#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
ATAD3A	55210	broad.mit.edu;ucsc.edu	37	1	1459280	1459280	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr1:1459280G>A	ENST00000378755.5	+	10	1263	c.1169G>A	c.(1168-1170)cGc>cAc	p.R390H	ATAD3A_ENST00000536055.1_Missense_Mutation_p.R263H|ATAD3A_ENST00000378756.3_Missense_Mutation_p.R342H	NM_018188.3	NP_060658.3	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	390					cell growth (GO:0016049)|negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)	p.R390H(1)		endometrium(4)|kidney(6)|large_intestine(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.12e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.18e-22)|Colorectal(212;0.000164)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00233)|BRCA - Breast invasive adenocarcinoma(365;0.00469)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0347)|Lung(427;0.147)		AAGAAGAACCGCAGCCTGTAC	0.627																																																	1	Substitution - Missense(1)	kidney(1)											122.0	116.0	118.0					1																	1459280		2203	4300	6503	SO:0001583	missense	55210			AK025865	CCDS31.1, CCDS53259.1, CCDS53260.1	1p36.33	2010-04-21		2007-02-08	ENSG00000197785	ENSG00000197785		"""ATPases / AAA-type"""	25567	protein-coding gene	gene with protein product		612316				12477932	Standard	NM_018188		Approved	FLJ10709	uc001afz.2	Q9NVI7	OTTHUMG00000000575	ENST00000378755.5:c.1169G>A	1.37:g.1459280G>A	ENSP00000368030:p.Arg390His	Somatic		WXS	Illumina GAIIx	Phase_I	B3KPB3|D2K8Q1|G3V1I6|Q5SV23|Q8N275|Q96A50	Missense_Mutation	SNP	ENST00000378755.5	37	CCDS31.1	.	.	.	.	.	.	.	.	.	.	g	5.448	0.267669	0.10294	.	.	ENSG00000197785	ENST00000378756;ENST00000378755;ENST00000536055	T;T;T	0.79247	-1.25;-1.25;-1.25	4.7	-6.11	0.02131	.	0.705172	0.13304	N	0.398006	T	0.68961	0.3058	L	0.56769	1.78	0.09310	N	1	B;B	0.16166	0.006;0.016	B;B	0.13407	0.003;0.009	T	0.53669	-0.8406	10	0.40728	T	0.16	.	13.3235	0.60447	0.8635:0.0:0.1365:0.0	.	342;390	D2K8Q1;Q9NVI7	.;ATD3A_HUMAN	H	342;390;263	ENSP00000368031:R342H;ENSP00000368030:R390H;ENSP00000439290:R263H	ENSP00000368030:R390H	R	+	2	0	ATAD3A	1449143	0.002000	0.14202	0.001000	0.08648	0.003000	0.03518	0.106000	0.15354	-1.079000	0.03113	-0.471000	0.05019	CGC		0.627	ATAD3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000001365.1		NM_018188	
BRD2	6046	broad.mit.edu;hgsc.bcm.edu	37	6	32943251	32943251	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr6:32943251A>G	ENST00000374825.4	+	4	2125	c.424A>G	c.(424-426)Atg>Gtg	p.M142V	BRD2_ENST00000395289.2_Missense_Mutation_p.M142V|BRD2_ENST00000374831.4_Missense_Mutation_p.M142V|BRD2_ENST00000395287.1_Missense_Mutation_p.M142V|BRD2_ENST00000449085.2_Missense_Mutation_p.M95V|XXbac-BPG181M17.6_ENST00000580587.1_RNA|BRD2_ENST00000443797.2_Missense_Mutation_p.M22V	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	142	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)	p.M142V(1)		central_nervous_system(3)|stomach(2)	5						TTCAGAGTGTATGCAAGATTT	0.333																																																	1	Substitution - Missense(1)	kidney(1)											93.0	90.0	91.0					6																	32943251		1510	2709	4219	SO:0001583	missense	6046			X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"""bromodomain-containing 2"""			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.424A>G	6.37:g.32943251A>G	ENSP00000363958:p.Met142Val	Somatic		WXS	Illumina HiSeq	Phase_I	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Missense_Mutation	SNP	ENST00000374825.4	37	CCDS4762.1	.	.	.	.	.	.	.	.	.	.	A	17.05	3.290775	0.59976	.	.	ENSG00000204256	ENST00000374825;ENST00000374831;ENST00000395289;ENST00000443797;ENST00000395287;ENST00000449085	T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62	5.63	5.63	0.86233	Bromodomain (6);Bromodomain, conserved site (1);	0.000000	0.64402	D	0.000008	T	0.08223	0.0205	N	0.03304	-0.355	0.80722	D	1	B;B	0.30870	0.298;0.124	B;B	0.35278	0.199;0.199	T	0.22417	-1.0217	10	0.29301	T	0.29	-21.5421	13.8401	0.63432	1.0:0.0:0.0:0.0	.	142;142	A2AAU0;P25440	.;BRD2_HUMAN	V	142;142;142;22;142;95	ENSP00000363958:M142V;ENSP00000363964:M142V;ENSP00000378704:M142V;ENSP00000413495:M22V;ENSP00000378702:M142V;ENSP00000409145:M95V	ENSP00000363958:M142V	M	+	1	0	BRD2	33051229	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.093000	0.76937	2.363000	0.80096	0.523000	0.50628	ATG		0.333	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2			
CAD	790	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	27457500	27457500	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr2:27457500G>A	ENST00000403525.1	+	22	3688	c.3544G>A	c.(3544-3546)Gaa>Aaa	p.E1182K	CAD_ENST00000264705.4_Missense_Mutation_p.E1245K			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)	p.E1245K(1)		NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CATCATGGGGGAAGAAGTGGA	0.517																																																	1	Substitution - Missense(1)	kidney(1)											111.0	105.0	107.0					2																	27457500		2203	4300	6503	SO:0001583	missense	790			D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.3544G>A	2.37:g.27457500G>A	ENSP00000384510:p.Glu1182Lys	Somatic		WXS	Illumina HiSeq	Phase_I	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	37		.	.	.	.	.	.	.	.	.	.	G	14.13	2.443227	0.43429	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	T;T	0.62364	0.03;0.03	5.43	5.43	0.79202	ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);	0.000000	0.85682	D	0.000000	T	0.51278	0.1665	N	0.25286	0.73	0.80722	D	1	B;P	0.44521	0.074;0.837	B;B	0.44315	0.064;0.446	T	0.45527	-0.9255	10	0.07813	T	0.8	-1.8425	18.1729	0.89752	0.0:0.0:1.0:0.0	.	1182;1245	F8VPD4;P27708	.;PYR1_HUMAN	K	1245;1182	ENSP00000264705:E1245K;ENSP00000384510:E1182K	ENSP00000264705:E1245K	E	+	1	0	CAD	27311004	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.231000	0.78106	2.696000	0.92011	0.655000	0.94253	GAA		0.517	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			
CHUK	1147	hgsc.bcm.edu;ucsc.edu	37	10	101961883	101961883	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr10:101961883delA	ENST00000370397.7	-	14	1617	c.1531delT	c.(1531-1533)tggfs	p.W511fs		NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	511					anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	ATTTCTTTCCATGCTTTTAGC	0.348																																					Ovarian(159;52 1904 10536 35305 37148)												0													197.0	176.0	183.0					10																	101961883		2202	4300	6502	SO:0001589	frameshift_variant	1147			AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.1531delT	10.37:g.101961883delA	ENSP00000359424:p.Trp511fs	Somatic		WXS	Illumina HiSeq	Phase_I	O14666|Q13132|Q5W0I4|Q92467	Frame_Shift_Del	DEL	ENST00000370397.7	37	CCDS7488.1																																																																																				0.348	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1		NM_001278	
