764	ENSP00000369599:S764L;ENSP00000344307:S764L	ENSP00000344307:S764L	S	+	2	0	KIAA1797	20864780	0.018000	0.18449	0.801000	0.32222	0.491000	0.33493	0.534000	0.23098	2.786000	0.95864	0.650000	0.86243	TCA		0.403	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1		NM_017794	
KIF3B	9371	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	30897808	30897808	+	Silent	SNP	G	G	C	rs377463465		TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr20:30897808G>C	ENST00000375712.3	+	2	395	c.228G>C	c.(226-228)acG>acC	p.T76T	KIF3B_ENST00000418717.2_5'Flank	NM_004798.3	NP_004789.1	O15066	KIF3B_HUMAN	kinesin family member 3B	76	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytoskeleton-dependent intracellular transport (GO:0030705)|determination of left/right symmetry (GO:0007368)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic spindle organization (GO:0007052)|plus-end-directed vesicle transport along microtubule (GO:0072383)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|plus-end kinesin complex (GO:0005873)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|Rho GTPase binding (GO:0017048)	p.T76T(1)		NS(2)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(9)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			ACGATGAGACGTTCCGACCAC	0.483																																																	1	Substitution - coding silent(1)	kidney(1)											153.0	133.0	140.0					20																	30897808		2203	4300	6503	SO:0001819	synonymous_variant	9371			AB002357	CCDS13200.1	20q11.21	2012-08-01			ENSG00000101350	ENSG00000101350		"""Kinesins"""	6320	protein-coding gene	gene with protein product		603754				9205841	Standard	NM_004798		Approved	KIAA0359, FLA8, KLP-11	uc002wxq.3	O15066	OTTHUMG00000032214	ENST00000375712.3:c.228G>C	20.37:g.30897808G>C		Somatic		WXS	Illumina HiSeq	Phase_I	B2RMP4|B4DSR5|E1P5M5	Silent	SNP	ENST00000375712.3	37	CCDS13200.1																																																																																				0.483	KIF3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078619.1		NM_004798	
LCMT2	9836	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	43621613	43621613	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr15:43621613C>A	ENST00000305641.5	-	1	1190	c.1075G>T	c.(1075-1077)Ggc>Tgc	p.G359C	ADAL_ENST00000428046.3_5'Flank|ADAL_ENST00000389651.4_5'Flank|ADAL_ENST00000422466.2_5'Flank|LCMT2_ENST00000567039.1_3'UTR|LCMT2_ENST00000544735.1_5'UTR	NM_014793.4	NP_055608.2	O60294	TYW4_HUMAN	leucine carboxyl methyltransferase 2	359					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)	p.G359C(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|liver(1)|lung(9)|skin(1)|urinary_tract(1)	20		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.1e-07)	L-Leucine(DB00149)	GAGGCGTGGCCATATCTCTTC	0.567																																																	1	Substitution - Missense(1)	kidney(1)											46.0	45.0	46.0					15																	43621613		2201	4299	6500	SO:0001583	missense	9836			AF265443	CCDS10094.1	15q15.3	2007-01-26			ENSG00000168806	ENSG00000168806			17558	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 4"""	611246				9628581, 17150819	Standard	NM_014793		Approved	KIAA0547, MGC9534, TYW4, PPM2	uc001zrg.3	O60294	OTTHUMG00000130705	ENST00000305641.5:c.1075G>T	15.37:g.43621613C>A	ENSP00000307214:p.Gly359Cys	Somatic		WXS	Illumina HiSeq	Phase_I	Q4JFT6|Q96B55|Q9NR10	Missense_Mutation	SNP	ENST00000305641.5	37	CCDS10094.1	.	.	.	.	.	.	.	.	.	.	C	14.81	2.647278	0.47258	.	.	ENSG00000168806	ENST00000305641	T	0.75704	-0.96	5.54	5.54	0.83059	.	0.056761	0.64402	D	0.000001	D	0.86785	0.6016	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.87896	0.2687	10	0.87932	D	0	-21.8914	14.8538	0.70319	0.0:1.0:0.0:0.0	.	359	O60294	LCMT2_HUMAN	C	359	ENSP00000307214:G359C	ENSP00000307214:G359C	G	-	1	0	LCMT2	41408905	0.987000	0.35691	0.570000	0.28473	0.365000	0.29674	2.838000	0.48199	2.885000	0.99019	0.655000	0.94253	GGC		0.567	LCMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253205.1		NM_014793	
BMS1P20	96610	broad.mit.edu	37	22	22664606	22664606	+	RNA	SNP	A	A	G	rs187344612		TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr22:22664606A>G	ENST00000426066.1	+	0	787					NR_027293.1				BMS1 pseudogene 20																		GTCTTCATGCAAACTTGGTAT	0.398																																																	0																																												96610					22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22664606A>G		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000426066.1	37																																																																																					0.398	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			
LTBP2	4053	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	74967715	74967715	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr14:74967715C>T	ENST00000261978.4	-	36	5724	c.5338G>A	c.(5338-5340)Gac>Aac	p.D1780N	LTBP2_ENST00000556690.1_Missense_Mutation_p.D1736N	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	1780	EGF-like 20; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.D1780N(1)		breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		CCGTTCAAGTCATCACACTCA	0.577											OREG0022805	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - Missense(1)	kidney(1)											46.0	40.0	42.0					14																	74967715		2203	4300	6503	SO:0001583	missense	4053				CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"""Latent transforming growth factor, beta binding proteins"""	6715	protein-coding gene	gene with protein product		602091	"""chromosome 14 open reading frame 141"""	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.5338G>A	14.37:g.74967715C>T	ENSP00000261978:p.Asp1780Asn	Somatic	1156	WXS	Illumina HiSeq	Phase_I	Q99907|Q9NS51	Missense_Mutation	SNP	ENST00000261978.4	37	CCDS9831.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.236380	0.79800	.	.	ENSG00000119681	ENST00000261978;ENST00000556690	D;D	0.92199	-2.99;-2.99	5.54	5.54	0.83059	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.44483	D	0.000446	D	0.87245	0.6129	N	0.16567	0.415	0.51767	D	0.999938	B	0.25351	0.124	B	0.28465	0.09	T	0.82329	-0.0511	10	0.37606	T	0.19	.	19.6787	0.95950	0.0:1.0:0.0:0.0	.	1780	Q14767	LTBP2_HUMAN	N	1780;1736	ENSP00000261978:D1780N;ENSP00000451477:D1736N	ENSP00000261978:D1780N	D	-	1	0	LTBP2	74037468	1.000000	0.71417	0.995000	0.50966	0.977000	0.68977	4.465000	0.60141	2.884000	0.98904	0.655000	0.94253	GAC		0.577	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1		NM_000428	
LY75	4065	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	160667078	160667078	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr2:160667078A>G	ENST00000263636.4	-	32	4685	c.4658T>C	c.(4657-4659)tTg>tCg	p.L1553S	LY75_ENST00000553424.1_Missense_Mutation_p.L1553S|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.L1553S|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.L1553S|LY75_ENST00000554112.1_Missense_Mutation_p.L1553S	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1553	C-type lectin 10. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.L1553S(1)		NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		AAAACTGTGCAATGCCTGATC	0.373																																																	1	Substitution - Missense(1)	kidney(1)											192.0	199.0	196.0					2																	160667078		2203	4300	6503	SO:0001583	missense	100526664			AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"""CD molecules"", ""C-type lectin domain containing"""	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.4658T>C	2.37:g.160667078A>G	ENSP00000263636:p.Leu1553Ser	Somatic		WXS	Illumina HiSeq	Phase_I	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	A	15.61	2.884402	0.51908	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.07908	3.15;3.15;3.15;3.15;3.15	4.91	4.91	0.64330	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.000000	0.26859	U	0.022130	T	0.26011	0.0634	M	0.73598	2.24	0.43394	D	0.995514	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.986;0.985;0.999	T	0.03493	-1.1031	10	0.21014	T	0.42	-9.962	13.0771	0.59093	1.0:0.0:0.0:0.0	.	1553;1553;1553	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	S	1553	ENSP00000451511:L1553S;ENSP00000451446:L1553S;ENSP00000263636:L1553S;ENSP00000423463:L1553S;ENSP00000421035:L1553S	ENSP00000423463:L1553S	L	-	2	0	LY75;LY75-CD302	160375324	1.000000	0.71417	0.987000	0.45799	0.417000	0.31264	5.395000	0.66291	1.976000	0.57569	0.402000	0.26972	TTG		0.373	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			
