#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
NLRP14	338323	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	7064302	7064302	+	Missense_Mutation	SNP	G	G	A			TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr11:7064302G>A	ENST00000299481.4	+	4	1391	c.1045G>A	c.(1045-1047)Gcc>Acc	p.A349T		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	349	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		TAAGAGGTGGGCCATGAAAGT	0.428																																																0													100.0	104.0	102.0					11																	7064302		2201	4296	6497	SO:0001583	missense	338323			BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"""Nucleotide-binding domain and leucine rich repeat containing"""	22939	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"""	609665	"""NACHT, leucine rich repeat and PYD containing 14"""	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.1045G>A	11.37:g.7064302G>A	ENSP00000299481:p.Ala349Thr		Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	.	.	.	.	.	.	.	.	.	.	G	14.66	2.601915	0.46423	.	.	ENSG00000158077	ENST00000299481	T	0.79033	-1.23	4.5	2.56	0.30785	NACHT nucleoside triphosphatase (1);	0.427086	0.20093	N	0.099389	T	0.75759	0.3893	M	0.75264	2.295	0.09310	N	1	D	0.54047	0.964	P	0.45310	0.476	T	0.67007	-0.5779	10	0.48119	T	0.1	.	7.0214	0.24916	0.0937:0.0:0.7339:0.1724	.	349	Q86W24	NAL14_HUMAN	T	349	ENSP00000299481:A349T	ENSP00000299481:A349T	A	+	1	0	NLRP14	7020878	0.998000	0.40836	0.003000	0.11579	0.495000	0.33615	5.043000	0.64208	0.610000	0.30035	0.650000	0.86243	GCC		0.428	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822		27	209	27	209
NCKAP1L	3071	hgsc.bcm.edu;ucsc.edu	37	12	54914539	54914539	+	Missense_Mutation	SNP	C	C	T			TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr12:54914539C>T	ENST00000293373.6	+	17	1766	c.1687C>T	c.(1687-1689)Cgt>Tgt	p.R563C	NCKAP1L_ENST00000545638.2_Missense_Mutation_p.R513C	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	563					actin polymerization-dependent cell motility (GO:0070358)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|chemotaxis (GO:0006935)|cortical actin cytoskeleton organization (GO:0030866)|erythrocyte development (GO:0048821)|maintenance of cell polarity (GO:0030011)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of myosin-light-chain-phosphatase activity (GO:0035509)|neutrophil chemotaxis (GO:0030593)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of lymphocyte differentiation (GO:0045621)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|response to drug (GO:0042493)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)|protein kinase activator activity (GO:0030295)|Rac GTPase activator activity (GO:0030675)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(37)|ovary(3)|prostate(3)|skin(3)|stomach(2)	80						TGCCATGTTGCGTTATGCCAT	0.463																																																0													422.0	358.0	380.0					12																	54914539		2203	4300	6503	SO:0001583	missense	3071			AI924363	CCDS31813.1, CCDS53799.1	12q13.1	2005-10-11	2005-10-11	2005-10-11		ENSG00000123338			4862	protein-coding gene	gene with protein product		141180	"""hematopoietic protein 1"""	HEM1		1932118	Standard	NM_005337		Approved		uc001sgc.4	P55160	OTTHUMG00000169843	ENST00000293373.6:c.1687C>T	12.37:g.54914539C>T	ENSP00000293373:p.Arg563Cys		B4DUT5|Q52LW0	Missense_Mutation	SNP	ENST00000293373.6	37	CCDS31813.1	.	.	.	.	.	.	.	.	.	.	C	16.58	3.162972	0.57476	.	.	ENSG00000123338	ENST00000293373;ENST00000545638	T;T	0.39056	1.1;1.1	5.46	4.56	0.56223	.	0.112873	0.64402	D	0.000016	T	0.42449	0.1203	M	0.71036	2.16	0.80722	D	1	B	0.26635	0.155	B	0.23852	0.049	T	0.47114	-0.9142	10	0.87932	D	0	-12.4671	11.6594	0.51337	0.0:0.914:0.0:0.086	.	563	P55160	NCKPL_HUMAN	C	563;513	ENSP00000293373:R563C;ENSP00000445596:R513C	ENSP00000293373:R563C	R	+	1	0	NCKAP1L	53200806	1.000000	0.71417	0.998000	0.56505	0.883000	0.51084	1.357000	0.34090	2.750000	0.94351	0.549000	0.68633	CGT		0.463	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406195.1	NM_005337		231	495	231	495
LGR5	8549	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	71978453	71978453	+	Missense_Mutation	SNP	C	C	T	rs369268162		TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr12:71978453C>T	ENST00000266674.5	+	18	2974	c.2663C>T	c.(2662-2664)cCa>cTa	p.P888L	LGR5_ENST00000536515.1_Missense_Mutation_p.P816L|RP11-186F10.2_ENST00000546601.1_RNA|LGR5_ENST00000540815.2_Missense_Mutation_p.P864L			O75473	LGR5_HUMAN	leucine-rich repeat containing G protein-coupled receptor 5	888					G-protein coupled receptor signaling pathway (GO:0007186)|inner ear development (GO:0048839)|positive regulation of canonical Wnt signaling pathway (GO:0090263)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)		NUP107/LGR5(2)	endometrium(2)|kidney(3)|large_intestine(2)|lung(24)|ovary(1)|pancreas(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	48						GTGCCATCACCAGCTTATCCA	0.458																																																0								C	LEU/PRO	0,4406		0,0,2203	137.0	130.0	132.0		2663	5.8	0.1	12		132	2,8598	2.2+/-6.3	0,2,4298	no	missense	LGR5	NM_003667.2	98	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging	888/908	71978453	2,13004	2203	4300	6503	SO:0001583	missense	8549			AF062006	CCDS9000.1, CCDS61194.1, CCDS61195.1	12q22-q23	2012-08-21	2011-01-25	2004-11-12				"""GPCR / Class A : Orphans"""	4504	protein-coding gene	gene with protein product		606667	"""G protein-coupled receptor 49"", ""leucine-rich repeat-containing G protein-coupled receptor 5"""	GPR67, GPR49		9642114	Standard	NM_003667		Approved	HG38, FEX	uc001swl.4	O75473	OTTHUMG00000169543	ENST00000266674.5:c.2663C>T	12.37:g.71978453C>T	ENSP00000266674:p.Pro888Leu		D8MCT0|Q4VAM0|Q4VAM2|Q9UP75	Missense_Mutation	SNP	ENST00000266674.5	37	CCDS9000.1	.	.	.	.	.	.	.	.	.	.	C	10.30	1.312005	0.23821	0.0	2.33E-4	ENSG00000139292	ENST00000266674;ENST00000536515;ENST00000540815	T;T;T	0.57273	0.47;0.41;0.54	5.82	5.82	0.92795	.	0.396843	0.24599	N	0.037141	T	0.43166	0.1235	N	0.22421	0.69	0.38556	D	0.949576	B;B	0.30361	0.277;0.181	B;B	0.27380	0.079;0.036	T	0.36335	-0.9752	10	0.39692	T	0.17	.	20.1016	0.97878	0.0:1.0:0.0:0.0	.	864;888	O75473-2;O75473	.;LGR5_HUMAN	L	888;816;864	ENSP00000266674:P888L;ENSP00000443033:P816L;ENSP00000441035:P864L	ENSP00000266674:P888L	P	+	2	0	LGR5	70264720	0.280000	0.24249	0.109000	0.21407	0.198000	0.23893	4.078000	0.57606	2.748000	0.94277	0.585000	0.79938	CCA		0.458	LGR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404744.1	NM_003667		95	187	95	187