DEGS1	8560	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	224377767	224377767	+	Missense_Mutation	SNP	G	G	A	rs188450448		TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr1:224377767G>A	ENST00000323699.4	+	2	737	c.571G>A	c.(571-573)Gtg>Atg	p.V191M	DEGS1_ENST00000391877.3_Missense_Mutation_p.V191M	NM_003676.3	NP_003667.1	O15121	DEGS1_HUMAN	delta(4)-desaturase, sphingolipid 1	191					small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|unsaturated fatty acid biosynthetic process (GO:0006636)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)	p.V191M(1)		breast(1)|kidney(3)|large_intestine(2)|lung(4)	10	Breast(184;0.193)			GBM - Glioblastoma multiforme(131;0.00643)		TATCAATACCGTGGCACAGGT	0.393													G|||	1	0.000199681	0.0	0.0	5008	,	,		19389	0.001		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)						G	MET/VAL	0,4406		0,0,2203	179.0	181.0	180.0		571	4.0	0.0	1		180	1,8599	1.2+/-3.3	0,1,4299	no	missense	DEGS1	NM_003676.2	21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	191/324	224377767	1,13005	2203	4300	6503	SO:0001583	missense	8560			AF002668	CCDS1540.1	1q42.11	2013-09-02	2011-12-09	2004-12-14	ENSG00000143753	ENSG00000143753		"""Fatty acid desaturases"""	13709	protein-coding gene	gene with protein product	"""sphingolipid delta(4)-desaturase 1"", ""dihydroceramide desaturase 1"""	615843	"""degenerative spermatocyte homolog 1, lipid desaturase (Drosophila)"""			9188692, 20105137	Standard	NM_003676		Approved	MLD, Des-1, DES1, FADS7, DEGS-1	uc001hoj.3	O15121	OTTHUMG00000037496	ENST00000323699.4:c.571G>A	1.37:g.224377767G>A	ENSP00000316476:p.Val191Met	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000323699.4	37	CCDS1540.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	5.557	0.287687	0.10513	0.0	1.16E-4	ENSG00000143753	ENST00000415210;ENST00000323699;ENST00000391877	T;T;T	0.18657	2.2;2.2;2.2	6.02	4.02	0.46733	Fatty acid desaturase, type 1 (1);	0.389827	0.28677	N	0.014514	T	0.21509	0.0518	L	0.57536	1.79	0.09310	N	1	P;B	0.34662	0.462;0.216	B;B	0.33254	0.16;0.058	T	0.14254	-1.0479	10	0.49607	T	0.09	.	11.3647	0.49664	0.0765:0.0:0.7567:0.1669	.	191;170	O15121;E7EMA0	DEGS1_HUMAN;.	M	170;191;191	ENSP00000400545:V170M;ENSP00000316476:V191M;ENSP00000375749:V191M	ENSP00000316476:V191M	V	+	1	0	DEGS1	222444390	0.000000	0.05858	0.016000	0.15963	0.003000	0.03518	0.035000	0.13797	1.566000	0.49654	0.549000	0.68633	GTG		0.393	DEGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091285.2			
EPHA5	2044	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	66213782	66213782	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr4:66213782G>C	ENST00000273854.3	-	15	3248	c.2648C>G	c.(2647-2649)aCc>aGc	p.T883S	EPHA5_ENST00000432638.2_Missense_Mutation_p.T720S|EPHA5_ENST00000511294.1_Missense_Mutation_p.T884S|EPHA5_ENST00000354839.4_Missense_Mutation_p.T861S	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	883	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)	p.T883S(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						ATCTTGATTGGTCATCTCCCA	0.398										TSP Lung(17;0.13)																																							1	Substitution - Missense(1)	kidney(1)											179.0	162.0	168.0					4																	66213782		2203	4300	6503	SO:0001583	missense	2044			L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3389	protein-coding gene	gene with protein product		600004	"""EphA5"""			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.2648C>G	4.37:g.66213782G>C	ENSP00000273854:p.Thr883Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	37	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	G	6.897	0.534950	0.13188	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	T;T;T;T	0.60797	0.16;0.16;0.16;0.16	5.86	5.86	0.93980	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000005	T	0.32164	0.0820	N	0.02539	-0.55	0.46631	D	0.999135	B;B;B;B	0.06786	0.0;0.001;0.0;0.001	B;B;B;B	0.09377	0.002;0.004;0.001;0.003	T	0.40757	-0.9546	10	0.02654	T	1	.	20.1823	0.98208	0.0:0.0:1.0:0.0	.	862;884;861;883	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	S	883;720;861;884	ENSP00000273854:T883S;ENSP00000389208:T720S;ENSP00000346899:T861S;ENSP00000427638:T884S	ENSP00000273854:T883S	T	-	2	0	EPHA5	65896377	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.278000	0.65592	2.771000	0.95319	0.650000	0.86243	ACC		0.398	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2		NM_004439	
ENAM	10117	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	71510239	71510239	+	Silent	SNP	C	C	A			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr4:71510239C>A	ENST00000396073.3	+	9	3377	c.3096C>A	c.(3094-3096)ggC>ggA	p.G1032G	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	1032					amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)		p.G1032G(1)		haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			ATCCAGAAGGCATCCAAAGTC	0.428																																																	1	Substitution - coding silent(1)	kidney(1)											121.0	105.0	110.0					4																	71510239		2203	4300	6503	SO:0001819	synonymous_variant	10117			AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"""amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"""	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.3096C>A	4.37:g.71510239C>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q17RI5|Q9H3D1	Silent	SNP	ENST00000396073.3	37	CCDS3544.2																																																																																				0.428	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3		NM_031889	
EPS15L1	58513	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	16536069	16536069	+	Missense_Mutation	SNP	G	G	A	rs370990400		TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr19:16536069G>A	ENST00000248070.6	-	9	756	c.617C>T	c.(616-618)cCg>cTg	p.P206L	EPS15L1_ENST00000594975.1_Missense_Mutation_p.P206L|EPS15L1_ENST00000535753.2_Missense_Mutation_p.P206L|EPS15L1_ENST00000602009.1_Missense_Mutation_p.P52L|EPS15L1_ENST00000597937.1_Missense_Mutation_p.P206L|EPS15L1_ENST00000455140.2_Missense_Mutation_p.P206L	NM_021235.2	NP_067058.1	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway substrate 15-like 1	206	EH 2. {ECO:0000255|PROSITE- ProRule:PRU00077}.|Interaction with DAB2. {ECO:0000250}.				endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	clathrin coat of coated pit (GO:0030132)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P206L(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(4)|skin(2)	30						GATGAGGGACGGGGGCAGGGC	0.652																																																	1	Substitution - Missense(1)	kidney(1)						G	LEU/PRO	0,4406		0,0,2203	20.0	21.0	21.0		617	4.9	0.9	19		21	1,8597		0,1,4298	no	missense	EPS15L1	NM_021235.1	98	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	206/865	16536069	1,13003	2203	4299	6502	SO:0001583	missense	58513			AF110265	CCDS32944.1, CCDS58653.1, CCDS58654.1, CCDS59363.1	19p13.12	2013-01-10				ENSG00000127527		"""EF-hand domain containing"""	24634	protein-coding gene	gene with protein product							Standard	NM_001258374		Approved	eps15R	uc002ndx.4	Q9UBC2		ENST00000248070.6:c.617C>T	19.37:g.16536069G>A	ENSP00000248070:p.Pro206Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A2RRF3|A5PL29|B4DKA3	Missense_Mutation	SNP	ENST00000248070.6	37	CCDS32944.1	.	.	.	.	.	.	.	.	.	.	G	12.17	1.858819	0.32884	0.0	1.16E-4	ENSG00000127527	ENST00000455140;ENST00000248070;ENST00000535753	T;T;T	0.33216	1.42;1.42;1.42	4.91	4.91	0.64330	EPS15 homology (EH) (2);EF-hand-like domain (1);	0.117673	0.64402	D	0.000014	T	0.38746	0.1052	M	0.73598	2.24	0.80722	D	1	B;B;B;B;B;B	0.32188	0.231;0.359;0.047;0.047;0.123;0.046	B;B;B;B;B;B	0.32465	0.146;0.103;0.016;0.024;0.077;0.03	T	0.42327	-0.9458	10	0.66056	D	0.02	.	17.2637	0.87079	0.0:0.0:1.0:0.0	.	206;206;205;206;206;206	A8K5P4;A5PL29;A5PKY0;A2RRF3;Q9UBC2;G3V0H2	.;.;.;.;EP15R_HUMAN;.	L	206	ENSP00000393313:P206L;ENSP00000248070:P206L;ENSP00000440103:P206L	ENSP00000248070:P206L	P	-	2	0	EPS15L1	16397069	0.998000	0.40836	0.906000	0.35671	0.005000	0.04900	6.320000	0.72876	2.557000	0.86248	0.655000	0.94253	CCG		0.652	EPS15L1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461040.1		NM_021235	