MAGEB3	4114	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	30254882	30254882	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chrX:30254882G>C	ENST00000361644.2	+	5	1578	c.841G>C	c.(841-843)Gct>Cct	p.A281P		NM_002365.4	NP_002356.2	O15480	MAGB3_HUMAN	melanoma antigen family B, 3	281	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.A281P(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	25						AAGAGCCCATGCTGAAACCAG	0.488																																																	1	Substitution - Missense(1)	kidney(1)											90.0	81.0	84.0					X																	30254882		2202	4300	6502	SO:0001583	missense	4114			AK057441	CCDS14220.1	Xp21.3	2009-03-17			ENSG00000198798	ENSG00000198798			6810	protein-coding gene	gene with protein product	"""cancer/testis antigen family 3, member 5"""	300152				9441743	Standard	NM_002365		Approved	CT3.5	uc004dca.2	O15480	OTTHUMG00000021320	ENST00000361644.2:c.841G>C	X.37:g.30254882G>C	ENSP00000355198:p.Ala281Pro	Somatic		WXS	Illumina HiSeq	Phase_I	A0AVE4|B3KQ52|O75861	Missense_Mutation	SNP	ENST00000361644.2	37	CCDS14220.1	.	.	.	.	.	.	.	.	.	.	G	10.57	1.385975	0.25031	.	.	ENSG00000198798	ENST00000378986;ENST00000361644	T;T	0.06068	3.35;3.35	4.3	2.54	0.30619	.	0.971903	0.08372	U	0.955888	T	0.32285	0.0824	H	0.94503	3.545	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.05419	-1.0886	10	0.87932	D	0	.	5.6488	0.17604	0.2483:0.0:0.7517:0.0	.	281	O15480	MAGB3_HUMAN	P	281	ENSP00000368271:A281P;ENSP00000355198:A281P	ENSP00000355198:A281P	A	+	1	0	MAGEB3	30164803	0.035000	0.19736	0.007000	0.13788	0.007000	0.05969	1.823000	0.39062	0.554000	0.29061	0.600000	0.82982	GCT		0.488	MAGEB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056158.2		NM_002365	
MAPK3	5595	broad.mit.edu;ucsc.edu	37	16	30133218	30133218	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr16:30133218G>A	ENST00000263025.4	-	2	364	c.280C>T	c.(280-282)Cgc>Tgc	p.R94C	MAPK3_ENST00000403394.1_Missense_Mutation_p.R94C|MAPK3_ENST00000395202.1_Missense_Mutation_p.R94C|MAPK3_ENST00000395200.1_Missense_Mutation_p.R65C|MAPK3_ENST00000395199.3_Missense_Mutation_p.R94C|MAPK3_ENST00000484663.1_5'UTR|MAPK3_ENST00000322266.5_Missense_Mutation_p.R94C	NM_002746.2	NP_002737.2	P27361	MK03_HUMAN	mitogen-activated protein kinase 3	94	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|caveolin-mediated endocytosis (GO:0072584)|cell cycle (GO:0007049)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage induced protein phosphorylation (GO:0006975)|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)|gene expression (GO:0010467)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|interleukin-1-mediated signaling pathway (GO:0070498)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apolipoprotein binding (GO:2000657)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of cytoskeleton organization (GO:0051493)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of stress-activated MAPK cascade (GO:0032872)|response to epidermal growth factor (GO:0070849)|response to exogenous dsRNA (GO:0043330)|sensory perception of pain (GO:0019233)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	caveola (GO:0005901)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|phosphatase binding (GO:0019902)	p.R94C(1)								Arsenic trioxide(DB01169)|Sulindac(DB00605)	TGGCGGAAGCGCAGCAGGATC	0.592																																																	1	Substitution - Missense(1)	kidney(1)											71.0	58.0	62.0					16																	30133218		2197	4300	6497	SO:0001583	missense	5595			M84490	CCDS10672.1, CCDS42148.1, CCDS42149.1	16p11.2	2011-06-10			ENSG00000102882	ENSG00000102882	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6877	protein-coding gene	gene with protein product		601795		PRKM3		9628824	Standard	NM_001109891		Approved	ERK1, p44mapk, p44erk1	uc002dws.3	P27361	OTTHUMG00000132149	ENST00000263025.4:c.280C>T	16.37:g.30133218G>A	ENSP00000263025:p.Arg94Cys	Somatic		WXS	Illumina GAIIx	Phase_I	A8CZ58|B0LPG3|Q8NHX1	Missense_Mutation	SNP	ENST00000263025.4	37	CCDS10672.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.812316	0.70912	.	.	ENSG00000102882	ENST00000263025;ENST00000322266;ENST00000403394;ENST00000395200;ENST00000395202;ENST00000395199	T;T;T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28;-0.28;-0.28	5.63	5.63	0.86233	Serine/threonine-protein kinase-like domain (1);MAP kinase, conserved site (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.65154	0.2664	M	0.64567	1.98	0.80722	D	1	B;P;P	0.36027	0.06;0.519;0.533	B;B;B	0.30855	0.033;0.121;0.093	T	0.69811	-0.5044	10	0.87932	D	0	-11.4158	18.4484	0.90695	0.0:0.0:1.0:0.0	.	94;94;94	P27361-2;P27361-3;P27361	.;.;MK03_HUMAN	C	94;94;94;65;94;94	ENSP00000263025:R94C;ENSP00000327293:R94C;ENSP00000384895:R94C;ENSP00000378626:R65C;ENSP00000378628:R94C;ENSP00000378625:R94C	ENSP00000263025:R94C	R	-	1	0	MAPK3	30040719	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.803000	0.85983	2.655000	0.90218	0.462000	0.41574	CGC		0.592	MAPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255196.2			
MCM7	4176	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	99693535	99693535	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr7:99693535G>T	ENST00000303887.5	-	11	2102	c.1457C>A	c.(1456-1458)gCt>gAt	p.A486D	MCM7_ENST00000354230.3_Missense_Mutation_p.A310D|MCM7_ENST00000343023.6_Intron|MIR93_ENST00000385024.1_RNA|MIR106B_ENST00000385301.1_RNA|MIR25_ENST00000384816.1_RNA	NM_005916.3	NP_005907.3	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	486	MCM.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of phosphorylation (GO:0042325)|response to drug (GO:0042493)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)	p.A486D(1)|p.A310D(1)		endometrium(1)|kidney(5)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GTTGGCGGCAGCCAGGATGGA	0.632																																																	2	Substitution - Missense(2)	kidney(2)											94.0	85.0	88.0					7																	99693535		2203	4300	6503	SO:0001583	missense	4176				CCDS5683.1, CCDS5684.1	7q21.3-q22.1	2014-06-12	2007-04-04		ENSG00000166508	ENSG00000166508			6950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 104"""	600592	"""minichromosome maintenance deficient (S. cerevisiae) 7"", ""MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)"""	MCM2		7842741	Standard	NM_005916		Approved	CDC47, PPP1R104	uc003usw.1	P33993	OTTHUMG00000154671	ENST00000303887.5:c.1457C>A	7.37:g.99693535G>T	ENSP00000307288:p.Ala486Asp	Somatic		WXS	Illumina HiSeq	Phase_I	A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1	Missense_Mutation	SNP	ENST00000303887.5	37	CCDS5683.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.665940	0.88251	.	.	ENSG00000166508	ENST00000303887;ENST00000542483;ENST00000362082;ENST00000354230	T;T	0.12879	2.64;2.64	5.28	5.28	0.74379	ATPase, AAA+ type, core (1);	0.059289	0.64402	D	0.000003	T	0.60130	0.2245	H	0.99619	4.66	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.79001	-0.1981	10	0.87932	D	0	-19.1517	16.4558	0.84012	0.0:0.0:1.0:0.0	.	486	P33993	MCM7_HUMAN	D	486;423;379;310	ENSP00000307288:A486D;ENSP00000346171:A310D	ENSP00000307288:A486D	A	-	2	0	MCM7	99531471	1.000000	0.71417	0.981000	0.43875	0.636000	0.38137	9.550000	0.98110	2.738000	0.93877	0.655000	0.94253	GCT		0.632	MCM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336534.3			
MLANA	2315	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	5897599	5897600	+	Missense_Mutation	DNP	AC	AC	GA			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr9:5897599_5897600AC>GA	ENST00000381477.3	+	3	280_281	c.120_121AC>GA	c.(118-123)ttACtg>ttGAtg	p.L41M	MLANA_ENST00000381471.1_Missense_Mutation_p.L41M|KIAA2026_ENST00000443149.2_5'Flank|MLANA_ENST00000490518.1_3'UTR|MLANA_ENST00000381476.1_Missense_Mutation_p.L41M	NM_005511.1	NP_005502.1	Q16655	MAR1_HUMAN	melan-A	41						endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|melanosome (GO:0042470)|trans-Golgi network (GO:0005802)		p.L40>?(1)|p.L41M(1)|p.L40L(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(1)	8		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(1;1.15e-06)|Lung(218;0.103)		TGGGAGTCTTACTGCTCATCGG	0.485																																																	3	Substitution - Missense(1)|Substitution - coding silent(1)|Complex(1)	kidney(3)																																								SO:0001583	missense	2315				CCDS6466.1	9p24.1	2008-02-05			ENSG00000120215	ENSG00000120215			7124	protein-coding gene	gene with protein product		605513					Standard	NM_005511		Approved	MART1	uc003zjo.1	Q16655	OTTHUMG00000019510	Exception_encountered	9.37:g.5897599_5897600delinsGA	ENSP00000370886:p.Leu41Met	Somatic		WXS	Illumina HiSeq	Phase_I	Q6ICU4	Silent|Missense_Mutation	SNP	ENST00000381477.3	37	CCDS6466.1																																																																																				0.485	MLANA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051643.1			