IDH2	3418	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	90631838	90631838	+	Missense_Mutation	SNP	C	C	T	rs121913503		TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr15:90631838C>T	ENST00000330062.3	-	4	628	c.515G>A	c.(514-516)aGg>aAg	p.R172K	IDH2_ENST00000559482.1_Intron|IDH2_ENST00000539790.1_Missense_Mutation_p.R42K|IDH2_ENST00000540499.2_Missense_Mutation_p.R120K	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	172					2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)	p.R172K(116)|p.R172M(21)|p.R172N(1)		biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			ATGGGCGTGCCTGCCAATGGT	0.632			M		GBM																																		Dom	yes		15	15q26.1	3418	"""socitrate dehydrogenase 2 (NADP+), mitochondrial """		M	138	Substitution - Missense(138)	haematopoietic_and_lymphoid_tissue(67)|central_nervous_system(65)|biliary_tract(6)											85.0	81.0	82.0					15																	90631838		2200	4298	6498	SO:0001583	missense	3418				CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.515G>A	15.37:g.90631838C>T	ENSP00000331897:p.Arg172Lys		B2R6L6|B4DFL2|Q96GT3	Missense_Mutation	SNP	ENST00000330062.3	37	CCDS10359.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.957149	0.53293	.	.	ENSG00000182054	ENST00000330062;ENST00000539790;ENST00000540499	D;D;D	0.86432	-2.12;-2.12;-2.12	5.93	4.07	0.47477	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.95217	0.8449	H	0.96889	3.9	0.49687	D	0.999812	D	0.89917	1.0	D	0.91635	0.999	D	0.95096	0.8226	10	0.87932	D	0	.	10.781	0.46377	0.0:0.8464:0.0:0.1536	.	172	P48735	IDHP_HUMAN	K	172;42;120	ENSP00000331897:R172K;ENSP00000438457:R42K;ENSP00000446147:R120K	ENSP00000331897:R172K	R	-	2	0	IDH2	88432842	1.000000	0.71417	0.025000	0.17156	0.001000	0.01503	7.797000	0.85911	0.862000	0.35528	-0.258000	0.10820	AGG		0.632	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313426.1			51	82	51	82
KRT36	8689	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	39642800	39642800	+	Missense_Mutation	SNP	G	G	A	rs369076801		TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr17:39642800G>A	ENST00000328119.6	-	7	1231	c.1232C>T	c.(1231-1233)aCg>aTg	p.T411M	KRT36_ENST00000393986.2_Missense_Mutation_p.T361M	NM_003771.4	NP_003762.1	O76013	KRT36_HUMAN	keratin 36	411	Tail.				regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural constituent of epidermis (GO:0030280)			breast(2)|cervix(1)|kidney(2)|large_intestine(3)|lung(8)|skin(1)	17		Breast(137;0.000286)				CTTGCATGCCGTGGCACAAGG	0.577																																																0								G	MET/THR	0,4406		0,0,2203	32.0	30.0	30.0		1232	1.3	0.7	17		30	1,8597	1.2+/-3.3	0,1,4298	no	missense	KRT36	NM_003771.4	81	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	411/468	39642800	1,13003	2203	4299	6502	SO:0001583	missense	8689			Y16792	CCDS11395.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000126337	ENSG00000126337		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6454	protein-coding gene	gene with protein product		604540	"""keratin, hair, acidic, 6"""	KRTHA6		9756910, 16831889	Standard	XM_005257762		Approved		uc002hwt.3	O76013	OTTHUMG00000133431	ENST00000328119.6:c.1232C>T	17.37:g.39642800G>A	ENSP00000329165:p.Thr411Met		Q86XG4	Missense_Mutation	SNP	ENST00000328119.6	37	CCDS11395.1	.	.	.	.	.	.	.	.	.	.	G	7.972	0.749269	0.15710	0.0	1.16E-4	ENSG00000126337	ENST00000393986;ENST00000328119	D;D	0.82711	-1.64;-1.52	5.41	1.26	0.21427	.	0.399288	0.21333	N	0.076276	T	0.73753	0.3627	L	0.46157	1.445	0.26795	N	0.969323	P	0.38250	0.624	B	0.32864	0.154	T	0.65348	-0.6190	10	0.66056	D	0.02	.	10.0377	0.42139	0.2271:0.0:0.7729:0.0	.	411	O76013	KRT36_HUMAN	M	361;411	ENSP00000377555:T361M;ENSP00000329165:T411M	ENSP00000329165:T411M	T	-	2	0	KRT36	36896326	0.097000	0.21791	0.723000	0.30687	0.101000	0.19017	0.140000	0.16056	0.130000	0.18549	-1.267000	0.01435	ACG		0.577	KRT36-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259508.1	NM_003771		5	27	5	27
CDH20	28316	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	59174700	59174700	+	Silent	SNP	G	G	A			TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr18:59174700G>A	ENST00000262717.4	+	6	1322	c.924G>A	c.(922-924)gaG>gaA	p.E308E	CDH20_ENST00000536675.2_Silent_p.E308E|CDH20_ENST00000538374.1_Silent_p.E308E			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	308	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				TCAATGCAGAGATGAAATATA	0.433																																																0													182.0	157.0	165.0					18																	59174700		2203	4300	6503	SO:0001819	synonymous_variant	28316			AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"""Cadherins / Major cadherins"""	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.924G>A	18.37:g.59174700G>A			Q495S3	Silent	SNP	ENST00000262717.4	37	CCDS11977.1																																																																																				0.433	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891		15	144	15	144
SERPINB3	6317	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	61323264	61323264	+	Missense_Mutation	SNP	A	A	C			TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr18:61323264A>C	ENST00000283752.5	-	8	943	c.800T>G	c.(799-801)aTg>aGg	p.M267R	SERPINB3_ENST00000332821.8_Missense_Mutation_p.M215R|SERPINB11_ENST00000489748.1_RNA	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	267					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						TGTCCATTCCATCAATTTCTC	0.378																																																0													91.0	82.0	85.0					18																	61323264		2203	4300	6503	SO:0001583	missense	6317			U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"""Serine (or cysteine) peptidase inhibitors"""	10569	protein-coding gene	gene with protein product		600517	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"""	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.800T>G	18.37:g.61323264A>C	ENSP00000283752:p.Met267Arg		A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Missense_Mutation	SNP	ENST00000283752.5	37	CCDS11987.1	.	.	.	.	.	.	.	.	.	.	A	1.818	-0.472988	0.04445	.	.	ENSG00000057149	ENST00000283752;ENST00000332821	D;D	0.83506	-1.73;-1.73	3.07	0.594	0.17485	Serpin domain (3);	1.832770	0.03174	N	0.171210	T	0.65668	0.2713	N	0.11000	0.08	0.09310	N	1	B;B	0.22746	0.074;0.02	B;B	0.28553	0.091;0.026	T	0.53078	-0.8489	10	0.16420	T	0.52	.	0.7547	0.00996	0.4638:0.1679:0.2048:0.1635	.	215;267	P29508-2;P29508	.;SPB3_HUMAN	R	267;215	ENSP00000283752:M267R;ENSP00000329498:M215R	ENSP00000283752:M267R	M	-	2	0	SERPINB3	59474244	0.000000	0.05858	0.001000	0.08648	0.092000	0.18411	-1.060000	0.03475	0.132000	0.18615	0.369000	0.22263	ATG		0.378	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919		29	131	29	131