F11	2160	broad.mit.edu;hgsc.bcm.edu	37	4	187208887	187208887	+	Silent	SNP	C	C	T			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr4:187208887C>T	ENST00000403665.2	+	14	1978	c.1626C>T	c.(1624-1626)aaC>aaT	p.N542N	F11_ENST00000264692.4_Silent_p.N490N|F11-AS1_ENST00000505103.1_RNA	NM_000128.3	NP_000119.1	P03951	FA11_HUMAN	coagulation factor XI	542	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)	p.N542N(2)		NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	32		all_cancers(14;6.2e-52)|all_epithelial(14;1.62e-38)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;2.13e-11)|BRCA - Breast invasive adenocarcinoma(30;4.59e-06)|GBM - Glioblastoma multiforme(59;0.000149)|STAD - Stomach adenocarcinoma(60;0.000314)|LUSC - Lung squamous cell carcinoma(40;0.00112)|READ - Rectum adenocarcinoma(43;0.176)	Coagulation Factor IX(DB00100)	TAGTGACCAACGAAGAGTGCC	0.403																																																	2	Substitution - coding silent(2)	kidney(1)|central_nervous_system(1)											91.0	89.0	90.0					4																	187208887		2203	4300	6503	SO:0001819	synonymous_variant	2160			M13142	CCDS3847.1	4q35	2008-08-01	2008-08-01		ENSG00000088926	ENSG00000088926	3.4.21.27		3529	protein-coding gene	gene with protein product	"""plasma thromboplastin antecedent"""	264900					Standard	NM_000128		Approved	FXI	uc003iza.1	P03951	OTTHUMG00000150311	ENST00000403665.2:c.1626C>T	4.37:g.187208887C>T		Somatic		WXS	Illumina HiSeq	Phase_I	D3DP64|Q4W5C2|Q9Y495	Silent	SNP	ENST00000403665.2	37	CCDS3847.1	.	.	.	.	.	.	.	.	.	.	C	0.016	-1.528329	0.00959	.	.	ENSG00000088926	ENST00000264691	.	.	.	4.92	-3.09	0.05331	.	.	.	.	.	T	0.29288	0.0729	.	.	.	0.21184	N	0.999763	.	.	.	.	.	.	T	0.36040	-0.9764	4	.	.	.	.	7.9248	0.29867	0.1095:0.4067:0.0:0.4839	.	.	.	.	M	76	.	.	T	+	2	0	F11	187445881	0.004000	0.15560	0.030000	0.17652	0.019000	0.09904	-0.087000	0.11215	-0.367000	0.08052	-0.415000	0.06103	ACG		0.403	F11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317519.4			
FREM2	341640	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	39451280	39451280	+	Silent	SNP	T	T	C			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr13:39451280T>C	ENST00000280481.7	+	21	8787	c.8571T>C	c.(8569-8571)ttT>ttC	p.F2857F		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2857					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F2857F(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CTGCTGAGTTTAGCTTGAACA	0.438																																																	1	Substitution - coding silent(1)	kidney(1)											268.0	233.0	245.0					13																	39451280		2203	4300	6503	SO:0001819	synonymous_variant	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.8571T>C	13.37:g.39451280T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																				0.438	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2		NM_207361	
IL2RA	3559	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	6054846	6054846	+	Silent	SNP	T	T	G			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr10:6054846T>G	ENST00000379959.3	-	8	981	c.808A>C	c.(808-810)Aga>Cga	p.R270R	IL2RA_ENST00000256876.6_Silent_p.R261R|IL2RA_ENST00000379954.1_Silent_p.R198R	NM_000417.2	NP_000408.1	P01589	IL2RA_HUMAN	interleukin 2 receptor, alpha	270					activation-induced cell death of T cells (GO:0006924)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-2-mediated signaling pathway (GO:0038110)|negative regulation of defense response to virus (GO:0050687)|negative regulation of immune response (GO:0050777)|negative regulation of inflammatory response (GO:0050728)|negative regulation of T cell proliferation (GO:0042130)|Notch signaling pathway (GO:0007219)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of T cell differentiation (GO:0045582)|regulation of T cell homeostatic proliferation (GO:0046013)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|interleukin-2 receptor activity (GO:0004911)	p.R270R(1)		endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	17					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	TAGATTGTTCTTCTACTCTTC	0.428																																																	1	Substitution - coding silent(1)	kidney(1)											177.0	159.0	165.0					10																	6054846		2203	4300	6503	SO:0001819	synonymous_variant	3559			X01057	CCDS7076.1	10p15-p14	2014-09-17			ENSG00000134460	ENSG00000134460		"""Interleukins and interleukin receptors"", ""CD molecules"""	6008	protein-coding gene	gene with protein product		147730	"""insulin-dependent diabetes mellitus 10"""	IL2R, IDDM10		3925551, 17676041	Standard	NM_000417		Approved	CD25	uc001iiz.2	P01589	OTTHUMG00000017616	ENST00000379959.3:c.808A>C	10.37:g.6054846T>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q5W007	Silent	SNP	ENST00000379959.3	37	CCDS7076.1																																																																																				0.428	IL2RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046627.1		NM_000417	
ITIH5	80760	hgsc.bcm.edu	37	10	7608335	7608336	+	Frame_Shift_Ins	INS	-	-	G	rs543300408		TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr10:7608335_7608336insG	ENST00000256861.6	-	13	2262_2263	c.2184_2185insC	c.(2182-2187)cccgccfs	p.A729fs	ITIH5_ENST00000298441.6_Frame_Shift_Ins_p.A515fs|ITIH5_ENST00000446830.2_Frame_Shift_Ins_p.A511fs|ITIH5_ENST00000397146.2_Intron	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	729					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						TTTGGAGGGGCGGGTGCCCCAA	0.51																																																	0																																										SO:0001589	frameshift_variant	80760					10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"""inter-alpha (globulin) inhibitor H5"""			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.2185dupC	10.37:g.7608338_7608338dupG	ENSP00000256861:p.Ala729fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Frame_Shift_Ins	INS	ENST00000256861.6	37																																																																																					0.510	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1		NM_030569	