MLH3	27030	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	75513898	75513898	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr14:75513898C>A	ENST00000556740.1	-	1	2496	c.2461G>T	c.(2461-2463)Gca>Tca	p.A821S	MLH3_ENST00000555671.1_5'UTR|MLH3_ENST00000238662.7_Missense_Mutation_p.A821S|MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000355774.2_Missense_Mutation_p.A821S|MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000556257.1_Missense_Mutation_p.A821S			Q9UHC1	MLH3_HUMAN	mutL homolog 3	821					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)	p.A821S(2)		breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		ATGTGGCTTGCTGGTTGACAA	0.408								Mismatch excision repair (MMR)																																									2	Substitution - Missense(2)	kidney(2)											83.0	85.0	84.0					14																	75513898		2203	4300	6503	SO:0001583	missense	27030			AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"""mutL (E. coli) homolog 3"", ""mutL homolog 3 (E. coli)"""			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.2461G>T	14.37:g.75513898C>A	ENSP00000452316:p.Ala821Ser	Somatic		WXS	Illumina HiSeq	Phase_I	P49751|Q56DK9|Q9P292|Q9UHC0	Missense_Mutation	SNP	ENST00000556740.1	37	CCDS32123.1	.	.	.	.	.	.	.	.	.	.	C	3.154	-0.173512	0.06421	.	.	ENSG00000119684	ENST00000355774;ENST00000238662;ENST00000556257;ENST00000556740	T;T;T;T	0.80653	-1.35;-1.35;-1.4;-1.35	5.93	1.94	0.25998	.	0.728099	0.12405	N	0.471814	T	0.68238	0.2979	L	0.36672	1.1	0.09310	N	0.999998	B;B	0.29301	0.241;0.011	B;B	0.29785	0.107;0.018	T	0.54302	-0.8314	10	0.32370	T	0.25	3.8711	4.6062	0.12378	0.1501:0.499:0.2726:0.0783	.	821;821	Q9UHC1-2;Q9UHC1	.;MLH3_HUMAN	S	821	ENSP00000348020:A821S;ENSP00000238662:A821S;ENSP00000451540:A821S;ENSP00000452316:A821S	ENSP00000238662:A821S	A	-	1	0	MLH3	74583651	0.046000	0.20272	0.029000	0.17559	0.028000	0.11728	0.472000	0.22116	0.074000	0.16767	0.655000	0.94253	GCA		0.408	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1		NM_014381	
NEURL1	9148	broad.mit.edu	37	10	105344764	105344764	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr10:105344764C>A	ENST00000369780.4	+	4	1530	c.1121C>A	c.(1120-1122)cCt>cAt	p.P374H	NEURL_ENST00000369777.2_Missense_Mutation_p.P357H	NM_004210.4	NP_004201.3	O76050	NEUL1_HUMAN		374	NHR 2. {ECO:0000255|PROSITE- ProRule:PRU00400}.				brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|lactation (GO:0007595)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Notch signaling pathway (GO:0045746)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse maturation (GO:0090129)|protein monoubiquitination (GO:0006513)|skeletal muscle tissue development (GO:0007519)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)	apical dendrite (GO:0097440)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|translation factor activity, non-nucleic acid binding (GO:0045183)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P374H(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	17				Epithelial(162;2.12e-09)|all cancers(201;6.99e-08)|BRCA - Breast invasive adenocarcinoma(275;0.125)		CCTTTCAGCCCTGAGGCCCTG	0.746																																																	1	Substitution - Missense(1)	kidney(1)											6.0	6.0	6.0					10																	105344764		1985	3970	5955	SO:0001583	missense	9148																														ENST00000369780.4:c.1121C>A	10.37:g.105344764C>A	ENSP00000358795:p.Pro374His	Somatic		WXS	Illumina GAIIx	Phase_I	Q5TDR2|Q5TDR3|Q8TAN0|Q9H463	Missense_Mutation	SNP	ENST00000369780.4	37	CCDS7551.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.611588	0.87258	.	.	ENSG00000107954	ENST00000369780;ENST00000369777	.	.	.	4.7	4.7	0.59300	NEUZ (2);	0.052809	0.85682	D	0.000000	T	0.79028	0.4377	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.67231	0.95	T	0.82303	-0.0524	9	0.62326	D	0.03	-17.6939	17.6584	0.88184	0.0:1.0:0.0:0.0	.	374	O76050	NEU1A_HUMAN	H	374;357	.	ENSP00000358792:P357H	P	+	2	0	NEURL	105334754	1.000000	0.71417	0.995000	0.50966	0.774000	0.43823	7.813000	0.86123	2.167000	0.68274	0.491000	0.48974	CCT		0.746	NEURL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050170.1			
NOX3	50508	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	155743887	155743887	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr6:155743887G>A	ENST00000159060.2	-	10	1351	c.1249C>T	c.(1249-1251)Ctt>Ttt	p.L417F		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	417					detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)	p.L417F(1)		cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		GATTTCAGAAGAGCAGCGAAG	0.512																																																	1	Substitution - Missense(1)	kidney(1)											156.0	146.0	149.0					6																	155743887		2203	4300	6503	SO:0001583	missense	50508			AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.1249C>T	6.37:g.155743887G>A	ENSP00000159060:p.Leu417Phe	Somatic		WXS	Illumina HiSeq	Phase_I	Q9HBJ9	Missense_Mutation	SNP	ENST00000159060.2	37	CCDS5250.1	.	.	.	.	.	.	.	.	.	.	G	16.17	3.048032	0.55110	.	.	ENSG00000074771	ENST00000159060	T	0.64438	-0.1	5.81	2.61	0.31194	Ferric reductase, NAD binding (1);	0.305394	0.28146	N	0.016430	T	0.49253	0.1546	L	0.43152	1.355	0.37076	D	0.898751	P	0.47841	0.901	P	0.51777	0.679	T	0.55811	-0.8082	10	0.72032	D	0.01	-21.2904	8.1031	0.30870	0.0:0.3283:0.3934:0.2782	.	417	Q9HBY0	NOX3_HUMAN	F	417	ENSP00000159060:L417F	ENSP00000159060:L417F	L	-	1	0	NOX3	155785579	0.861000	0.29849	0.528000	0.27938	0.483000	0.33249	1.331000	0.33793	1.430000	0.47334	0.643000	0.83706	CTT		0.512	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1			
NR5A2	2494	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	200014591	200014591	+	Silent	SNP	C	C	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr1:200014591C>A	ENST00000367362.3	+	4	588	c.342C>A	c.(340-342)gtC>gtA	p.V114V	NR5A2_ENST00000236914.3_Silent_p.V68V|NR5A2_ENST00000544748.1_Silent_p.V42V	NM_001276464.1|NM_205860.1	NP_001263393.1|NP_995582.1	O00482	NR5A2_HUMAN	nuclear receptor subfamily 5, group A, member 2	114					bile acid metabolic process (GO:0008206)|cholesterol homeostasis (GO:0042632)|embryo development (GO:0009790)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|homeostatic process (GO:0042592)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral genome replication (GO:0045070)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.V114V(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31	Prostate(682;0.19)					AGCGAACAGTCCAAAATAATA	0.328																																					Melanoma(179;1138 2773 15678 26136)												1	Substitution - coding silent(1)	kidney(1)											94.0	96.0	95.0					1																	200014591		2203	4300	6503	SO:0001819	synonymous_variant	2494			U93553	CCDS1400.1, CCDS1401.1, CCDS60383.1	1q32.11	2013-01-16			ENSG00000116833	ENSG00000116833		"""Nuclear hormone receptors"""	7984	protein-coding gene	gene with protein product	"""liver receptor homolog-1"""	604453		FTF		9858833, 7680097	Standard	NM_205860		Approved	FTZ-F1beta, hB1F, LRH-1, FTZ-F1, hB1F-2, B1F2	uc001gvb.4	O00482	OTTHUMG00000035635	ENST00000367362.3:c.342C>A	1.37:g.200014591C>A		Somatic		WXS	Illumina HiSeq	Phase_I	B4E2P3|O95642|Q147U3	Silent	SNP	ENST00000367362.3	37	CCDS1401.1	.	.	.	.	.	.	.	.	.	.	C	9.821	1.185770	0.21870	.	.	ENSG00000116833	ENST00000367357	.	.	.	5.5	4.57	0.56435	.	.	.	.	.	T	0.62060	0.2397	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58137	-0.7689	4	.	.	.	.	11.5027	0.50448	0.0:0.8581:0.0:0.1419	.	.	.	.	Y	35	.	.	S	+	2	0	NR5A2	198281214	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.268000	0.33062	2.742000	0.94016	0.655000	0.94253	TCC		0.328	NR5A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086497.2			