GBP5	115362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	89728016	89728016	+	Missense_Mutation	SNP	C	C	T			TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr1:89728016C>T	ENST00000370459.3	-	10	1661	c.1534G>A	c.(1534-1536)Gag>Aag	p.E512K	GBP5_ENST00000343435.5_Missense_Mutation_p.E512K|RP4-620F22.2_ENST00000437128.1_RNA|GBP5_ENST00000471171.1_5'Flank			Q96PP8	GBP5_HUMAN	guanylate binding protein 5	512						cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|endometrium(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)	24				all cancers(265;0.00784)|Epithelial(280;0.0286)		ATCATTTGCTCGTTCTGCCTT	0.463																																																0													189.0	167.0	175.0					1																	89728016		2203	4300	6503	SO:0001583	missense	115362			AF430642	CCDS722.1	1p22.2	2008-02-05			ENSG00000154451	ENSG00000154451			19895	protein-coding gene	gene with protein product		611467					Standard	NM_052942		Approved		uc001dnd.3	Q96PP8	OTTHUMG00000010006	ENST00000370459.3:c.1534G>A	1.37:g.89728016C>T	ENSP00000359488:p.Glu512Lys		B2RCE1|Q86TM5	Missense_Mutation	SNP	ENST00000370459.3	37	CCDS722.1	.	.	.	.	.	.	.	.	.	.	C	12.67	2.008102	0.35415	.	.	ENSG00000154451	ENST00000343435;ENST00000370459	T;T	0.02301	4.35;4.35	4.86	-0.172	0.13327	Guanylate-binding protein, C-terminal (3);	0.552403	0.18469	N	0.140290	T	0.00754	0.0025	L	0.41961	1.31	0.09310	N	1	P	0.37548	0.599	B	0.29663	0.105	T	0.49634	-0.8919	10	0.39692	T	0.17	-9.5852	11.602	0.51008	0.0822:0.6539:0.2638:0.0	.	512	Q96PP8	GBP5_HUMAN	K	512	ENSP00000340396:E512K;ENSP00000359488:E512K	ENSP00000340396:E512K	E	-	1	0	GBP5	89500604	0.003000	0.15002	0.003000	0.11579	0.004000	0.04260	-0.007000	0.12810	0.188000	0.20168	-0.150000	0.13652	GAG		0.463	GBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027700.1	NM_052942		66	80	66	80
PCNXL2	80003	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	233344354	233344354	+	Missense_Mutation	SNP	C	C	T			TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr1:233344354C>T	ENST00000258229.9	-	13	3007	c.2773G>A	c.(2773-2775)Gcc>Acc	p.A925T	PCNXL2_ENST00000430153.1_Missense_Mutation_p.A224T|PCNXL2_ENST00000488780.2_Missense_Mutation_p.A58T	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	925						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				CTGGCTTTGGCCCCTGTATCA	0.423																																																0													113.0	109.0	110.0					1																	233344354		1906	4125	6031	SO:0001583	missense	80003			AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"""pecanex (Drosophila)-like 2"""			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.2773G>A	1.37:g.233344354C>T	ENSP00000258229:p.Ala925Thr		O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	37	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.678749	0.88542	.	.	ENSG00000135749	ENST00000258229;ENST00000488780;ENST00000518351;ENST00000430153	T;T;T;T	0.59906	0.23;0.23;0.23;0.23	5.8	4.84	0.62591	.	.	.	.	.	T	0.58235	0.2108	L	0.58101	1.795	0.33421	D	0.579887	P;P	0.45531	0.86;0.594	P;B	0.44561	0.453;0.164	T	0.69499	-0.5129	9	0.42905	T	0.14	.	14.1667	0.65480	0.2205:0.7795:0.0:0.0	.	224;925	A6NKB5-2;A6NKB5	.;PCX2_HUMAN	T	925;58;94;224	ENSP00000258229:A925T;ENSP00000430820:A58T;ENSP00000429231:A94T;ENSP00000394703:A224T	ENSP00000258229:A925T	A	-	1	0	PCNXL2	231410977	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.815000	0.48018	2.735000	0.93741	0.655000	0.94253	GCC		0.423	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801		14	93	14	93
PCSK2	5126	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	20	17434533	17434533	+	Silent	SNP	C	C	T			TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr20:17434533C>T	ENST00000262545.2	+	9	1347	c.1032C>T	c.(1030-1032)gaC>gaT	p.D344D	PCSK2_ENST00000536609.1_Silent_p.D309D|PCSK2_ENST00000377899.1_Silent_p.D325D	NM_002594.3	NP_002585.2	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	344	Peptidase S8.				cellular protein metabolic process (GO:0044267)|embryo development (GO:0009790)|enkephalin processing (GO:0034230)|insulin processing (GO:0030070)|islet amyloid polypeptide processing (GO:0034231)|nervous system development (GO:0007399)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	dendrite (GO:0030425)|extracellular space (GO:0005615)|membrane (GO:0016020)|perikaryon (GO:0043204)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)	p.D344D(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|lung(17)|ovary(3)|pancreas(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	53					"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	CCCTGTACGACGAGAGCTGCT	0.597																																																1	Substitution - coding silent(1)	kidney(1)											144.0	108.0	120.0					20																	17434533		2203	4300	6503	SO:0001819	synonymous_variant	5126			AK312341	CCDS13125.1, CCDS56179.1, CCDS56180.1	20p11.2	2008-08-01			ENSG00000125851	ENSG00000125851			8744	protein-coding gene	gene with protein product	"""neuroendocrine convertase 2"", ""KEX2-like endoprotease 2"""	162151		NEC2		1765368	Standard	NM_001201528		Approved	PC2, SPC2	uc002wpm.3	P16519	OTTHUMG00000031941	ENST00000262545.2:c.1032C>T	20.37:g.17434533C>T			B1ANH9|B4DFQ3|Q14927|Q5JYQ1|Q8IWA8|Q9NQG3|Q9NUG1|Q9UJC6	Silent	SNP	ENST00000262545.2	37	CCDS13125.1																																																																																				0.597	PCSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078120.2	NM_002594		26	152	26	152