CEP162	22832	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	84894950	84894950	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr6:84894950T>C	ENST00000403245.3	-	13	1732	c.1618A>G	c.(1618-1620)Aaa>Gaa	p.K540E	KIAA1009_ENST00000257766.4_Missense_Mutation_p.K464E|KIAA1009_ENST00000461137.1_5'UTR	NM_014895.2	NP_055710.2												p.K540E(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		CTCAAGTTTTTGCTTTTTATA	0.348																																																	1	Substitution - Missense(1)	kidney(1)											87.0	84.0	85.0					6																	84894950		2203	4300	6503	SO:0001583	missense	22832																														ENST00000403245.3:c.1618A>G	6.37:g.84894950T>C	ENSP00000385215:p.Lys540Glu	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000403245.3	37	CCDS34494.2	.	.	.	.	.	.	.	.	.	.	T	3.444	-0.113421	0.06881	.	.	ENSG00000135315	ENST00000257766;ENST00000403245	T;T	0.17528	2.27;2.27	5.34	4.02	0.46733	.	0.421904	0.24996	N	0.033941	T	0.04770	0.0129	L	0.37561	1.115	0.09310	N	1	B;B	0.18310	0.001;0.027	B;B	0.16289	0.002;0.015	T	0.20240	-1.0281	10	0.36615	T	0.2	-20.3598	7.2992	0.26411	0.0:0.1391:0.0:0.8609	.	540;540	Q5TB80;C9JFM9	QN1_HUMAN;.	E	464;540	ENSP00000257766:K464E;ENSP00000385215:K540E	ENSP00000257766:K464E	K	-	1	0	KIAA1009	84951669	0.706000	0.27856	0.457000	0.27056	0.007000	0.05969	1.244000	0.32778	2.150000	0.67090	0.519000	0.50382	AAA		0.348	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1			
KLHDC7A	127707	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	18807868	18807868	+	Silent	SNP	G	G	A			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr1:18807868G>A	ENST00000400664.1	+	1	445	c.393G>A	c.(391-393)tcG>tcA	p.S131S		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	131						integral component of membrane (GO:0016021)		p.S131S(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GGCAGGGCTCGGACTCTGAGC	0.632																																																	1	Substitution - coding silent(1)	kidney(1)											25.0	31.0	29.0					1																	18807868		2030	4181	6211	SO:0001819	synonymous_variant	127707			AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.393G>A	1.37:g.18807868G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q8N8W6	Silent	SNP	ENST00000400664.1	37	CCDS185.2																																																																																				0.632	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3		NM_152375	
MGA	23269	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	42035185	42035185	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr15:42035185C>G	ENST00000570161.1	+	14	5027	c.5027C>G	c.(5026-5028)cCt>cGt	p.P1676R	MGA_ENST00000389936.4_Missense_Mutation_p.P1676R|MGA_ENST00000545763.1_Intron|MGA_ENST00000219905.7_Missense_Mutation_p.P1676R|MGA_ENST00000566586.1_Intron			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.P1725R(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GTTGCTTTTCCTAAGTCTTTG	0.483																																																	1	Substitution - Missense(1)	kidney(1)											167.0	156.0	159.0					15																	42035185		1968	4177	6145	SO:0001583	missense	23269			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.5027C>G	15.37:g.42035185C>G	ENSP00000457035:p.Pro1676Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	C	13.23	2.174318	0.38413	.	.	ENSG00000174197	ENST00000219905;ENST00000389936	D;D	0.85171	-1.91;-1.95	4.8	4.8	0.61643	.	0.245209	0.28706	N	0.014408	T	0.75213	0.3819	N	0.08118	0	0.80722	D	1	P;P	0.48911	0.917;0.736	P;B	0.46659	0.523;0.221	T	0.79902	-0.1607	10	0.87932	D	0	.	11.5201	0.50546	0.0:0.9179:0.0:0.0821	.	292;1676	B4DVS1;E7ENI0	.;.	R	1676	ENSP00000219905:P1676R;ENSP00000374586:P1676R	ENSP00000219905:P1676R	P	+	2	0	MGA	39822477	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.162000	0.50755	2.485000	0.83878	0.563000	0.77884	CCT		0.483	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1		NM_001164273.1	
MYO1E	4643	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	59506883	59506883	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr15:59506883A>G	ENST00000288235.4	-	11	1543	c.1144T>C	c.(1144-1146)Tac>Cac	p.Y382H	RNU4-80P_ENST00000363200.1_RNA|AC092756.1_ENST00000401164.1_RNA	NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	382	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)	p.Y382H(1)		breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		CCAATGTTGTATTCTTCATGG	0.423																																																	1	Substitution - Missense(1)	kidney(1)											204.0	193.0	197.0					15																	59506883		2190	4290	6480	SO:0001583	missense	4643			U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483		"""Myosins / Myosin superfamily : Class I"""	7599	protein-coding gene	gene with protein product	"""myosin-IC"""	601479				8884266	Standard	NM_004998		Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.1144T>C	15.37:g.59506883A>G	ENSP00000288235:p.Tyr382His	Somatic		WXS	Illumina HiSeq	Phase_I	Q14778	Missense_Mutation	SNP	ENST00000288235.4	37	CCDS32254.1	.	.	.	.	.	.	.	.	.	.	A	11.19	1.565651	0.27915	.	.	ENSG00000157483	ENST00000288235	D	0.87256	-2.23	5.14	5.14	0.70334	Myosin head, motor domain (2);	0.164455	0.56097	D	0.000035	D	0.89298	0.6675	L	0.43598	1.365	0.48571	D	0.999671	D	0.55385	0.971	D	0.64687	0.928	D	0.86078	0.1542	10	0.16896	T	0.51	.	15.4162	0.74970	1.0:0.0:0.0:0.0	.	382	Q12965	MYO1E_HUMAN	H	382	ENSP00000288235:Y382H	ENSP00000288235:Y382H	Y	-	1	0	MYO1E	57294175	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.028000	0.76470	2.285000	0.76669	0.533000	0.62120	TAC		0.423	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1		NM_004998	
NCF2	4688	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	183532672	183532672	+	Nonsense_Mutation	SNP	T	T	A			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr1:183532672T>A	ENST00000367535.3	-	12	1326	c.1075A>T	c.(1075-1077)Aag>Tag	p.K359*	NCF2_ENST00000469280.1_5'UTR|NCF2_ENST00000367536.1_Nonsense_Mutation_p.K359*|NCF2_ENST00000418089.1_Nonsense_Mutation_p.K278*|NCF2_ENST00000413720.1_Nonsense_Mutation_p.K314*	NM_000433.3	NP_000424.2	P19878	NCF2_HUMAN	neutrophil cytosolic factor 2	359	OPR.				aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cellular response to hormone stimulus (GO:0032870)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron apoptotic process (GO:0043525)|respiratory burst (GO:0045730)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to hyperoxia (GO:0055093)|response to laminar fluid shear stress (GO:0034616)|response to lipopolysaccharide (GO:0032496)|response to progesterone (GO:0032570)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|NADPH oxidase complex (GO:0043020)|nucleolus (GO:0005730)|phagolysosome (GO:0032010)	electron carrier activity (GO:0009055)|protein C-terminus binding (GO:0008022)	p.K359*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30					Dextromethorphan(DB00514)	ACCGTGTACTTGTAGTGCACC	0.542																																																	1	Substitution - Nonsense(1)	kidney(1)											125.0	109.0	115.0					1																	183532672		2203	4300	6503	SO:0001587	stop_gained	4688			BC001606	CCDS1356.1, CCDS53446.1, CCDS53447.1	1q25	2014-09-17	2008-07-31		ENSG00000116701	ENSG00000116701		"""Tetratricopeptide (TTC) repeat domain containing"""	7661	protein-coding gene	gene with protein product	"""NADPH oxidase activator 2"", ""chronic granulomatous disease, autosomal 2"""	608515	"""neutrophil cytosolic factor 2 (65kD, chronic granulomatous disease, autosomal 2)"""				Standard	NM_000433		Approved	p67phox, NOXA2	uc001gqk.4	P19878	OTTHUMG00000035329	ENST00000367535.3:c.1075A>T	1.37:g.183532672T>A	ENSP00000356505:p.Lys359*	Somatic		WXS	Illumina HiSeq	Phase_I	B2R6Q1|B4DKQ7|B4DQA7|E9PHJ2|E9PHX3|Q2PP06|Q8NFC7|Q9BV51	Nonsense_Mutation	SNP	ENST00000367535.3	37	CCDS1356.1	.	.	.	.	.	.	.	.	.	.	T	40	7.952327	0.98580	.	.	ENSG00000116701	ENST00000367536;ENST00000392014;ENST00000413720;ENST00000418089;ENST00000367535;ENST00000420553;ENST00000419402	.	.	.	5.74	5.74	0.90152	.	0.196194	0.52532	D	0.000067	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-59.1101	14.6438	0.68745	0.0:0.0:0.0:1.0	.	.	.	.	X	359;431;314;278;359;10;98	.	ENSP00000356505:K359X	K	-	1	0	NCF2	181799295	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.266000	0.65525	2.202000	0.70862	0.529000	0.55759	AAG		0.542	NCF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085483.1		NM_000433	