NRP2	8828	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	206640998	206640998	+	Silent	SNP	C	C	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr2:206640998C>T	ENST00000357118.4	+	16	2485	c.2454C>T	c.(2452-2454)ccC>ccT	p.P818P	NRP2_ENST00000540841.1_Intron|NRP2_ENST00000540178.1_Intron|NRP2_ENST00000272849.3_Silent_p.P823P|NRP2_ENST00000357785.5_Intron|NRP2_ENST00000360409.3_Intron|NRP2_ENST00000412873.2_Intron	NM_201267.1	NP_957719	Q99435	NELL2_HUMAN	neuropilin 2	0						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.P823P(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(14)|lung(19)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	52						GGACCGAGCCCACAGTGGACA	0.597											OREG0015157	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - coding silent(1)	kidney(1)											82.0	86.0	84.0					2																	206640998		2203	4300	6503	SO:0001819	synonymous_variant	8828			AF016098	CCDS2364.1, CCDS2365.1, CCDS46496.1, CCDS46497.1, CCDS46498.1, CCDS46499.1	2q33.3	2008-05-23			ENSG00000118257	ENSG00000118257			8005	protein-coding gene	gene with protein product		602070				9529250, 9331348	Standard	NM_003872		Approved	VEGF165R2	uc002vaw.3	O60462	OTTHUMG00000132893	ENST00000357118.4:c.2454C>T	2.37:g.206640998C>T		Somatic	2161	WXS	Illumina HiSeq	Phase_I	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Silent	SNP	ENST00000357118.4	37	CCDS46498.1																																																																																				0.597	NRP2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336465.1			
NSD1	64324	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	176631295	176631295	+	Splice_Site	SNP	T	T	C			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr5:176631295T>C	ENST00000439151.2	+	4	1281		c.e4+2		NSD1_ENST00000354179.4_Splice_Site|NSD1_ENST00000361032.4_Intron|NSD1_ENST00000347982.4_Splice_Site	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1						gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.?(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		AGGCATAAGGTAGGAAACGAA	0.378			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																														Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	2	Unknown(2)	kidney(2)											80.0	74.0	76.0					5																	176631295		2203	4300	6503	SO:0001630	splice_region_variant	64324	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.1236+2T>C	5.37:g.176631295T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q96PD8|Q96RN7	Splice_Site	SNP	ENST00000439151.2	37	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.077383	0.76415	.	.	ENSG00000165671	ENST00000354179;ENST00000355783;ENST00000508896;ENST00000439151;ENST00000347982	.	.	.	5.35	5.35	0.76521	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2975	0.73922	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	NSD1	176563901	1.000000	0.71417	0.994000	0.49952	0.865000	0.49528	7.165000	0.77544	2.155000	0.67459	0.533000	0.62120	.		0.378	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2		NM_172349	Intron
PCDH18	54510	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	138450943	138450943	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr4:138450943C>T	ENST00000344876.4	-	1	2686	c.2300G>A	c.(2299-2301)gGc>gAc	p.G767D	PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000510305.1_Intron|PCDH18_ENST00000507846.1_Missense_Mutation_p.G547D|PCDH18_ENST00000412923.2_Missense_Mutation_p.G767D	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	767					brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G767D(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					GGGCAGAGTGCCATTTATGGT	0.517																																																	1	Substitution - Missense(1)	kidney(1)											207.0	173.0	185.0					4																	138450943		2203	4300	6503	SO:0001583	missense	54510			AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"""Cadherins / Protocadherins : Non-clustered"""	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.2300G>A	4.37:g.138450943C>T	ENSP00000355082:p.Gly767Asp	Somatic		WXS	Illumina HiSeq	Phase_I	A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	37	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	C	15.55	2.868109	0.51588	.	.	ENSG00000189184	ENST00000344876;ENST00000412923;ENST00000507846	T;T;T	0.54479	0.68;0.68;0.57	5.53	5.53	0.82687	.	0.000000	0.44285	D	0.000477	T	0.72653	0.3487	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.984;0.994;0.984	T	0.69650	-0.5088	10	0.40728	T	0.16	.	19.663	0.95879	0.0:1.0:0.0:0.0	.	547;767;767	D6RIG4;Q9HCL0-2;Q9HCL0	.;.;PCD18_HUMAN	D	767;767;547	ENSP00000355082:G767D;ENSP00000390688:G767D;ENSP00000425903:G547D	ENSP00000355082:G767D	G	-	2	0	PCDH18	138670393	1.000000	0.71417	0.954000	0.39281	0.981000	0.71138	7.269000	0.78482	2.871000	0.98454	0.655000	0.94253	GGC		0.517	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1		NM_019035	
PCDHB13	56123	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	140594887	140594887	+	Nonsense_Mutation	SNP	G	G	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr5:140594887G>T	ENST00000341948.4	+	1	1379	c.1192G>T	c.(1192-1194)Gaa>Taa	p.E398*		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	398	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E398*(1)|p.E398K(1)		NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GAAATCCGCGGAAAACTTTTA	0.453																																																	2	Substitution - Missense(1)|Substitution - Nonsense(1)	lung(1)|kidney(1)											89.0	88.0	88.0					5																	140594887		2203	4300	6503	SO:0001587	stop_gained	56123			AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"""Cadherins / Protocadherins : Clustered"""	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.1192G>T	5.37:g.140594887G>T	ENSP00000345491:p.Glu398*	Somatic		WXS	Illumina HiSeq	Phase_I	A8K9V6	Nonsense_Mutation	SNP	ENST00000341948.4	37	CCDS4255.1	.	.	.	.	.	.	.	.	.	.	N	24.2	4.509698	0.85282	.	.	ENSG00000187372	ENST00000341948;ENST00000430318;ENST00000419217	.	.	.	3.5	0.507	0.16967	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	7.9544	0.30033	0.4429:0.0:0.5571:0.0	.	.	.	.	X	398	.	ENSP00000345491:E398X	E	+	1	0	PCDHB13	140575071	0.000000	0.05858	0.001000	0.08648	0.249000	0.25844	-0.604000	0.05667	0.135000	0.18707	0.298000	0.19748	GAA		0.453	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1		NM_018933	
PIK3C2G	5288	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	18435099	18435099	+	Missense_Mutation	SNP	T	T	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr12:18435099T>G	ENST00000266497.5	+	1	122	c.84T>G	c.(82-84)aaT>aaG	p.N28K	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.N28K|PIK3C2G_ENST00000535651.1_Missense_Mutation_p.N28K|RERGL_ENST00000541632.1_Intron|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.N28K			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	28					chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)	p.N28K(2)		breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				TCTTTGTAAATCAACCCCATT	0.363																																																	2	Substitution - Missense(2)	kidney(2)											63.0	59.0	60.0					12																	18435099		1864	4104	5968	SO:0001583	missense	5288			AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.84T>G	12.37:g.18435099T>G	ENSP00000266497:p.Asn28Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	T	9.956	1.221550	0.22457	.	.	ENSG00000139144	ENST00000535651;ENST00000433979;ENST00000266497;ENST00000538779	T;T;T;T	0.64991	1.25;-0.06;-0.06;-0.13	4.53	-0.538	0.11868	.	2.266350	0.02170	N	0.059606	T	0.46054	0.1373	L	0.29908	0.895	0.09310	N	1	P;B	0.35272	0.493;0.361	B;B	0.31101	0.124;0.058	T	0.35895	-0.9770	10	0.56958	D	0.05	-5.5696	2.4599	0.04538	0.3527:0.2028:0.0:0.4445	.	28;28	F5H369;O75747	.;P3C2G_HUMAN	K	28	ENSP00000443850:N28K;ENSP00000404845:N28K;ENSP00000266497:N28K;ENSP00000445381:N28K	ENSP00000266497:N28K	N	+	3	2	PIK3C2G	18326366	0.012000	0.17670	0.001000	0.08648	0.037000	0.13140	0.098000	0.15189	-0.082000	0.12640	-0.336000	0.08194	AAT		0.363	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1		NM_004570	
PLCB3	5331	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	64028903	64028903	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr11:64028903A>T	ENST00000540288.1	+	15	1866	c.1763A>T	c.(1762-1764)gAg>gTg	p.E588V	PLCB3_ENST00000279230.6_Missense_Mutation_p.E588V|PLCB3_ENST00000325234.5_Missense_Mutation_p.E521V	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	588					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.E588V(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						AATGCCACTGAGGAGATGTCC	0.617																																																	1	Substitution - Missense(1)	kidney(1)											153.0	119.0	131.0					11																	64028903		2201	4297	6498	SO:0001583	missense	5331			Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.1763A>T	11.37:g.64028903A>T	ENSP00000443631:p.Glu588Val	Somatic		WXS	Illumina HiSeq	Phase_I	A5PKZ6|G5E960|Q8N1A4	Missense_Mutation	SNP	ENST00000540288.1	37	CCDS8064.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.462688	0.84425	.	.	ENSG00000149782	ENST00000279230;ENST00000540288;ENST00000325234	T;T;T	0.52295	0.67;0.67;0.67	4.85	4.85	0.62838	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.274139	0.39985	N	0.001212	T	0.62405	0.2425	M	0.64404	1.975	0.58432	D	0.999997	D;D	0.69078	0.997;0.983	P;P	0.62885	0.892;0.908	T	0.65639	-0.6119	10	0.59425	D	0.04	.	13.3947	0.60843	1.0:0.0:0.0:0.0	.	521;588	G5E960;Q01970	.;PLCB3_HUMAN	V	588;588;521	ENSP00000279230:E588V;ENSP00000443631:E588V;ENSP00000324660:E521V	ENSP00000279230:E588V	E	+	2	0	PLCB3	63785479	1.000000	0.71417	0.996000	0.52242	0.780000	0.44128	9.187000	0.94912	1.824000	0.53156	0.254000	0.18369	GAG		0.617	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1			