PI4KA	5297	hgsc.bcm.edu;broad.mit.edu	37	22	21115635	21115635	+	Missense_Mutation	SNP	C	C	T			TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr22:21115635C>T	ENST00000572273.1	-	23	2804	c.2574G>A	c.(2572-2574)atG>atA	p.M858I	PI4KA_ENST00000255882.6_Missense_Mutation_p.M916I|PI4KA_ENST00000466162.1_5'UTR			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	858					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			AGTAGCAGAACATTACCTGGA	0.368																																					GBM(136;1332 1831 3115 23601 50806)											0													108.0	97.0	101.0					22																	21115635		2203	4300	6503	SO:0001583	missense	5297			L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.2574G>A	22.37:g.21115635C>T	ENSP00000458238:p.Met858Ile		Q7Z625|Q9UPG2	Missense_Mutation	SNP	ENST00000572273.1	37		.	.	.	.	.	.	.	.	.	.	C	9.732	1.162659	0.21538	.	.	ENSG00000241973	ENST00000255882	.	.	.	5.29	5.29	0.74685	.	0.037649	0.85682	D	0.000000	T	0.30166	0.0756	N	0.02158	-0.66	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37502	-0.9703	9	0.02654	T	1	-40.4864	19.1301	0.93402	0.0:1.0:0.0:0.0	.	858	P42356	PI4KA_HUMAN	I	858	.	ENSP00000255882:M858I	M	-	3	0	PI4KA	19445635	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.509000	0.67012	2.767000	0.95098	0.655000	0.94253	ATG		0.368	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004		11	127	11	127
SPECC1L	23384	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	22	24717648	24717648	+	Missense_Mutation	SNP	C	C	T	rs200267920		TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr22:24717648C>T	ENST00000314328.9	+	5	985	c.700C>T	c.(700-702)Cac>Tac	p.H234Y	SPECC1L-ADORA2A_ENST00000358654.2_Missense_Mutation_p.H234Y|SPECC1L_ENST00000541492.1_Missense_Mutation_p.H234Y|SPECC1L_ENST00000437398.1_Missense_Mutation_p.H234Y|SPECC1L_ENST00000416735.1_Intron	NM_001254733.1|NM_015330.3	NP_001241662.1|NP_056145	Q69YQ0	CYTSA_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1-like	234					actin cytoskeleton organization (GO:0030036)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|negative regulation of actin filament depolymerization (GO:0030835)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|gap junction (GO:0005921)|microtubule organizing center (GO:0005815)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(3)|stomach(2)|urinary_tract(1)	27						TATTATGGCTCACCAGCCGAC	0.438																																																0													112.0	116.0	115.0					22																	24717648		2203	4300	6503	SO:0001583	missense	23384			AK025531	CCDS33619.1, CCDS58797.1	22q11.23	2012-12-20	2010-09-17	2010-09-17	ENSG00000100014	ENSG00000100014			29022	protein-coding gene	gene with protein product	"""cytokinesis and spindle organization A"", ""cytospin A"""	614140	"""SPECC1-like"""			9205841	Standard	NM_001254733		Approved	KIAA0376, CYTSA	uc002zzv.4	Q69YQ0	OTTHUMG00000171450	ENST00000314328.9:c.700C>T	22.37:g.24717648C>T	ENSP00000325785:p.His234Tyr		B7Z758|F5H1H6|O15081	Missense_Mutation	SNP	ENST00000314328.9	37	CCDS33619.1	.	.	.	.	.	.	.	.	.	.	C	11.98	1.801713	0.31869	.	.	ENSG00000100014	ENST00000398280;ENST00000437398;ENST00000421374;ENST00000314328;ENST00000541492;ENST00000440893	T;T;T;T;T	0.59364	0.27;2.75;0.27;3.27;0.72	4.91	4.91	0.64330	.	0.164032	0.53938	D	0.000057	T	0.43743	0.1261	N	0.14661	0.345	0.38973	D	0.958796	P;B	0.41008	0.735;0.325	B;B	0.40256	0.324;0.042	T	0.51124	-0.8745	10	0.45353	T	0.12	-21.8987	16.1266	0.81400	0.0:1.0:0.0:0.0	.	234;234	F5H1H6;Q69YQ0	.;CYTSA_HUMAN	Y	262;234;234;234;234;173	ENSP00000393363:H234Y;ENSP00000405671:H234Y;ENSP00000325785:H234Y;ENSP00000439633:H234Y;ENSP00000414354:H173Y	ENSP00000325785:H234Y	H	+	1	0	SPECC1L	23047648	0.998000	0.40836	0.983000	0.44433	0.636000	0.38137	4.837000	0.62796	2.675000	0.91044	0.591000	0.81541	CAC		0.438	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330		86	187	86	187
C2orf71	388939	hgsc.bcm.edu;broad.mit.edu	37	2	29294007	29294007	+	Missense_Mutation	SNP	G	G	A			TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr2:29294007G>A	ENST00000331664.5	-	1	3120	c.3121C>T	c.(3121-3123)Cca>Tca	p.P1041S		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	1041	Pro-rich.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						GTGGTGGGTGGGCTTAGCACC	0.687																																																0													33.0	40.0	38.0					2																	29294007		1958	4120	6078	SO:0001583	missense	0				CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.3121C>T	2.37:g.29294007G>A	ENSP00000332809:p.Pro1041Ser			Missense_Mutation	SNP	ENST00000331664.5	37	CCDS42669.1	.	.	.	.	.	.	.	.	.	.	G	12.41	1.930356	0.34096	.	.	ENSG00000179270	ENST00000331664	T	0.24723	1.84	5.39	4.51	0.55191	.	0.160840	0.43260	D	0.000588	T	0.30324	0.0761	L	0.35854	1.095	0.30762	N	0.743926	P	0.52316	0.952	P	0.51550	0.673	T	0.15521	-1.0434	10	0.35671	T	0.21	-7.9898	14.1739	0.65527	0.0723:0.0:0.9277:0.0	.	1041	A6NGG8	CB071_HUMAN	S	1041	ENSP00000332809:P1041S	ENSP00000332809:P1041S	P	-	1	0	C2orf71	29147511	1.000000	0.71417	0.429000	0.26710	0.685000	0.39939	2.825000	0.48096	1.264000	0.44198	0.561000	0.74099	CCA		0.687	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		41	91	41	91