NDUFA4L2	56901	hgsc.bcm.edu	37	12	57630850	57630860	+	Frame_Shift_Del	DEL	CAAGACTGGCT	CAAGACTGGCT	-	rs373331973		TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	CAAGACTGGCT	CAAGACTGGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr12:57630850_57630860delCAAGACTGGCT	ENST00000554503.1	-	1	261_271	c.9_19delAGCCAGTCTTG	c.(7-21)ggagccagtcttgggfs	p.GASLG3fs	NDUFA4L2_ENST00000393825.1_Frame_Shift_Del_p.GASLG3fs|NDUFA4L2_ENST00000556732.1_Frame_Shift_Del_p.GASLG3fs|NDUFA4L2_ENST00000557276.1_5'Flank			Q9NRX3	NUA4L_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4-like 2	3										lung(1)|prostate(1)	2						AAGCGGGCCCCAAGACTGGCTCCTGCCATAT	0.602																																																	0																																										SO:0001589	frameshift_variant	56901			BC011910	CCDS8935.1	12q13.3	2014-05-29			ENSG00000185633	ENSG00000185633			29836	protein-coding gene	gene with protein product							Standard	NM_020142		Approved	NUOMS, FLJ26118	uc001sno.3	Q9NRX3	OTTHUMG00000171275	ENST00000554503.1:c.9_19delAGCCAGTCTTG	12.37:g.57630850_57630860delCAAGACTGGCT	ENSP00000450664:p.Gly3fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q6IAH9	Frame_Shift_Del	DEL	ENST00000554503.1	37	CCDS8935.1																																																																																				0.602	NDUFA4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412744.1		NM_020142	
NF2	4771	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	30032866	30032867	+	Splice_Site	DEL	GT	GT	-			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr22:30032866_30032867delGT	ENST00000338641.4	+	2	681		c.e2+1		NF2_ENST00000353887.4_Intron|NF2_ENST00000361452.4_Splice_Site|NF2_ENST00000397789.3_Splice_Site|NF2_ENST00000361166.4_Splice_Site|NF2_ENST00000413209.2_Splice_Site|NF2_ENST00000403435.1_Splice_Site|NF2_ENST00000403999.3_Splice_Site|NF2_ENST00000334961.7_Intron|NF2_ENST00000361676.4_Intron|NF2_ENST00000347330.5_Intron	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)						actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(6)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						GGACAAGAAGGTTGGGCTAGAA	0.535			"""D, Mis, N, F, S, O"""		"""meningioma, acoustic neuroma, renal """	"""meningioma, acoustic neuroma"""			Neurofibromatosis, type 2																														yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	6	Unknown(6)	meninges(2)|stomach(1)|large_intestine(1)|lung(1)|soft_tissue(1)	GRCh37	CS930848|CS941518	NF2	S																																				SO:0001630	splice_region_variant	4771	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"""A-kinase anchor proteins"""	7773	protein-coding gene	gene with protein product	"""moesin-ezrin-radixin like"", ""schwannomin"""	607379	"""neurofibromin 2 (bilateral acoustic neuroma)"""			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.240+1GT>-	22.37:g.30032866_30032867delGT		Somatic		WXS	Illumina HiSeq	Phase_I	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Frame_Shift_Del	DEL	ENST00000338641.4	37	CCDS13861.1																																																																																				0.535	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3		NM_000268	Intron
NGRN	51335	hgsc.bcm.edu;ucsc.edu	37	15	90815002	90815005	+	Frame_Shift_Del	DEL	CTTC	CTTC	-			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	CTTC	CTTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr15:90815002_90815005delCTTC	ENST00000379095.3	+	3	866_869	c.858_861delCTTC	c.(856-861)aacttcfs	p.NF286fs	RP11-697E2.6_ENST00000561573.1_3'UTR|NGRN_ENST00000331497.3_3'UTR	NM_001033088.1	NP_001028260.2	Q9NPE2	NGRN_HUMAN	neugrin, neurite outgrowth associated	286					neuron differentiation (GO:0030182)	extracellular region (GO:0005576)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(4)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	11	Melanoma(11;0.00551)|Lung NSC(78;0.0178)|all_lung(78;0.0378)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|BRCA - Breast invasive adenocarcinoma(143;0.0323)|Kidney(142;0.0514)			GCAACGGGAACTTCCTGTACAGAA	0.49																																																	0																																										SO:0001589	frameshift_variant	51335			AB029315	CCDS32329.1	15q26.1	2008-02-05			ENSG00000182768	ENSG00000182768			18077	protein-coding gene	gene with protein product						11118320	Standard	NR_028052		Approved	DSC92	uc002bpf.1	Q9NPE2	OTTHUMG00000149807	ENST00000379095.3:c.858_861delCTTC	15.37:g.90815002_90815005delCTTC	ENSP00000368389:p.Asn286fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2R6M8|Q4V9L7|Q9HBL4	Frame_Shift_Del	DEL	ENST00000379095.3	37	CCDS32329.1																																																																																				0.490	NGRN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313418.1			
NGRN	51335	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	90815014	90815014	+	Silent	SNP	A	A	G			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr15:90815014A>G	ENST00000379095.3	+	3	878	c.870A>G	c.(868-870)agA>agG	p.R290R	RP11-697E2.6_ENST00000561573.1_3'UTR|NGRN_ENST00000331497.3_3'UTR	NM_001033088.1	NP_001028260.2	Q9NPE2	NGRN_HUMAN	neugrin, neurite outgrowth associated	290					neuron differentiation (GO:0030182)	extracellular region (GO:0005576)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R218R(1)|p.R290R(1)		kidney(2)|large_intestine(4)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	11	Melanoma(11;0.00551)|Lung NSC(78;0.0178)|all_lung(78;0.0378)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|BRCA - Breast invasive adenocarcinoma(143;0.0323)|Kidney(142;0.0514)			TCCTGTACAGAATTTGAGTCG	0.493																																																	2	Substitution - coding silent(2)	kidney(2)											46.0	46.0	46.0					15																	90815014		2199	4298	6497	SO:0001819	synonymous_variant	51335			AB029315	CCDS32329.1	15q26.1	2008-02-05			ENSG00000182768	ENSG00000182768			18077	protein-coding gene	gene with protein product						11118320	Standard	NR_028052		Approved	DSC92	uc002bpf.1	Q9NPE2	OTTHUMG00000149807	ENST00000379095.3:c.870A>G	15.37:g.90815014A>G		Somatic		WXS	Illumina HiSeq	Phase_I	B2R6M8|Q4V9L7|Q9HBL4	Silent	SNP	ENST00000379095.3	37	CCDS32329.1																																																																																				0.493	NGRN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313418.1			