POLQ	10721	broad.mit.edu;ucsc.edu	37	3	121208173	121208173	+	Missense_Mutation	SNP	T	T	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr3:121208173T>G	ENST00000264233.5	-	16	3733	c.3605A>C	c.(3604-3606)gAa>gCa	p.E1202A		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1202					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)	p.E1337A(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		GCTTGTCTGTTCATGAGATTG	0.348								DNA polymerases (catalytic subunits)																													Pancreas(152;907 1925 26081 31236 36904)												1	Substitution - Missense(1)	kidney(1)											200.0	206.0	204.0					3																	121208173		2203	4300	6503	SO:0001583	missense	10721			AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.3605A>C	3.37:g.121208173T>G	ENSP00000264233:p.Glu1202Ala	Somatic		WXS	Illumina GAIIx	Phase_I	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	T	5.547	0.285890	0.10513	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.46451	0.87	5.21	1.49	0.22878	.	1.020640	0.07821	N	0.959775	T	0.21186	0.0510	N	0.19112	0.55	0.09310	N	1	B;B	0.28258	0.085;0.205	B;B	0.24394	0.039;0.053	T	0.24977	-1.0145	10	0.17832	T	0.49	.	0.6244	0.00783	0.1679:0.1929:0.1747:0.4645	.	1202;374	O75417;O75417-2	DPOLQ_HUMAN;.	A	825;1202;1338	ENSP00000264233:E1202A	ENSP00000264233:E1202A	E	-	2	0	POLQ	122690863	0.001000	0.12720	0.004000	0.12327	0.092000	0.18411	0.694000	0.25512	1.007000	0.39238	0.460000	0.39030	GAA		0.348	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1		NM_199420	
PPP1R16A	84988	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	145724303	145724303	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr8:145724303G>A	ENST00000292539.4	+	4	1252	c.335G>A	c.(334-336)tGc>tAc	p.C112Y	PPP1R16A_ENST00000435887.1_Missense_Mutation_p.C112Y|CTD-2517M14.5_ENST00000569326.1_RNA|CTD-2517M22.14_ENST00000532766.1_RNA			Q96I34	PP16A_HUMAN	protein phosphatase 1, regulatory subunit 16A	112						plasma membrane (GO:0005886)		p.C112Y(1)		NS(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			TTGCAGTGCTGCATTGATGAT	0.652																																																	1	Substitution - Missense(1)	kidney(1)											65.0	54.0	58.0					8																	145724303		2203	4300	6503	SO:0001583	missense	84988				CCDS6429.1	8q24.3	2013-01-10	2011-10-04		ENSG00000160972	ENSG00000160972		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	14941	protein-coding gene	gene with protein product		609172	"""protein phosphatase 1, regulatory (inhibitor) subunit 16A"""			11948623	Standard	NM_032902		Approved	MGC14333, MYPT3	uc003zdf.3	Q96I34	OTTHUMG00000165173	ENST00000292539.4:c.335G>A	8.37:g.145724303G>A	ENSP00000292539:p.Cys112Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	D3DWM5	Missense_Mutation	SNP	ENST00000292539.4	37	CCDS6429.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	20.8|20.8|20.8	4.055449|4.055449|4.055449	0.75960|0.75960|0.75960	.|.|.	.|.|.	ENSG00000255182|ENSG00000160972|ENSG00000255182	ENST00000532766|ENST00000292539;ENST00000435887|ENST00000527086	.|T;T|.	.|0.64803|.	.|-0.12;-0.12|.	4.76|4.76|4.76	4.76|4.76|4.76	0.60689|0.60689|0.60689	.|Ankyrin repeat-containing domain (4);|.	.|0.000000|.	.|0.85682|.	.|D|.	.|0.000000|.	D|D|.	0.83547|0.83547|.	0.5278|0.5278|.	M|M|M	0.90814|0.90814|0.90814	3.15|3.15|3.15	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|D|.	.|0.89917|.	.|1.0|.	.|D|.	.|0.87578|.	.|0.998|.	D|D|.	0.87601|0.87601|.	0.2497|0.2497|.	6|10|.	0.87932|0.87932|0.87932	D|D|D	0|0|0	.|.|.	15.2564|15.2564|15.2564	0.73588|0.73588|0.73588	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	.|112|.	.|Q96I34|.	.|PP16A_HUMAN|.	V|Y|X	31|112|46	.|ENSP00000292539:C112Y;ENSP00000391126:C112Y|.	ENSP00000435686:A31V|ENSP00000292539:C112Y|ENSP00000437304:Q46X	A|C|Q	-|+|-	2|2|1	0|0|0	CTD-2517M22.14|PPP1R16A|CTD-2517M22.14	145695111|145695111|145695111	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.555000|0.555000|0.555000	0.35460|0.35460|0.35460	5.314000|5.314000|5.314000	0.65804|0.65804|0.65804	2.198000|2.198000|2.198000	0.70561|0.70561|0.70561	0.462000|0.462000|0.462000	0.41574|0.41574|0.41574	GCA|TGC|CAG		0.652	PPP1R16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382459.1		NM_032902	
PRPF38B	55119	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	109238748	109238749	+	Nonsense_Mutation	DNP	GC	GC	TT			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr1:109238748_109238749GC>TT	ENST00000370025.4	+	3	698_699	c.429_430GC>TT	c.(427-432)aaGCaa>aaTTaa	p.143_144KQ>N*	PRPF38B_ENST00000370021.1_Nonsense_Mutation_p.32_33KQ>N*|PRPF38B_ENST00000370022.5_Nonsense_Mutation_p.143_144KQ>N*|PRPF38B_ENST00000467302.1_3'UTR	NM_018061.2	NP_060531.2	Q5VTL8	PR38B_HUMAN	pre-mRNA processing factor 38B	143					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)	p.K143>?(1)|p.Q144*(1)|p.K143N(1)		NS(1)|kidney(3)|large_intestine(5)|lung(8)|prostate(1)|skin(1)	19		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0149)|Lung(183;0.0888)|COAD - Colon adenocarcinoma(174;0.113)|Epithelial(280;0.161)		TAACTCGAAAGCAAGTGATGGG	0.376																																																	3	Substitution - Missense(1)|Substitution - Nonsense(1)|Complex(1)	kidney(3)																																								SO:0001587	stop_gained	55119			AL833950	CCDS788.1	1p13.3	2013-10-03	2013-10-03		ENSG00000134186	ENSG00000134186			25512	protein-coding gene	gene with protein product			"""PRP38 pre-mRNA processing factor 38 (yeast) domain containing B"""				Standard	NM_018061		Approved	FLJ10330, NET1	uc001dvv.4	Q5VTL8	OTTHUMG00000010991	Exception_encountered	1.37:g.109238748_109238749delinsTT	ENSP00000359042:p.K143_Q144delinsN*	Somatic		WXS	Illumina HiSeq	Phase_I	Q05DD6|Q32Q58|Q5VTL9|Q6PK39|Q7Z6E2|Q86WF3|Q8IWG9|Q9NW40	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000370025.4	37	CCDS788.1																																																																																				0.376	PRPF38B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030231.1		NM_018061	
PZP	5858	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	9344841	9344841	+	Silent	SNP	C	C	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr12:9344841C>T	ENST00000261336.2	-	13	1522	c.1494G>A	c.(1492-1494)aaG>aaA	p.K498K	PZP_ENST00000381997.2_Silent_p.K367K	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	498					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.K498K(1)|p.K367K(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						CGATGACTCCCTTAGCCATGA	0.463																																					Melanoma(125;1402 1695 4685 34487 38571)												2	Substitution - coding silent(2)	kidney(2)											100.0	88.0	92.0					12																	9344841		2203	4300	6503	SO:0001819	synonymous_variant	5858			X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.1494G>A	12.37:g.9344841C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A6ND27|Q15273|Q2NKL2|Q7M4N7	Silent	SNP	ENST00000261336.2	37	CCDS8600.1																																																																																				0.463	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1		NM_002864	