RIF1	55183	hgsc.bcm.edu;broad.mit.edu	37	2	152293371	152293371	+	Missense_Mutation	SNP	C	C	A			TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr2:152293371C>A	ENST00000243326.5	+	11	1709	c.1226C>A	c.(1225-1227)aCt>aAt	p.T409N	RIF1_ENST00000428287.2_Missense_Mutation_p.T409N|RIF1_ENST00000444746.2_Missense_Mutation_p.T409N|RIF1_ENST00000453091.2_Missense_Mutation_p.T409N|RIF1_ENST00000433166.2_Missense_Mutation_p.L339I|RIF1_ENST00000430328.2_Missense_Mutation_p.T409N			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		GCCCCGGGAACTCCCCGAATG	0.418																																																0													53.0	51.0	52.0					2																	152293371		2203	4300	6503	SO:0001583	missense	55183			AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"""RAP1 interacting factor homolog (yeast)"""			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.1226C>A	2.37:g.152293371C>A	ENSP00000243326:p.Thr409Asn		A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	37	CCDS2194.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	19.36|19.36|19.36	3.812264|3.812264|3.812264	0.70912|0.70912|0.70912	.|.|.	.|.|.	ENSG00000080345|ENSG00000080345|ENSG00000080345	ENST00000433166|ENST00000414861|ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	.|.|T;T;T;T;T	.|.|0.19394	.|.|2.15;2.16;2.16;2.15;2.16	5.33|5.33|5.33	3.46|3.46|3.46	0.39613|0.39613|0.39613	.|.|.	.|.|0.146288	.|.|0.64402	.|.|N	.|.|0.000010	T|T|T	0.40171|0.40171|0.40171	0.1106|0.1106|0.1106	M|M|M	0.62723|0.62723|0.62723	1.935|1.935|1.935	0.22199|0.22199|0.22199	N|N|N	0.999297|0.999297|0.999297	.|.|D;D	.|.|0.65815	.|.|0.995;0.993	.|.|D;P	.|.|0.63113	.|.|0.911;0.854	T|T|T	0.27468|0.27468|0.27468	-1.0073|-1.0073|-1.0073	6|5|10	0.15952|.|0.72032	T|.|D	0.53|.|0.01	-8.3635|-8.3635|-8.3635	13.8319|13.8319|13.8319	0.63386|0.63386|0.63386	0.2793:0.7207:0.0:0.0|0.2793:0.7207:0.0:0.0|0.2793:0.7207:0.0:0.0	.|.|.	.|.|409;409	.|.|Q5UIP0;Q5UIP0-2	.|.|RIF1_HUMAN;.	I|K|N	339|400|409	.|.|ENSP00000390181:T409N;ENSP00000414615:T409N;ENSP00000415691:T409N;ENSP00000243326:T409N;ENSP00000416123:T409N	ENSP00000396865:L339I|.|ENSP00000243326:T409N	L|N|T	+|+|+	1|3|2	0|2|0	RIF1|RIF1|RIF1	152001617|152001617|152001617	0.961000|0.961000|0.961000	0.32948|0.32948|0.32948	0.040000|0.040000|0.040000	0.18447|0.18447|0.18447	0.466000|0.466000|0.466000	0.32739|0.32739|0.32739	2.329000|2.329000|2.329000	0.43876|0.43876|0.43876	0.572000|0.572000|0.572000	0.29383|0.29383|0.29383	0.557000|0.557000|0.557000	0.71058|0.71058|0.71058	CTC|AAC|ACT		0.418	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			11	120	11	120
CHRNA1	1134	hgsc.bcm.edu;broad.mit.edu	37	2	175614763	175614763	+	Missense_Mutation	SNP	C	C	T	rs137852804		TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr2:175614763C>T	ENST00000261007.5	-	8	1054	c.988G>A	c.(988-990)Gtc>Atc	p.V330I	CHRNA1_ENST00000409542.1_Missense_Mutation_p.V223I|CHRNA1_ENST00000348749.5_Missense_Mutation_p.V305I|CHRNA1_ENST00000409219.1_Missense_Mutation_p.V305I|AC018890.6_ENST00000442996.1_RNA	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	330			V -> I (in FCCMS; abnormally slow channel opening and closing resulting in abnormally brief current). {ECO:0000269|PubMed:10195214}.		cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ion channel activity (GO:0005216)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	GAGGCAATGACGAACACCATG	0.537																																																0			GRCh37	CM994574	CHRNA1	M	rs137852804						246.0	186.0	206.0					2																	175614763		2203	4300	6503	SO:0001583	missense	1134			Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1955	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 1 (muscle)"""	100690	"""cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)"""	CHRNA			Standard	NM_001039523		Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000261007.5:c.988G>A	2.37:g.175614763C>T	ENSP00000261007:p.Val330Ile		B4DRV6|D3DPE8	Missense_Mutation	SNP	ENST00000261007.5	37	CCDS33331.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.223673	0.79576	.	.	ENSG00000138435	ENST00000348749;ENST00000261007;ENST00000409542;ENST00000409219	D;D;D;D	0.87887	-2.31;-2.31;-2.31;-2.31	5.4	5.4	0.78164	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.110841	0.64402	D	0.000010	D	0.92231	0.7536	L	0.55213	1.73	0.80722	A	1	D;D	0.89917	1.0;1.0	D;D	0.75484	0.986;0.976	D	0.92788	0.6246	9	0.87932	D	0	.	19.1684	0.93567	0.0:1.0:0.0:0.0	.	305;330	Q53SH4;P02708	.;ACHA_HUMAN	I	305;330;223;305	ENSP00000261008:V305I;ENSP00000261007:V330I;ENSP00000387026:V223I;ENSP00000386611:V305I	ENSP00000261007:V330I	V	-	1	0	CHRNA1	175323009	1.000000	0.71417	0.992000	0.48379	0.823000	0.46562	7.815000	0.86186	2.527000	0.85204	0.655000	0.94253	GTC		0.537	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1			9	148	9	148
PLXNB1	5364	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	48461210	48461210	+	Missense_Mutation	SNP	G	G	C			TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr3:48461210G>C	ENST00000358536.4	-	11	2754	c.2485C>G	c.(2485-2487)Cca>Gca	p.P829A	PLXNB1_ENST00000358459.4_Intron|PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000456774.1_Intron|PLXNB1_ENST00000296440.6_Missense_Mutation_p.P829A	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	829	Pro-rich.				axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		ATGGCCCCTGGGAAAGTGGTG	0.701																																																0													7.0	8.0	8.0					3																	48461210		2159	4249	6408	SO:0001583	missense	5364			X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"""Plexins"""	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.2485C>G	3.37:g.48461210G>C	ENSP00000351338:p.Pro829Ala		A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Missense_Mutation	SNP	ENST00000358536.4	37	CCDS2765.1	.	.	.	.	.	.	.	.	.	.	G	16.03	3.006111	0.54361	.	.	ENSG00000164050	ENST00000296440;ENST00000358536	T;T	0.02974	4.09;4.09	4.56	4.56	0.56223	.	0.420157	0.20409	N	0.092885	T	0.02012	0.0063	N	0.08118	0	0.80722	D	1	P	0.38504	0.634	B	0.33690	0.168	T	0.67534	-0.5646	10	0.41790	T	0.15	.	14.4884	0.67634	0.0:0.0:1.0:0.0	.	829	O43157	PLXB1_HUMAN	A	829	ENSP00000296440:P829A;ENSP00000351338:P829A	ENSP00000296440:P829A	P	-	1	0	PLXNB1	48436214	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	4.165000	0.58196	2.076000	0.62316	0.462000	0.41574	CCA		0.701	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		7	14	7	14