NKAPL	222698	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	28227271	28227271	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr6:28227271C>T	ENST00000343684.3	+	1	174	c.122C>T	c.(121-123)tCc>tTc	p.S41F	ZKSCAN4_ENST00000423974.2_5'Flank	NM_001007531.1	NP_001007532.1	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	41								p.S41F(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						GATGGCTGTTCCCGCTCTCAC	0.652																																																	1	Substitution - Missense(1)	kidney(1)											44.0	45.0	45.0					6																	28227271		2203	4300	6503	SO:0001583	missense	222698			BC038240	CCDS34353.1	6p21.33	2008-02-05	2007-08-16	2007-08-16	ENSG00000189134	ENSG00000189134			21584	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 194"""	C6orf194			Standard	NM_001007531		Approved	bA424I5.1	uc003nkt.4	Q5M9Q1	OTTHUMG00000014517	ENST00000343684.3:c.122C>T	6.37:g.28227271C>T	ENSP00000345716:p.Ser41Phe	Somatic		WXS	Illumina HiSeq	Phase_I	Q3MIV1|Q9H4Q7	Missense_Mutation	SNP	ENST00000343684.3	37	CCDS34353.1	.	.	.	.	.	.	.	.	.	.	C	10.67	1.414159	0.25465	.	.	ENSG00000189134	ENST00000343684	T	0.15372	2.43	4.11	0.367	0.16140	.	2.069380	0.02215	N	0.063533	T	0.05456	0.0144	L	0.51422	1.61	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.30387	-0.9980	10	0.39692	T	0.17	3.5053	3.6802	0.08308	0.0:0.4946:0.1919:0.3135	.	41	Q5M9Q1	NKAPL_HUMAN	F	41	ENSP00000345716:S41F	ENSP00000345716:S41F	S	+	2	0	NKAPL	28335250	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	0.051000	0.14141	-0.045000	0.13468	0.609000	0.83330	TCC		0.652	NKAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040185.1			
OR2T10	127069	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	248756885	248756885	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr1:248756885A>C	ENST00000330500.2	-	1	215	c.185T>G	c.(184-186)tTt>tGt	p.F62C	Y_RNA_ENST00000364732.1_RNA	NM_001004693.1	NP_001004693.1	Q8NGZ9	O2T10_HUMAN	olfactory receptor, family 2, subfamily T, member 10	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F62C(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(17)|skin(3)|upper_aerodigestive_tract(1)	26	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CTGGTTTATAAAGAAGTACAT	0.408																																																	1	Substitution - Missense(1)	kidney(1)											79.0	89.0	86.0					1																	248756885		2049	4235	6284	SO:0001583	missense	127069				CCDS31121.1	1q44	2012-08-09			ENSG00000184022	ENSG00000184022		"""GPCR / Class A : Olfactory receptors"""	19573	protein-coding gene	gene with protein product							Standard	NM_001004693		Approved		uc010pzn.2	Q8NGZ9	OTTHUMG00000040388	ENST00000330500.2:c.185T>G	1.37:g.248756885A>C	ENSP00000329210:p.Phe62Cys	Somatic		WXS	Illumina HiSeq	Phase_I	B2RNK7	Missense_Mutation	SNP	ENST00000330500.2	37	CCDS31121.1	.	.	.	.	.	.	.	.	.	.	.	11.68	1.710242	0.30322	.	.	ENSG00000184022	ENST00000330500	T	0.14766	2.48	2.34	1.1	0.20463	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.30696	0.0773	H	0.95224	3.64	0.21256	N	0.999743	P	0.36577	0.558	B	0.41894	0.369	T	0.21930	-1.0231	9	0.87932	D	0	.	7.1223	0.25453	0.7695:0.2305:0.0:0.0	.	62	Q8NGZ9	O2T10_HUMAN	C	62	ENSP00000329210:F62C	ENSP00000329210:F62C	F	-	2	0	OR2T10	246823508	0.966000	0.33281	0.483000	0.27378	0.940000	0.58332	5.209000	0.65208	0.027000	0.15297	0.362000	0.22060	TTT		0.408	OR2T10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097139.1		NM_001004693	
PAIP1	10605	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	43555964	43555964	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr5:43555964A>T	ENST00000306846.3	-	2	635	c.403T>A	c.(403-405)Ttt>Att	p.F135I	PAIP1_ENST00000436644.2_Missense_Mutation_p.F56I|PAIP1_ENST00000338972.4_Missense_Mutation_p.F23I|PAIP1_ENST00000514514.1_Missense_Mutation_p.F56I	NM_006451.4|NM_182789.3	NP_006442.2|NP_877590.1	Q9H074	PAIP1_HUMAN	poly(A) binding protein interacting protein 1	135	PABPC1-interacting motif-2 (PAM2).				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	RNA binding (GO:0003723)|translation activator activity (GO:0008494)	p.F135I(1)		endometrium(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Lung NSC(6;2.07e-05)					GAAGGGTAAAATTCAGGGGCA	0.418																																																	1	Substitution - Missense(1)	kidney(1)											133.0	144.0	140.0					5																	43555964		2203	4300	6503	SO:0001583	missense	10605			AF013758	CCDS3947.1, CCDS3948.1, CCDS47204.1	5p12	2008-02-05			ENSG00000172239	ENSG00000172239			16945	protein-coding gene	gene with protein product		605184				9548260, 11230166	Standard	NM_006451		Approved		uc003job.3	Q9H074	OTTHUMG00000096960	ENST00000306846.3:c.403T>A	5.37:g.43555964A>T	ENSP00000302768:p.Phe135Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A6NKV8|O60455|Q96B61|Q9BS63	Missense_Mutation	SNP	ENST00000306846.3	37	CCDS3947.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.904676	0.92035	.	.	ENSG00000172239	ENST00000306846;ENST00000436644;ENST00000338972;ENST00000514514;ENST00000511321;ENST00000508537;ENST00000515338	T;T;T;T;T;T	0.56611	1.3;1.34;0.59;1.36;0.45;0.61	5.63	5.63	0.86233	Ataxin-2, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.62816	0.2459	L	0.29908	0.895	0.48975	D	0.999738	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.91635	0.999;0.998;0.996	T	0.66901	-0.5806	10	0.87932	D	0	-9.2022	15.8204	0.78638	1.0:0.0:0.0:0.0	.	56;135;56	D6REB4;Q9H074;Q9H074-2	.;PAIP1_HUMAN;.	I	135;56;23;56;23;23;23	ENSP00000302768:F135I;ENSP00000387729:F56I;ENSP00000339622:F23I;ENSP00000425084:F56I;ENSP00000425675:F23I;ENSP00000425736:F23I	ENSP00000302768:F135I	F	-	1	0	PAIP1	43591721	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	6.657000	0.74402	2.142000	0.66516	0.459000	0.35465	TTT		0.418	PAIP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214024.1		NM_006451	
PCDHA9	9752	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	140230078	140230078	+	Silent	SNP	G	G	A			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr5:140230078G>A	ENST00000532602.1	+	1	3031	c.1998G>A	c.(1996-1998)ctG>ctA	p.L666L	PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA9_ENST00000378122.3_Silent_p.L666L|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	666	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L666L(2)		breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCACTGTGCTGGTGTCGCTGG	0.687																																					Melanoma(55;1800 1972 14909)												2	Substitution - coding silent(2)	kidney(2)											43.0	47.0	46.0					5																	140230078		2197	4268	6465	SO:0001819	synonymous_variant	9752			AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"""Cadherins / Protocadherins : Clustered"""	8675	other	complex locus constituent	"""KIAA0345-like 5"""	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.1998G>A	5.37:g.140230078G>A		Somatic		WXS	Illumina HiSeq	Phase_I	O15053|Q2M3S5	Silent	SNP	ENST00000532602.1	37	CCDS54920.1																																																																																				0.687	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2		NM_031857	