RAB24	53917	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	176729440	176729440	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr5:176729440G>A	ENST00000303251.6	-	5	810	c.391C>T	c.(391-393)Cgt>Tgt	p.R131C	RAB24_ENST00000393611.2_Missense_Mutation_p.R131C|PRELID1_ENST00000303204.4_5'Flank|RAB24_ENST00000303270.6_Missense_Mutation_p.R102C|PRELID1_ENST00000503216.1_5'Flank	NM_001031677.2	NP_001026847.1	Q969Q5	RAB24_HUMAN	RAB24, member RAS oncogene family	131					autophagy (GO:0006914)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	autophagic vacuole (GO:0005776)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)	p.R131C(1)				all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACACGTCGACGCCTCCGGTCT	0.577																																																	1	Substitution - Missense(1)	kidney(1)											108.0	111.0	110.0					5																	176729440		2203	4300	6503	SO:0001583	missense	53917			AF087904	CCDS34300.1	5q35.3	2009-10-06			ENSG00000169228	ENSG00000169228		"""RAB, member RAS oncogene"""	9765	protein-coding gene	gene with protein product		612415					Standard	NM_001031677		Approved		uc003mfw.3	Q969Q5	OTTHUMG00000130849	ENST00000303251.6:c.391C>T	5.37:g.176729440G>A	ENSP00000304376:p.Arg131Cys	Somatic		WXS	Illumina HiSeq	Phase_I	Q7Z4Z7	Missense_Mutation	SNP	ENST00000303251.6	37	CCDS34300.1	.	.	.	.	.	.	.	.	.	.	G	19.70	3.876950	0.72180	.	.	ENSG00000169228	ENST00000393611;ENST00000303251;ENST00000303270	T;T;T	0.77620	-1.11;-1.11;-1.11	5.13	5.13	0.70059	Small GTP-binding protein domain (1);	0.698769	0.13310	U	0.397551	T	0.72342	0.3448	N	0.19112	0.55	0.53688	D	0.999973	P;D	0.53885	0.948;0.963	P;P	0.48901	0.594;0.459	T	0.74520	-0.3638	10	0.72032	D	0.01	0.0455	13.4679	0.61266	0.0:0.0:0.8032:0.1968	.	131;102	Q969Q5;F8W8H5	RAB24_HUMAN;.	C	131;131;102	ENSP00000377235:R131C;ENSP00000304376:R131C;ENSP00000302085:R102C	ENSP00000304376:R131C	R	-	1	0	RAB24	176662046	0.298000	0.24417	0.945000	0.38365	0.894000	0.52154	2.504000	0.45416	2.388000	0.81334	0.555000	0.69702	CGT		0.577	RAB24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253416.1		NM_130781	
RASA2	5922	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	141278763	141278763	+	Silent	SNP	A	A	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr3:141278763A>G	ENST00000452898.1	+	9	824	c.789A>G	c.(787-789)ctA>ctG	p.L263L	RASA2_ENST00000286364.3_Silent_p.L263L	NM_006506.2	NP_006497.2	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	263	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)	p.L263L(2)		NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	34						ATGGAAACCTAGTCCAAGATG	0.393																																																	2	Substitution - coding silent(2)	kidney(2)											124.0	117.0	119.0					3																	141278763		2203	4300	6503	SO:0001819	synonymous_variant	5922			AF115573	CCDS3117.1	3q22-q23	2013-01-10			ENSG00000155903	ENSG00000155903		"""Pleckstrin homology (PH) domain containing"""	9872	protein-coding gene	gene with protein product		601589				8699317	Standard	NM_006506		Approved	GAP1M	uc003etz.1	Q15283	OTTHUMG00000160221	ENST00000452898.1:c.789A>G	3.37:g.141278763A>G		Somatic		WXS	Illumina HiSeq	Phase_I	A8K7K1|G3V0F9|O00695|Q15284|Q92594|Q99577|Q9UEQ2	Silent	SNP	ENST00000452898.1	37																																																																																					0.393	RASA2-201	KNOWN	basic	protein_coding	protein_coding			NM_006506	
RNH1	6050	broad.mit.edu	37	11	498772	498772	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr11:498772C>A	ENST00000534797.1	-	5	2183	c.776G>T	c.(775-777)aGg>aTg	p.R259M	RNH1_ENST00000533410.1_Missense_Mutation_p.R259M|RNH1_ENST00000397604.3_Missense_Mutation_p.R259M|RNH1_ENST00000397614.1_Missense_Mutation_p.R259M|RNH1_ENST00000354420.2_Missense_Mutation_p.R259M|RNH1_ENST00000356187.5_Missense_Mutation_p.R259M|RNH1_ENST00000397615.2_Missense_Mutation_p.R259M|RNH1_ENST00000533592.1_5'Flank|RNH1_ENST00000438658.2_Missense_Mutation_p.R259M			O60930	RNH1_HUMAN	ribonuclease/angiogenin inhibitor 1	0	RNase H. {ECO:0000255|PROSITE- ProRule:PRU00408}.				mitochondrial DNA replication (GO:0006264)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)	p.R259M(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.26e-26)|Epithelial(43;1.34e-25)|OV - Ovarian serous cystadenocarcinoma(40;5.31e-20)|BRCA - Breast invasive adenocarcinoma(625;8.01e-05)|Lung(200;0.0378)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CCACAGGGTCCTGAGCCTGGA	0.706																																																	1	Substitution - Missense(1)	kidney(1)											17.0	19.0	18.0					11																	498772		2201	4297	6498	SO:0001583	missense	6050				CCDS7697.1	11p15.5	2008-02-05	2005-06-01	2005-06-01	ENSG00000023191	ENSG00000023191			10074	protein-coding gene	gene with protein product		173320	"""ribonuclease/angiogenin inhibitor"""	RNH			Standard	NM_203386		Approved	RAI	uc001lpo.1	P13489	OTTHUMG00000119086	ENST00000534797.1:c.776G>T	11.37:g.498772C>A	ENSP00000433999:p.Arg259Met	Somatic		WXS	Illumina GAIIx	Phase_I	B3KQU4|O60523|O60857|Q57Z93|Q5U0C1|Q6FHD4	Missense_Mutation	SNP	ENST00000534797.1	37	CCDS7697.1	.	.	.	.	.	.	.	.	.	.	C	10.26	1.301117	0.23650	.	.	ENSG00000023191	ENST00000534797;ENST00000397614;ENST00000397615;ENST00000397604;ENST00000529768;ENST00000533410;ENST00000438658;ENST00000354420;ENST00000356187	T;T;T;T;T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55	3.49	-3.21	0.05140	.	1.306900	0.05143	N	0.494583	T	0.58793	0.2147	M	0.72894	2.215	0.09310	N	1	D	0.69078	0.997	P	0.50825	0.651	T	0.60047	-0.7339	10	0.62326	D	0.03	.	8.9225	0.35621	0.0:0.3421:0.0:0.6579	.	259	P13489	RINI_HUMAN	M	259;259;259;259;53;259;259;259;259	ENSP00000433999:R259M;ENSP00000380738:R259M;ENSP00000380739:R259M;ENSP00000380729:R259M;ENSP00000432170:R53M;ENSP00000435594:R259M;ENSP00000416589:R259M;ENSP00000346402:R259M;ENSP00000348515:R259M	ENSP00000346402:R259M	R	-	2	0	RNH1	488772	0.000000	0.05858	0.001000	0.08648	0.131000	0.20780	-1.732000	0.01851	-0.590000	0.05866	0.549000	0.68633	AGG		0.706	RNH1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384301.1		NM_203389	
RXFP1	59350	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	159549854	159549854	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr4:159549854G>A	ENST00000307765.5	+	11	1143	c.892G>A	c.(892-894)Gat>Aat	p.D298N	RXFP1_ENST00000460056.2_Missense_Mutation_p.D217N|RXFP1_ENST00000448688.2_Missense_Mutation_p.D193N|RXFP1_ENST00000343542.5_Missense_Mutation_p.D298N|RXFP1_ENST00000470033.1_Missense_Mutation_p.D265N	NM_001253727.1|NM_001253728.1|NM_001253730.1|NM_001253732.1|NM_001253733.1|NM_021634.3	NP_001240656.1|NP_001240657.1|NP_001240659.1|NP_001240661.1|NP_001240662.1|NP_067647.2	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	298					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|lung connective tissue development (GO:0060427)|nipple morphogenesis (GO:0060658)|parturition (GO:0007567)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)	p.D298N(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|liver(2)|lung(22)|prostate(1)|skin(10)	49	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		CCAGAAACTGGATGAATTGTA	0.264																																																	1	Substitution - Missense(1)	kidney(1)											39.0	39.0	39.0					4																	159549854		1794	4061	5855	SO:0001583	missense	59350			AF190500	CCDS43276.1, CCDS58929.1, CCDS58930.1, CCDS75204.1, CCDS75205.1, CCDS75206.1	4q31.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000171509	ENSG00000171509		"""GPCR / Class A : Relaxin family peptide receptors"""	19718	protein-coding gene	gene with protein product		606654	"""leucine-rich repeat-containing G protein-coupled receptor 7"""	LGR7		15956688, 16507880	Standard	NM_021634		Approved	RXFPR1	uc003ipz.3	Q9HBX9	OTTHUMG00000149973	ENST00000307765.5:c.892G>A	4.37:g.159549854G>A	ENSP00000303248:p.Asp298Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B4DHD1|B4DTV2|Q2M215|Q3KU24|Q3KU25|Q3KU26	Missense_Mutation	SNP	ENST00000307765.5	37	CCDS43276.1	.	.	.	.	.	.	.	.	.	.	G	11.13	1.547749	0.27652	.	.	ENSG00000171509	ENST00000460056;ENST00000307765;ENST00000448688;ENST00000343542;ENST00000470033;ENST00000440678	T;T;T;T;T	0.58210	0.4;0.35;0.41;0.35;0.35	5.21	1.37	0.22104	.	0.318925	0.38005	N	0.001855	T	0.26702	0.0653	N	0.05351	-0.065	0.30577	N	0.762903	B;B;B;B;B;B;B;B;B	0.32467	0.089;0.271;0.04;0.072;0.143;0.001;0.076;0.372;0.173	B;B;B;B;B;B;B;B;B	0.37198	0.158;0.158;0.063;0.098;0.098;0.003;0.102;0.243;0.158	T	0.20338	-1.0278	10	0.17832	T	0.49	.	4.1558	0.10260	0.084:0.2953:0.4685:0.1522	.	309;325;193;298;265;217;168;235;298	B3KV27;B4DGP2;B4DHD1;Q9HBX9-4;Q9HBX9-2;E9PCA3;Q59H16;Q4W5D9;Q9HBX9	.;.;.;.;.;.;.;.;RXFP1_HUMAN	N	217;298;193;298;265;168	ENSP00000423306:D217N;ENSP00000303248:D298N;ENSP00000414885:D193N;ENSP00000345889:D298N;ENSP00000420712:D265N	ENSP00000303248:D298N	D	+	1	0	RXFP1	159769304	1.000000	0.71417	0.990000	0.47175	0.911000	0.54048	1.195000	0.32186	0.001000	0.14605	0.460000	0.39030	GAT		0.264	RXFP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314865.1		NM_021634	