NIPBL	25836	hgsc.bcm.edu;broad.mit.edu	37	5	37008732	37008732	+	Nonsense_Mutation	SNP	C	C	G			TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr5:37008732C>G	ENST00000282516.8	+	20	4827	c.4328C>G	c.(4327-4329)tCa>tGa	p.S1443*	NIPBL_ENST00000448238.2_Nonsense_Mutation_p.S1443*	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	1443					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			CAGGTATTCTCAAGATATGAA	0.274																																																0													50.0	62.0	58.0					5																	37008732		2188	4279	6467	SO:0001587	stop_gained	25836			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"""sister chromatid cohesion 2 homolog (yeast)"""	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.4328C>G	5.37:g.37008732C>G	ENSP00000282516:p.Ser1443*		Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Nonsense_Mutation	SNP	ENST00000282516.8	37	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	C	47	13.340239	0.99735	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	.	.	.	5.01	5.01	0.66863	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	.	18.6684	0.91501	0.0:1.0:0.0:0.0	.	.	.	.	X	1443	.	ENSP00000282516:S1443X	S	+	2	0	NIPBL	37044489	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.417000	0.80156	2.456000	0.83038	0.591000	0.81541	TCA		0.274	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		12	224	12	224
C5orf34	375444	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	43506030	43506030	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr5:43506030C>T	ENST00000306862.2	-	4	1127	c.752G>A	c.(751-753)tGg>tAg	p.W251*	RP11-159F24.3_ENST00000505645.1_RNA	NM_198566.2	NP_940968	Q96MH7	CE034_HUMAN	chromosome 5 open reading frame 34	251										breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|stomach(2)	21	Lung NSC(6;2.07e-05)					AGGATATTTCCATTCCTCTGG	0.408																																																0													113.0	115.0	114.0					5																	43506030		2203	4300	6503	SO:0001587	stop_gained	0			AK056925	CCDS3946.1	5p12	2012-02-23			ENSG00000172244	ENSG00000172244			24738	protein-coding gene	gene with protein product						12477932	Standard	XM_006714473		Approved	FLJ32363	uc003jnz.2	Q96MH7	OTTHUMG00000131151	ENST00000306862.2:c.752G>A	5.37:g.43506030C>T	ENSP00000303490:p.Trp251*			Nonsense_Mutation	SNP	ENST00000306862.2	37	CCDS3946.1	.	.	.	.	.	.	.	.	.	.	C	38	7.032519	0.98017	.	.	ENSG00000172244	ENST00000306862;ENST00000509489	.	.	.	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.2296	16.5572	0.84488	0.0:1.0:0.0:0.0	.	.	.	.	X	251;137	.	ENSP00000303490:W251X	W	-	2	0	C5orf34	43541787	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.472000	0.66768	2.351000	0.79841	0.591000	0.81541	TGG		0.408	C5orf34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253843.1	NM_198566		22	269	22	269
ADRB2	154	hgsc.bcm.edu;broad.mit.edu	37	5	148206922	148206922	+	Silent	SNP	C	C	T			TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr5:148206922C>T	ENST00000305988.4	+	1	767	c.528C>T	c.(526-528)gcC>gcT	p.A176A		NM_000024.5	NP_000015	P07550	ADRB2_HUMAN	adrenoceptor beta 2, surface	176					activation of adenylate cyclase activity (GO:0007190)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|bone resorption (GO:0045453)|brown fat cell differentiation (GO:0050873)|cell surface receptor signaling pathway (GO:0007166)|desensitization of G-protein coupled receptor protein signaling pathway by arrestin (GO:0002032)|diet induced thermogenesis (GO:0002024)|endosome to lysosome transport (GO:0008333)|heat generation (GO:0031649)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor-mediated endocytosis (GO:0006898)|regulation of sodium ion transport (GO:0002028)|regulation of vasodilation (GO:0042312)|response to cold (GO:0009409)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	beta2-adrenergic receptor activity (GO:0004941)|norepinephrine binding (GO:0051380)|potassium channel regulator activity (GO:0015459)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(3)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Acebutolol(DB01193)|Alprenolol(DB00866)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Arformoterol(DB01274)|Asenapine(DB06216)|Atenolol(DB00335)|Bambuterol(DB01408)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dipivefrin(DB00449)|Dobutamine(DB00841)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Indacaterol(DB05039)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenoxybenzamine(DB00925)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Sotalol(DB00489)|Terbutaline(DB00871)|Timolol(DB00373)|Trimipramine(DB00726)	GGTACCGGGCCACCCACCAGG	0.537																																																0													205.0	181.0	189.0					5																	148206922		2203	4300	6503	SO:0001819	synonymous_variant	154			AF022953	CCDS4292.1	5q31-q32	2012-08-08	2012-05-09		ENSG00000169252	ENSG00000169252		"""GPCR / Class A : Adrenoceptors : beta"""	286	protein-coding gene	gene with protein product		109690	"""adrenergic, beta-2-, receptor, surface"""	ADRB2R			Standard	NM_000024		Approved	ADRBR, BAR, B2AR	uc003lpr.2	P07550	OTTHUMG00000129933	ENST00000305988.4:c.528C>T	5.37:g.148206922C>T			B0LPE4|B2R7X2|O14823|O14824|O14825|O14826|Q4JG18|Q53GA6|Q6GMT4|Q6P4D8|Q8NEQ9|Q96EC3|Q9UCZ0|Q9UCZ1|Q9UCZ2|Q9UCZ3|Q9UH95|Q9UHA1|Q9UMZ5	Silent	SNP	ENST00000305988.4	37	CCDS4292.1																																																																																				0.537	ADRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252189.1	NM_000024		20	288	20	288
GRM1	2911	hgsc.bcm.edu;broad.mit.edu	37	6	146720659	146720659	+	Silent	SNP	G	G	C			TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr6:146720659G>C	ENST00000282753.1	+	7	2719	c.2484G>C	c.(2482-2484)ggG>ggC	p.G828G	GRM1_ENST00000492807.2_Silent_p.G828G|GRM1_ENST00000507907.1_Silent_p.G828G|GRM1_ENST00000361719.2_Silent_p.G828G|GRM1_ENST00000392299.2_Silent_p.G828G|GRM1_ENST00000355289.4_Silent_p.G828G			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	828					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		TGGCTCTGGGGTGCATGTTCA	0.488																																																0													142.0	113.0	123.0					6																	146720659		2203	4300	6503	SO:0001819	synonymous_variant	2911			U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4593	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 85"""	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.2484G>C	6.37:g.146720659G>C			B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Silent	SNP	ENST00000282753.1	37	CCDS5209.1																																																																																				0.488	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		9	128	9	128