PIGC	5279	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	172411549	172411549	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr1:172411549A>T	ENST00000367728.1	-	1	1677	c.214T>A	c.(214-216)Tgg>Agg	p.W72R	PIGC_ENST00000344529.4_Missense_Mutation_p.W72R|C1orf105_ENST00000367727.4_Intron|PIGC_ENST00000484368.1_Intron|PIGC_ENST00000258324.1_Missense_Mutation_p.W72R			Q92535	PIGC_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class C	72					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)|phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)	p.W72R(1)		breast(1)|endometrium(1)|kidney(1)|lung(1)	4						ATATACCACCAGATAACCACA	0.458																																																	1	Substitution - Missense(1)	kidney(1)											108.0	110.0	109.0					1																	172411549		2203	4300	6503	SO:0001583	missense	5279			BC006539	CCDS1302.1	1q23-q25	2013-02-26	2006-06-28		ENSG00000135845	ENSG00000135845	2.4.1.198	"""Phosphatidylinositol glycan anchor biosynthesis"""	8960	protein-coding gene	gene with protein product	"""phosphatidylinositol N-acetylglucosaminyltransferase"""	601730	"""phosphatidylinositol glycan, class C"""			8806613, 9325057	Standard	NM_153747		Approved		uc001gio.3	Q92535	OTTHUMG00000034751	ENST00000367728.1:c.214T>A	1.37:g.172411549A>T	ENSP00000356702:p.Trp72Arg	Somatic		WXS	Illumina HiSeq	Phase_I	O14491	Missense_Mutation	SNP	ENST00000367728.1	37	CCDS1302.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.184581	0.78677	.	.	ENSG00000135845	ENST00000344529;ENST00000367728;ENST00000258324	T;T;T	0.46451	0.87;0.87;0.87	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.44329	0.1288	M	0.66939	2.045	0.80722	D	1	P	0.35107	0.484	P	0.47786	0.557	T	0.50955	-0.8766	10	0.66056	D	0.02	-15.1063	13.8968	0.63778	1.0:0.0:0.0:0.0	.	72	Q92535	PIGC_HUMAN	R	72	ENSP00000356701:W72R;ENSP00000356702:W72R;ENSP00000258324:W72R	ENSP00000258324:W72R	W	-	1	0	PIGC	170678172	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.793000	0.91862	1.970000	0.57323	0.533000	0.62120	TGG		0.458	PIGC-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084068.1		NM_153747	
PLEC	5339	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	145007369	145007369	+	Missense_Mutation	SNP	G	G	A	rs559590378		TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr8:145007369G>A	ENST00000322810.4	-	13	1994	c.1825C>T	c.(1825-1827)Cgc>Tgc	p.R609C	PLEC_ENST00000354958.2_Missense_Mutation_p.R450C|PLEC_ENST00000356346.3_Missense_Mutation_p.R458C|PLEC_ENST00000398774.2_Missense_Mutation_p.R440C|PLEC_ENST00000527096.1_Missense_Mutation_p.R495C|PLEC_ENST00000345136.3_Missense_Mutation_p.R472C|PLEC_ENST00000354589.3_Missense_Mutation_p.R472C|PLEC_ENST00000436759.2_Missense_Mutation_p.R499C|PLEC_ENST00000357649.2_Missense_Mutation_p.R476C	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	609	Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)	p.R609C(1)|p.R472C(1)|p.R499C(1)		NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GCCCACCTGCGGTACATCTGC	0.662													G|||	1	0.000199681	0.0	0.0	5008	,	,		15123	0.001		0.0	False		,,,				2504	0.0																3	Substitution - Missense(3)	kidney(3)											39.0	49.0	45.0					8																	145007369		2034	4158	6192	SO:0001583	missense	5339			U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.1825C>T	8.37:g.145007369G>A	ENSP00000323856:p.Arg609Cys	Somatic		WXS	Illumina HiSeq	Phase_I	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	G	14.16	2.453182	0.43531	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096;ENST00000528025	D;D;D;D;D;D;D;D;D;D	0.92647	-3.08;-3.08;-3.08;-3.08;-3.08;-3.08;-3.08;-3.08;-3.08;-3.08	5.08	5.08	0.68730	.	0.000000	0.64402	U	0.000016	D	0.94755	0.8307	M	0.63428	1.95	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.83275	0.996;0.996;0.996;0.991;0.996;0.996;0.996;0.996	D	0.94847	0.8010	10	0.72032	D	0.01	.	12.3656	0.55226	0.0:0.0:0.8311:0.1688	.	499;458;450;609;440;472;476;472	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	C	472;476;472;440;609;450;458;499;495;516	ENSP00000344848:R472C;ENSP00000350277:R476C;ENSP00000346602:R472C;ENSP00000381756:R440C;ENSP00000323856:R609C;ENSP00000347044:R450C;ENSP00000348702:R458C;ENSP00000388180:R499C;ENSP00000434583:R495C;ENSP00000437303:R516C	ENSP00000323856:R609C	R	-	1	0	PLEC	145079357	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.169000	0.42434	2.378000	0.81104	0.549000	0.68633	CGC		0.662	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1		NM_000445	
PNPLA8	50640	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	108155092	108155092	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr7:108155092A>C	ENST00000422087.1	-	4	1250	c.844T>G	c.(844-846)Tca>Gca	p.S282A	PNPLA8_ENST00000436062.1_Missense_Mutation_p.S282A|PNPLA8_ENST00000388728.5_Missense_Mutation_p.S282A|PNPLA8_ENST00000257694.8_Missense_Mutation_p.S282A|PNPLA8_ENST00000453144.1_Missense_Mutation_p.S182A|PNPLA8_ENST00000426128.2_Missense_Mutation_p.S282A|PNPLA8_ENST00000483879.1_Intron	NM_015723.3	NP_056538.1	Q9NP80	PLPL8_HUMAN	patatin-like phospholipase domain containing 8	282					arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|cell death (GO:0008219)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|linoleic acid metabolic process (GO:0043651)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylcholine catabolic process (GO:0034638)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylethanolamine catabolic process (GO:0046338)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)	p.S282A(1)		breast(5)|endometrium(1)|kidney(3)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(3)	29						TGTTTAGTTGAAACTTGAAGA	0.433																																																	1	Substitution - Missense(1)	kidney(1)											115.0	111.0	112.0					7																	108155092		2203	4300	6503	SO:0001583	missense	50640			AF217519	CCDS34733.1, CCDS59075.1, CCDS59508.1	7q31	2012-07-31			ENSG00000135241	ENSG00000135241		"""Patatin-like phospholipase domain containing"""	28900	protein-coding gene	gene with protein product		612123				10744668, 10833412, 16799181, 19029121	Standard	NM_015723		Approved	IPLA2G, IPLA2-2, iPLA2gamma	uc003vfj.2	Q9NP80	OTTHUMG00000154870	ENST00000422087.1:c.844T>G	7.37:g.108155092A>C	ENSP00000410804:p.Ser282Ala	Somatic		WXS	Illumina HiSeq	Phase_I	A4D0S1|C9JZI4|O95035|Q8N3I3|Q9H7T5|Q9NR17|Q9NUN2|Q9NZ79	Missense_Mutation	SNP	ENST00000422087.1	37	CCDS34733.1	.	.	.	.	.	.	.	.	.	.	A	10.39	1.336704	0.24253	.	.	ENSG00000135241	ENST00000426128;ENST00000257694;ENST00000388728;ENST00000422087;ENST00000453144;ENST00000436062;ENST00000453085	D;D;D;D;D;D;D	0.98531	-3.85;-4.98;-3.84;-4.98;-4.9;-4.98;-4.9	5.48	5.48	0.80851	.	0.107617	0.64402	D	0.000004	D	0.96867	0.8977	M	0.68952	2.095	0.49687	D	0.999818	P	0.34662	0.462	B	0.31946	0.138	D	0.96614	0.9454	10	0.36615	T	0.2	.	15.8623	0.79035	1.0:0.0:0.0:0.0	.	282	Q9NP80	PLPL8_HUMAN	A	282;282;282;282;182;282;182	ENSP00000394988:S282A;ENSP00000257694:S282A;ENSP00000373380:S282A;ENSP00000410804:S282A;ENSP00000387789:S182A;ENSP00000406779:S282A;ENSP00000402274:S182A	ENSP00000257694:S282A	S	-	1	0	PNPLA8	107942328	1.000000	0.71417	0.253000	0.24343	0.079000	0.17450	5.927000	0.70080	2.205000	0.71048	0.482000	0.46254	TCA		0.433	PNPLA8-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337475.1		NM_015723	