SIK3	23387	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	116746997	116746997	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr11:116746997A>G	ENST00000292055.4	-	8	928	c.893T>C	c.(892-894)aTg>aCg	p.M298T	SIK3_ENST00000375300.1_Missense_Mutation_p.M356T|SIK3_ENST00000375288.1_5'UTR|SIK3_ENST00000542607.1_Missense_Mutation_p.M298T|SIK3_ENST00000434315.2_Missense_Mutation_p.M197T|SIK3_ENST00000446921.2_Missense_Mutation_p.M356T	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	298	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.M356T(1)		breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	57						GTCCAGTCCCATGTCCTCCAT	0.463																																																	1	Substitution - Missense(1)	kidney(1)											230.0	183.0	199.0					11																	116746997		2201	4296	6497	SO:0001583	missense	23387			AB023216	CCDS8379.1, CCDS60974.1, CCDS8379.2	11q23.3	2010-02-17			ENSG00000160584	ENSG00000160584			29165	protein-coding gene	gene with protein product		614776				10231032, 8889548	Standard	NM_025164		Approved	FLJ12240, L19, KIAA0999, QSK	uc001ppy.3	Q9Y2K2	OTTHUMG00000066628	ENST00000292055.4:c.893T>C	11.37:g.116746997A>G	ENSP00000292055:p.Met298Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Missense_Mutation	SNP	ENST00000292055.4	37	CCDS8379.1	.	.	.	.	.	.	.	.	.	.	A	15.63	2.891709	0.52014	.	.	ENSG00000160584	ENST00000375300;ENST00000292055;ENST00000542607;ENST00000434315	T;T;T;T	0.71341	-0.53;-0.56;-0.5;-0.16	5.59	5.59	0.84812	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (1);Protein kinase-like domain (1);	0.000000	0.50627	U	0.000120	T	0.70211	0.3198	M	0.67953	2.075	0.80722	D	1	B;B;B	0.30793	0.295;0.003;0.132	B;B;B	0.28991	0.097;0.011;0.065	T	0.72283	-0.4339	10	0.87932	D	0	.	15.7466	0.77949	1.0:0.0:0.0:0.0	.	298;197;298	A1A5A8;A1A5A9;Q9Y2K2	.;.;SIK3_HUMAN	T	356;298;298;197	ENSP00000364449:M356T;ENSP00000292055:M298T;ENSP00000438108:M298T;ENSP00000415873:M197T	ENSP00000292055:M298T	M	-	2	0	SIK3	116252207	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.746000	0.74866	2.117000	0.64856	0.528000	0.53228	ATG		0.463	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding			NM_025164	
SUPT5H	6829	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	39955501	39955501	+	Missense_Mutation	SNP	T	T	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr19:39955501T>A	ENST00000599117.1	+	12	1055	c.688T>A	c.(688-690)Tac>Aac	p.Y230N	SUPT5H_ENST00000359191.6_Missense_Mutation_p.Y226N|SUPT5H_ENST00000432763.2_Missense_Mutation_p.Y230N|SUPT5H_ENST00000598725.1_Missense_Mutation_p.Y230N|SUPT5H_ENST00000402194.2_Missense_Mutation_p.Y226N			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	230	Interaction with SUPT4H1.				7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)	p.Y230N(1)		breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CGTGGAGGCCTACAAGCAGAC	0.582																																																	1	Substitution - Missense(1)	kidney(1)											105.0	91.0	96.0					19																	39955501		2203	4300	6503	SO:0001583	missense	6829			U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"""suppressor of Ty (S.cerevisiae) 5 homolog"""			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.688T>A	19.37:g.39955501T>A	ENSP00000470252:p.Tyr230Asn	Somatic		WXS	Illumina HiSeq	Phase_I	O43279|Q59G52|Q99639	Missense_Mutation	SNP	ENST00000599117.1	37	CCDS12536.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.848089	0.91277	.	.	ENSG00000196235	ENST00000432763;ENST00000402194;ENST00000378524;ENST00000359191	.	.	.	5.62	5.62	0.85841	Transcription antitermination protein, NusG, N-terminal (1);	0.188964	0.46145	D	0.000308	T	0.74137	0.3677	L	0.55103	1.725	0.80722	D	1	D;D	0.71674	0.997;0.998	D;D	0.73708	0.968;0.981	T	0.73553	-0.3946	8	.	.	.	-16.4543	14.8054	0.69952	0.0:0.0:0.0:1.0	.	226;230	O00267-2;O00267	.;SPT5H_HUMAN	N	230;226;208;230	.	.	Y	+	1	0	SUPT5H	44647341	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.885000	0.87282	2.137000	0.66172	0.533000	0.62120	TAC		0.582	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1		NM_003169	
TACC3	10460	hgsc.bcm.edu	37	4	1729795	1729795	+	Silent	SNP	A	A	G	rs200539908	byFrequency	TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr4:1729795A>G	ENST00000313288.4	+	4	772	c.666A>G	c.(664-666)gaA>gaG	p.E222E		NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	222					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|cytoplasmic sequestering of transcription factor (GO:0042994)|hemopoiesis (GO:0030097)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of cell cycle (GO:0051726)|regulation of microtubule-based process (GO:0032886)|response to hypoxia (GO:0001666)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	25		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126)			GAGCCGAGGAAGAATGCAAAG	0.617													-|||	192	0.0383387	0.056	0.0173	5008	,	,		16940	0.0129		0.0199	False		,,,				2504	0.0746				Ovarian(120;482 2294 11894 35824)												0								A		135,4267		4,127,2070	20.0	22.0	21.0		666	0.8	0.0	4		21	86,8506		2,82,4212	no	coding-synonymous	TACC3	NM_006342.1		6,209,6282	GG,GA,AA		1.0009,3.0668,1.7008		222/839	1729795	221,12773	2201	4296	6497	SO:0001819	synonymous_variant	10460			AF093543	CCDS3352.1	4p16.3	2008-07-29			ENSG00000013810	ENSG00000013810			11524	protein-coding gene	gene with protein product		605303				17675670	Standard	NM_006342		Approved	ERIC1	uc003gdo.3	Q9Y6A5	OTTHUMG00000089535	ENST00000313288.4:c.666A>G	4.37:g.1729795A>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q2NKK4|Q3KQS5|Q9UMQ1	Silent	SNP	ENST00000313288.4	37	CCDS3352.1																																																																																				0.617	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2			
TLK1	9874	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	171902831	171902831	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr2:171902831C>T	ENST00000431350.2	-	11	1426	c.1022G>A	c.(1021-1023)aGg>aAg	p.R341K	TLK1_ENST00000521943.1_Missense_Mutation_p.R293K|TLK1_ENST00000360843.3_Missense_Mutation_p.R362K|TLK1_ENST00000442919.2_Missense_Mutation_p.R293K|TLK1_ENST00000434911.2_Missense_Mutation_p.R245K			Q9UKI8	TLK1_HUMAN	tousled-like kinase 1	341					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R341K(1)|p.R293K(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						TTTCCTTTGCCTTTCAATATC	0.378																																																	2	Substitution - Missense(2)	kidney(2)											203.0	183.0	190.0					2																	171902831		2203	4300	6503	SO:0001583	missense	9874			AB004885	CCDS2241.1, CCDS46447.1, CCDS46448.1	2q31.1	2010-04-19			ENSG00000198586	ENSG00000198586			11841	protein-coding gene	gene with protein product		608438				9427565, 12660173	Standard	NM_012290		Approved	KIAA0137, PKU-BETA	uc002ugp.2	Q9UKI8	OTTHUMG00000132243	ENST00000431350.2:c.1022G>A	2.37:g.171902831C>T	ENSP00000411099:p.Arg341Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B3KR15|B4DX87|Q14150|Q8N591|Q9NYH2|Q9Y4F6	Missense_Mutation	SNP	ENST00000431350.2	37	CCDS2241.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.361296	0.82353	.	.	ENSG00000198586	ENST00000442919;ENST00000431350;ENST00000360843;ENST00000521943;ENST00000434911	T;T;T;T;T	0.63744	-0.03;-0.06;-0.03;-0.03;0.01	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.77096	0.4080	L	0.58428	1.81	0.80722	D	1	B;B;D	0.67145	0.1;0.357;0.996	B;B;D	0.77004	0.109;0.219;0.989	T	0.76061	-0.3097	10	0.46703	T	0.11	-5.903	19.3879	0.94565	0.0:1.0:0.0:0.0	.	245;362;341	B4DX87;Q9UKI8-2;Q9UKI8	.;.;TLK1_HUMAN	K	293;341;362;293;245	ENSP00000402165:R293K;ENSP00000411099:R341K;ENSP00000354089:R362K;ENSP00000428113:R293K;ENSP00000409222:R245K	ENSP00000354089:R362K	R	-	2	0	TLK1	171611077	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.776000	0.85560	2.652000	0.90054	0.591000	0.81541	AGG		0.378	TLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255314.1		NM_012290	
TMPRSS3	64699	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	21	43803192	43803192	+	Silent	SNP	G	G	A			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr21:43803192G>A	ENST00000291532.3	-	8	1687	c.732C>T	c.(730-732)ggC>ggT	p.G244G	TMPRSS3_ENST00000474596.1_5'UTR|TMPRSS3_ENST00000433957.2_Silent_p.G244G|TMPRSS3_ENST00000398405.1_Silent_p.G242G|TMPRSS3_ENST00000380399.1_Silent_p.G328G|TMPRSS3_ENST00000398397.3_Silent_p.G244G	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	244	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)	p.G244G(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						TGATGACAGAGCCCCCGCACA	0.597																																																	1	Substitution - coding silent(1)	kidney(1)											79.0	67.0	71.0					21																	43803192		2203	4300	6503	SO:0001819	synonymous_variant	64699			AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"""Serine peptidases / Transmembrane"""	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.732C>T	21.37:g.43803192G>A		Somatic		WXS	Illumina HiSeq	Phase_I	D3DSJ6|Q5USC7|Q6ZMC3	Silent	SNP	ENST00000291532.3	37	CCDS13686.1																																																																																				0.597	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1			