RALYL	138046	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	85774590	85774590	+	Missense_Mutation	SNP	G	G	A	rs371267637		TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr8:85774590G>A	ENST00000521268.1	+	6	1578	c.473G>A	c.(472-474)cGt>cAt	p.R158H	RALYL_ENST00000521695.1_Missense_Mutation_p.R158H|RALYL_ENST00000517638.1_Missense_Mutation_p.R171H|RALYL_ENST00000523850.1_Missense_Mutation_p.R85H|RALYL_ENST00000518566.1_Missense_Mutation_p.R147H|RALYL_ENST00000521376.1_Missense_Mutation_p.R69H|RALYL_ENST00000522455.1_Missense_Mutation_p.R158H	NM_173848.5	NP_776247.3	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like	158							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)	24						CCGCTGAAGCGTCCCAGAGTG	0.507													G|||	1	0.000199681	0.0008	0.0	5008	,	,		15673	0.0		0.0	False		,,,				2504	0.0															0								G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	2,3846		0,2,1922	59.0	61.0	60.0		512,473,473,473	5.2	1.0	8		60	1,8273		0,1,4136	no	missense,missense,missense,missense	RALYL	NM_001100391.1,NM_001100392.1,NM_001100393.1,NM_173848.5	29,29,29,29	0,3,6058	AA,AG,GG		0.0121,0.052,0.0247	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	171/305,158/292,158/292,158/292	85774590	3,12119	1924	4137	6061	SO:0001583	missense	138046				CCDS55252.1, CCDS55253.1, CCDS75760.1, CCDS75761.1	8q21.2	2013-07-16			ENSG00000184672	ENSG00000184672		"""RNA binding motif (RRM) containing"""	27036	protein-coding gene	gene with protein product		614648				12688537	Standard	NM_001100391		Approved	HNRPCL3	uc003yct.4	Q86SE5	OTTHUMG00000164628	ENST00000521268.1:c.473G>A	8.37:g.85774590G>A	ENSP00000430367:p.Arg158His		B3KTH2|G3V129|Q6ZW87|Q8N1C2	Missense_Mutation	SNP	ENST00000521268.1	37	CCDS55253.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.409671	0.83340	5.2E-4	1.21E-4	ENSG00000184672	ENST00000522455;ENST00000521695;ENST00000521268;ENST00000518566;ENST00000517638;ENST00000523850;ENST00000521376	T;T;T;T;T;T;T	0.25749	2.31;2.31;2.31;2.39;2.29;1.94;1.78	5.25	5.25	0.73442	.	0.048014	0.85682	D	0.000000	T	0.49762	0.1576	L	0.58810	1.83	0.43275	D	0.995234	P;D;P;P;D	0.89917	0.755;1.0;0.953;0.939;1.0	B;D;B;P;D	0.79784	0.312;0.993;0.267;0.565;0.993	T	0.47433	-0.9118	10	0.62326	D	0.03	-4.6088	19.1979	0.93696	0.0:0.0:1.0:0.0	.	147;158;85;171;158	B3KT61;B3KSX3;Q86SE5-2;G3V129;Q86SE5	.;.;.;.;RALYL_HUMAN	H	158;158;158;147;171;85;69	ENSP00000430394:R158H;ENSP00000428667:R158H;ENSP00000430367:R158H;ENSP00000430065:R147H;ENSP00000430128:R171H;ENSP00000428807:R85H;ENSP00000428310:R69H	ENSP00000430128:R171H	R	+	2	0	RALYL	85937145	1.000000	0.71417	0.995000	0.50966	0.777000	0.43975	7.074000	0.76791	2.599000	0.87857	0.551000	0.68910	CGT		0.507	RALYL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379448.1			7	49	7	49
KLF4	9314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	110249405	110249405	+	Missense_Mutation	SNP	G	G	A			TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr9:110249405G>A	ENST00000374672.4	-	4	1641	c.1168C>T	c.(1168-1170)Cgg>Tgg	p.R390W		NM_004235.4	NP_004226.3	O43474	KLF4_HUMAN	Kruppel-like factor 4 (gut)	424	Pro-rich.				cellular response to cycloheximide (GO:0071409)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to peptide (GO:1901653)|epidermal cell differentiation (GO:0009913)|epidermis morphogenesis (GO:0048730)|fat cell differentiation (GO:0045444)|mesodermal cell fate determination (GO:0007500)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000342)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of muscle hyperplasia (GO:0014740)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of hemoglobin biosynthetic process (GO:0046985)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic camera-type eye development (GO:0031077)|post-embryonic hemopoiesis (GO:0035166)|regulation of cell differentiation (GO:0045595)|response to retinoic acid (GO:0032526)|stem cell maintenance (GO:0019827)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding transcription factor activity (GO:0003700)|sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001010)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(5)|large_intestine(1)|lung(3)|pancreas(1)|prostate(2)	16						GTCCTTTTCCGGGGCCACGAT	0.587																																																0													200.0	182.0	188.0					9																	110249405		2203	4300	6503	SO:0001583	missense	9314			AF022184	CCDS6770.2	9q31	2013-01-08			ENSG00000136826	ENSG00000136826		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	6348	protein-coding gene	gene with protein product		602253				9422764, 16372018	Standard	NM_004235		Approved	EZF, GKLF	uc004bdg.3	O43474	OTTHUMG00000020449	ENST00000374672.4:c.1168C>T	9.37:g.110249405G>A	ENSP00000363804:p.Arg390Trp		B2R8S4|B3KT79|L0R3I6|L0R4N5|P78338|Q5T3J8|Q5T3J9|Q8N717|Q9UNP3	Missense_Mutation	SNP	ENST00000374672.4	37	CCDS6770.2	.	.	.	.	.	.	.	.	.	.	G	22.3	4.265729	0.80358	.	.	ENSG00000136826	ENST00000374672	T	0.07908	3.15	5.44	4.46	0.54185	.	0.221517	0.22687	N	0.056880	T	0.28200	0.0696	M	0.80616	2.505	0.51482	D	0.999925	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.992	T	0.00923	-1.1513	10	0.87932	D	0	.	10.7709	0.46321	0.0:0.0:0.5946:0.4054	.	424;390	O43474;O43474-1	KLF4_HUMAN;.	W	390	ENSP00000363804:R390W	ENSP00000363804:R390W	R	-	1	2	KLF4	109289226	0.998000	0.40836	1.000000	0.80357	0.916000	0.54674	2.082000	0.41605	2.547000	0.85894	0.561000	0.74099	CGG		0.587	KLF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053556.2	NM_004235		88	177	88	177