LOC442028	442028	broad.mit.edu	37	2	95552625	95552625	+	RNA	SNP	C	C	T	rs556537904		TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr2:95552625C>T	ENST00000568768.1	-	0	476																											GAACATACAGCCAAAAATCCA	0.333													C|||	1	0.000199681	0.0	0.0	5008	,	,		18318	0.0		0.0	False		,,,				2504	0.001																0																																												0																															2.37:g.95552625C>T		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000568768.1	37																																																																																					0.333	AC097374.2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000431504.1			
UPF3A	65110	broad.mit.edu	37	13	115047559	115047559	+	Silent	SNP	C	C	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr13:115047559C>T	ENST00000375299.3	+	2	327	c.271C>T	c.(271-273)Ctg>Ttg	p.L91L	UPF3A_ENST00000351487.5_Silent_p.L91L	NM_023011.3	NP_075387.1	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A (yeast)	91	Required for interaction with UPF2.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nucleocytoplasmic transport (GO:0006913)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.L91L(8)		autonomic_ganglia(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	16	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)		GCTGCGCCCGCTGCCAGCACA	0.731																																																	8	Substitution - coding silent(8)	lung(2)|prostate(2)|kidney(2)|central_nervous_system(2)											4.0	4.0	4.0					13																	115047559		1902	3804	5706	SO:0001819	synonymous_variant	65110			AF318575	CCDS9543.1, CCDS9544.1	13q34	2010-04-30			ENSG00000169062	ENSG00000169062			20332	protein-coding gene	gene with protein product		605530				11113196, 11163187	Standard	NM_023011		Approved	RENT3A, UPF3, HUPF3A	uc001vup.3	Q9H1J1	OTTHUMG00000017403	ENST00000375299.3:c.271C>T	13.37:g.115047559C>T		Somatic		WXS	Illumina GAIIx	Phase_I	A2A366|Q5T8C3|Q5T8C9|Q7Z6N3|Q86YK1|Q9BZI8	Silent	SNP	ENST00000375299.3	37	CCDS9543.1																																																																																				0.731	UPF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045968.2			
WHAMMP3	339005	broad.mit.edu	37	15	23205108	23205108	+	RNA	SNP	C	C	T			TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr15:23205108C>T	ENST00000400153.2	-	0	746					NR_003521.1		Q1A5X7	WHAL1_HUMAN	WAS protein homolog associated with actin, golgi membranes and microtubules pseudogene 3																		GTGGTTGCCACGGTAACTAAT	0.393																																																	0																																												0			BC048987		15q11.2	2014-03-20	2011-06-24	2011-06-24	ENSG00000187667	ENSG00000276141			27892	pseudogene	pseudogene			"""WAS protein homology region 2 domain containing 1-like 1"", ""WAS protein homolog associated with actin, golgi membranes and microtubules-like 1"", ""WAS protein homolog associated with actin, golgi membranes and microtubules-like 1 (pseudogene)"""	WHDC1L1, WHAMML1		18226259	Standard	NR_003521		Approved		uc001yvg.3	Q1A5X7	OTTHUMG00000171921		15.37:g.23205108C>T		Somatic		WXS	Illumina GAIIx	Phase_I	Q1A5X8|Q52M16|Q52M18	RNA	SNP	ENST00000400153.2	37																																																																																					0.393	WHAMMP3-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000415907.1		NR_003521	
ZCCHC3	85364	broad.mit.edu	37	20	278688	278690	+	In_Frame_Del	DEL	CGG	CGG	-	rs11468351|rs5839847|rs6147263	byFrequency	TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	CGG	CGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr20:278688_278690delCGG	ENST00000382352.3	+	1	952_954	c.461_463delCGG	c.(460-465)ccggcg>ccg	p.A159del		NM_033089.6	NP_149080	Q9NUD5	ZCHC3_HUMAN	zinc finger, CCHC domain containing 3	159	Poly-Ala.						poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.A159delA(3)		endometrium(2)|large_intestine(1)|lung(3)|prostate(2)	8		all_cancers(10;0.000209)|Lung NSC(37;0.0417)|all_lung(30;0.0713)|all_epithelial(17;0.0748)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			CAGGATGAgccggcggcggcggc	0.768														4335	0.865615	0.8343	0.9395	5008	,	,		8937	0.8065		0.9423	False		,,,				2504	0.8374																3	Deletion - In frame(3)	prostate(2)|large_intestine(1)																																								SO:0001651	inframe_deletion	85364			AL034548	CCDS42844.1	20p13-p12.2	2014-04-10	2004-07-14	2004-07-14	ENSG00000177764	ENSG00000247315		"""Zinc fingers, CCHC domain containing"""	16230	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 99"""	C20orf99			Standard	NM_033089		Approved	dJ1103G7.7	uc002wdf.3	Q9NUD5	OTTHUMG00000188280	ENST00000382352.3:c.461_463delCGG	20.37:g.278697_278699delCGG	ENSP00000371789:p.Ala159del	Somatic		WXS	Illumina GAIIx	Phase_I	Q3B7J3|Q6NT79	In_Frame_Del	DEL	ENST00000382352.3	37	CCDS42844.1																																																																																				0.768	ZCCHC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077447.1			
ZNF710	374655	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	90616473	90616473	+	Silent	SNP	C	C	G	rs146964408	byFrequency	TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr15:90616473C>G	ENST00000268154.4	+	3	1880	c.1629C>G	c.(1627-1629)ccC>ccG	p.P543P	RP11-617F23.1_ENST00000558334.1_RNA	NM_198526.2	NP_940928.2	Q8N1W2	ZN710_HUMAN	zinc finger protein 710	543					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P543P(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(1)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	19	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.00769)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.129)			TACACTCGCCCGTGAAGCCAT	0.592																																																	1	Substitution - coding silent(1)	kidney(1)											102.0	96.0	98.0					15																	90616473		2200	4298	6498	SO:0001819	synonymous_variant	374655			AK094712	CCDS10358.1	15q26.1	2013-01-08			ENSG00000140548	ENSG00000140548		"""Zinc fingers, C2H2-type"""	25352	protein-coding gene	gene with protein product							Standard	XM_005254905		Approved	DKFZp547K1113, FLJ37393, FLJ00306	uc002bov.2	Q8N1W2	OTTHUMG00000149812	ENST00000268154.4:c.1629C>G	15.37:g.90616473C>G		Somatic		WXS	Illumina HiSeq	Phase_I	A0AVS3|Q6ZMK9|Q8NDU0	Silent	SNP	ENST00000268154.4	37	CCDS10358.1																																																																																				0.592	ZNF710-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313423.1		NM_198526	
VHL	7428	hgsc.bcm.edu	37	3	10183859	10183859	+	Missense_Mutation	SNP	C	C	T	rs17855706		TCGA-CJ-6031-01A-11D-1669-08	TCGA-CJ-6031-11A-01D-1669-08	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM	.		Illumina GAIIx	a47debc7-700e-4c64-a9b3-1113609a1ddf	7ab7544e-efbe-4520-a5ad-1bb251253877	g.chr3:10183859C>T	ENST00000256474.2	+	1	1168	c.328C>T	c.(328-330)Cac>Tac	p.H110Y	VHL_ENST00000345392.2_Missense_Mutation_p.H110Y|snoU13_ENST00000458986.1_RNA	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	110	Involved in binding to CCT complex.		H -> Y (in dbSNP:rs17855706). {ECO:0000269|PubMed:15489334}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.?(2)|p.H110>RIN(1)|p.I109_R113del(1)|p.G106fs*49(1)|p.H110fs*49(1)|p.H110_S111del(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CCGCCGCATCCACAGCTACCG	0.692		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													.	yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	7	Deletion - Frameshift(2)|Deletion - In frame(2)|Unknown(2)|Complex - insertion inframe(1)	kidney(7)											11.0	12.0	12.0					3																	10183859		1772	3719	5491	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.328C>T	3.37:g.10183859C>T	ENSP00000256474:p.His110Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.510008	0.85282	.	.	ENSG00000134086	ENST00000256474;ENST00000345392	D;D	0.99811	-6.87;-6.87	5.17	4.21	0.49690	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.287952	0.36778	N	0.002409	D	0.99254	0.9740	N	0.22421	0.69	0.20873	N	0.999835	D;D	0.67145	0.994;0.996	P;D	0.65573	0.899;0.936	D	0.96283	0.9208	10	0.52906	T	0.07	-9.4471	11.8157	0.52209	0.2538:0.7462:0.0:0.0	rs17855706	110;110	P40337-2;P40337	.;VHL_HUMAN	Y	110	ENSP00000256474:H110Y;ENSP00000344757:H110Y	ENSP00000256474:H110Y	H	+	1	0	VHL	10158859	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.257000	0.32932	2.425000	0.82216	0.479000	0.44913	CAC		0.692	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