CHMP1A	5119	broad.mit.edu;ucsc.edu	37	16	89715806	89715806	+	Missense_Mutation	SNP	C	C	T			TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr16:89715806C>T	ENST00000397901.3	-	4	461	c.205G>A	c.(205-207)Gta>Ata	p.V69I	CHMP1A_ENST00000535997.2_Missense_Mutation_p.V5I|CHMP1A_ENST00000547614.1_5'UTR|CHMP1A_ENST00000550102.1_Missense_Mutation_p.V69I|CHMP1A_ENST00000253475.5_Missense_Mutation_p.R62H	NM_002768.3	NP_002759.2	Q9HD42	CHM1A_HUMAN	charged multivesicular body protein 1A	69					cytokinesis (GO:0000910)|gene silencing (GO:0016458)|mitotic chromosome condensation (GO:0007076)|negative regulation of transcription by glucose (GO:0045014)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|proteolysis (GO:0006508)|transcription, DNA-templated (GO:0006351)|vesicle-mediated transport (GO:0016192)	condensed nuclear chromosome (GO:0000794)|early endosome (GO:0005769)|endomembrane system (GO:0012505)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|nuclear matrix (GO:0016363)	metallopeptidase activity (GO:0008237)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|ovary(1)	3		all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.048)		ACTGCGTCTACGCGGGACGCC	0.597																																																0													91.0	107.0	101.0					16																	89715806		2164	4257	6421	SO:0001583	missense	5119			U58048	CCDS45552.1	16q24.3	2011-09-21	2011-09-21	2007-03-20	ENSG00000131165	ENSG00000131165		"""Charged multivesicular body proteins"""	8740	protein-coding gene	gene with protein product		164010	"""procollagen (type III) N-endopeptidase"", ""chromatin modifying protein 1A"""	PRSM1, PCOLN3		11559748, 11559747	Standard	NM_002768		Approved	KIAA0047, CHMP1, Vps46A	uc002fnu.4	Q9HD42	OTTHUMG00000169521	ENST00000397901.3:c.205G>A	16.37:g.89715806C>T	ENSP00000380998:p.Val69Ile		A2RU09|Q14468|Q15779|Q96G31	Missense_Mutation	SNP	ENST00000397901.3	37	CCDS45552.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.169|9.169	1.020546|1.020546	0.19433|0.19433	.|.	.|.	ENSG00000131165|ENSG00000131165	ENST00000253475|ENST00000397901;ENST00000535997;ENST00000550102	.|T;T;T	.|0.69561	.|-0.41;-0.41;-0.41	5.38|5.38	5.38|5.38	0.77491|0.77491	.|.	0.740232|.	0.11125|.	N|.	0.596967|.	T|T	0.54191|0.54191	0.1843|0.1843	L|L	0.28400|0.28400	0.85|0.85	0.30063|0.30063	N|N	0.810733|0.810733	D|B	0.61080|0.20368	0.989|0.044	P|B	0.44732|0.16722	0.459|0.016	T|T	0.42137|0.42137	-0.9469|-0.9469	9|9	0.87932|0.02654	D|T	0|1	-0.0527|-0.0527	19.1332|19.1332	0.93415|0.93415	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	62|69	A6NG32|Q9HD42	.|CHM1A_HUMAN	H|I	62|69;5;69	.|ENSP00000380998:V69I;ENSP00000442120:V5I;ENSP00000449243:V69I	ENSP00000253475:R62H|ENSP00000380998:V69I	R|V	-|-	2|1	0|0	CHMP1A|CHMP1A	88243307|88243307	1.000000|1.000000	0.71417|0.71417	0.918000|0.918000	0.36340|0.36340	0.675000|0.675000	0.39556|0.39556	5.469000|5.469000	0.66749|0.66749	2.516000|2.516000	0.84829|0.84829	0.561000|0.561000	0.74099|0.74099	CGT|GTA		0.597	CHMP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404581.1	NM_002768		70	151	70	151
CATSPER1	117144	broad.mit.edu;ucsc.edu	37	11	65790440	65790440	+	Missense_Mutation	SNP	G	G	A			TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr11:65790440G>A	ENST00000312106.5	-	2	1446	c.1309C>T	c.(1309-1311)Cgg>Tgg	p.R437W		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	437					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						ATCATTTCCCGGAAGCCCTGA	0.557											OREG0021092	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0													108.0	108.0	108.0					11																	65790440		2201	4296	6497	SO:0001583	missense	117144			AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"""Voltage-gated ion channels / Cation channels, sperm associated"""	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.1309C>T	11.37:g.65790440G>A	ENSP00000309052:p.Arg437Trp	1086	Q96P76	Missense_Mutation	SNP	ENST00000312106.5	37	CCDS8127.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.059850	0.55325	.	.	ENSG00000175294	ENST00000312106	D	0.97924	-4.61	5.1	2.14	0.27477	.	0.650151	0.11787	N	0.529615	D	0.93641	0.7969	L	0.42245	1.32	0.09310	N	1	P	0.37955	0.612	B	0.27170	0.077	D	0.87998	0.2754	10	0.87932	D	0	-10.5498	5.6372	0.17544	0.0914:0.0:0.559:0.3496	.	437	Q8NEC5	CTSR1_HUMAN	W	437	ENSP00000309052:R437W	ENSP00000309052:R437W	R	-	1	2	CATSPER1	65547016	0.022000	0.18835	0.002000	0.10522	0.048000	0.14542	0.931000	0.28871	0.299000	0.22661	0.563000	0.77884	CGG		0.557	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054		69	115	69	115
CIC	23152	broad.mit.edu	37	19	42797299	42797300	+	Frame_Shift_Del	DEL	TC	TC	-			TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr19:42797299_42797300delTC	ENST00000575354.2	+	15	3701_3702	c.3661_3662delTC	c.(3661-3663)tctfs	p.S1221fs	CIC_ENST00000160740.3_Frame_Shift_Del_p.S1219fs|CIC_ENST00000572681.2_Frame_Shift_Del_p.S2128fs	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1221	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				TGCCCCAGAGTCTGAGCTTGAG	0.718			"""Mis, F, S"""		oligodendroglioma																																		Rec	yes		19	19q13.2	23152	capicua homolog		O	0																																										SO:0001589	frameshift_variant	23152			AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.3661_3662delTC	19.37:g.42797299_42797300delTC	ENSP00000458663:p.Ser1221fs		Q7LGI1|Q9UEG5|Q9Y6T1	Frame_Shift_Del	DEL	ENST00000575354.2	37	CCDS12601.1																																																																																				0.718	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			9	7	9	7
IDH2	3418	hgsc.bcm.edu	37	15	90628591	90628591	+	Silent	SNP	G	G	A	rs61737003	byFrequency	TCGA-DH-5141-01A-01D-1468-08	TCGA-DH-5141-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b77c396b-3f9c-4f1a-864e-f92793906b9d	8ab5bff0-41b4-493c-9626-d706d1c6aa38	g.chr15:90628591G>A	ENST00000330062.3	-	8	1109	c.996C>T	c.(994-996)tcC>tcT	p.S332S	IDH2_ENST00000559482.1_Silent_p.S223S|IDH2_ENST00000539790.1_Silent_p.S202S|IDH2_ENST00000540499.2_Silent_p.S280S	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	332					2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)			biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			AGACCAGGACGGACGTCATCA	0.642			M		GBM								G|||	394	0.0786741	0.2511	0.0231	5008	,	,		16860	0.0		0.0258	False		,,,				2504	0.0204						Dom	yes		15	15q26.1	3418	"""socitrate dehydrogenase 2 (NADP+), mitochondrial """		M	0								G		859,3505		86,687,1409	56.0	44.0	48.0		996	-10.8	0.0	15	dbSNP_129	48	122,8408		1,120,4144	no	coding-synonymous	IDH2	NM_002168.2		87,807,5553	AA,AG,GG		1.4302,19.6838,7.6082		332/453	90628591	981,11913	2182	4265	6447	SO:0001819	synonymous_variant	3418				CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.996C>T	15.37:g.90628591G>A			B2R6L6|B4DFL2|Q96GT3	Silent	SNP	ENST00000330062.3	37	CCDS10359.1																																																																																				0.642	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313426.1			6	6	6	6