POLD1	5424	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	50905747	50905747	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr19:50905747G>A	ENST00000440232.2	+	7	848	c.795G>A	c.(793-795)tgG>tgA	p.W265*	POLD1_ENST00000595904.1_Nonsense_Mutation_p.W265*|POLD1_ENST00000599857.1_Nonsense_Mutation_p.W265*	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	265					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.W265*(2)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		GCTGCAACTGGCTGGAGCTCC	0.667								DNA polymerases (catalytic subunits)																																									2	Substitution - Nonsense(2)	kidney(2)											20.0	21.0	20.0					19																	50905747		2199	4298	6497	SO:0001587	stop_gained	5424				CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"""DNA polymerases"""	9175	protein-coding gene	gene with protein product	"""CDC2 homolog (S. cerevisiae)"""	174761	"""polymerase (DNA directed), delta 1, catalytic subunit (125kD)"""	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.795G>A	19.37:g.50905747G>A	ENSP00000406046:p.Trp265*	Somatic		WXS	Illumina HiSeq	Phase_I	Q8NER3|Q96H98	Nonsense_Mutation	SNP	ENST00000440232.2	37	CCDS12795.1	.	.	.	.	.	.	.	.	.	.	G	36	5.945684	0.97134	.	.	ENSG00000062822	ENST00000440232;ENST00000376930	.	.	.	4.23	4.23	0.50019	.	0.265227	0.33753	N	0.004581	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-30.9945	15.919	0.79544	0.0:0.0:1.0:0.0	.	.	.	.	X	265;266	.	ENSP00000366129:W266X	W	+	3	0	POLD1	55597559	1.000000	0.71417	1.000000	0.80357	0.777000	0.43975	5.488000	0.66869	2.365000	0.80145	0.491000	0.48974	TGG		0.667	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1			
PRKCE	5581	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	45879259	45879259	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr2:45879259T>A	ENST00000306156.3	+	1	347	c.20T>A	c.(19-21)cTt>cAt	p.L7H		NM_005400.2	NP_005391.1	Q02156	KPCE_HUMAN	protein kinase C, epsilon	7	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to ethanol (GO:0071361)|cellular response to hypoxia (GO:0071456)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|locomotory exploration behavior (GO:0035641)|macrophage activation involved in immune response (GO:0002281)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cellular glucuronidation (GO:2001031)|positive regulation of cytokinesis (GO:0032467)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of insulin secretion (GO:0032024)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|release of sequestered calcium ion into cytosol (GO:0051209)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|ethanol binding (GO:0035276)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|receptor activator activity (GO:0030546)|signal transducer activity (GO:0004871)	p.L7H(1)	MBOAT2/PRKCE(2)	breast(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(13)|ovary(3)|upper_aerodigestive_tract(2)	34		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)		Tamoxifen(DB00675)	TTCAATGGCCTTCTTAAGATC	0.652																																																	1	Substitution - Missense(1)	kidney(1)											36.0	41.0	39.0					2																	45879259		2201	4299	6500	SO:0001583	missense	5581				CCDS1824.1	2p21	2009-07-10			ENSG00000171132	ENSG00000171132	2.7.11.1		9401	protein-coding gene	gene with protein product		176975				1382605, 7877991	Standard	NM_005400		Approved		uc002rut.3	Q02156	OTTHUMG00000128817	ENST00000306156.3:c.20T>A	2.37:g.45879259T>A	ENSP00000306124:p.Leu7His	Somatic		WXS	Illumina HiSeq	Phase_I	B0LPH7|Q32MQ3|Q53SL4|Q53SM5|Q9UE81	Missense_Mutation	SNP	ENST00000306156.3	37	CCDS1824.1	.	.	.	.	.	.	.	.	.	.	T	13.93	2.382690	0.42207	.	.	ENSG00000171132	ENST00000421201;ENST00000306156	T;T	0.10668	2.85;2.85	4.71	3.46	0.39613	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.789478	0.10990	N	0.611648	T	0.11537	0.0281	L	0.42245	1.32	0.80722	D	1	P	0.37158	0.585	B	0.40329	0.326	T	0.14699	-1.0463	10	0.15952	T	0.53	.	10.2021	0.43089	0.1486:0.0:0.0:0.8514	.	7	Q02156	KPCE_HUMAN	H	7	ENSP00000394574:L7H;ENSP00000306124:L7H	ENSP00000306124:L7H	L	+	2	0	PRKCE	45732763	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.309000	0.51903	1.749000	0.51849	0.459000	0.35465	CTT		0.652	PRKCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250751.2			
RYR1	6261	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	38985048	38985048	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr19:38985048G>A	ENST00000359596.3	+	39	6331	c.6331G>A	c.(6331-6333)Gtg>Atg	p.V2111M	RYR1_ENST00000355481.4_Missense_Mutation_p.V2111M|RYR1_ENST00000360985.3_Missense_Mutation_p.V2111M			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2111	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.V2111M(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	AGAGGACTTCGTGCAGAGCCC	0.667																																																	1	Substitution - Missense(1)	kidney(1)											39.0	35.0	37.0					19																	38985048		2203	4300	6503	SO:0001583	missense	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.6331G>A	19.37:g.38985048G>A	ENSP00000352608:p.Val2111Met	Somatic		WXS	Illumina HiSeq	Phase_I	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.933607	0.52866	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.97016	-4.21;-4.21;-4.21	4.79	3.7	0.42460	.	0.088383	0.45126	U	0.000384	D	0.92987	0.7768	N	0.25647	0.755	0.35883	D	0.8291	D;D	0.59767	0.986;0.977	P;P	0.51833	0.681;0.483	D	0.92458	0.5975	10	0.59425	D	0.04	.	4.1571	0.10266	0.3105:0.0:0.6895:0.0	.	2111;2111	P21817-2;P21817	.;RYR1_HUMAN	M	2111	ENSP00000352608:V2111M;ENSP00000347667:V2111M;ENSP00000354254:V2111M	ENSP00000347667:V2111M	V	+	1	0	RYR1	43676888	1.000000	0.71417	0.978000	0.43139	0.869000	0.49853	3.809000	0.55606	2.477000	0.83638	0.313000	0.20887	GTG		0.667	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			
RYR1	6261	broad.mit.edu;hgsc.bcm.edu	37	19	39008218	39008218	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr19:39008218C>A	ENST00000359596.3	+	66	9905	c.9905C>A	c.(9904-9906)cCa>cAa	p.P3302Q	RYR1_ENST00000355481.4_Missense_Mutation_p.P3302Q|RYR1_ENST00000360985.3_Missense_Mutation_p.P3302Q			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3302					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.P3302Q(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGCGCCCCCCCACCCTGCACA	0.652																																																	1	Substitution - Missense(1)	kidney(1)											33.0	32.0	32.0					19																	39008218		2202	4300	6502	SO:0001583	missense	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.9905C>A	19.37:g.39008218C>A	ENSP00000352608:p.Pro3302Gln	Somatic		WXS	Illumina HiSeq	Phase_I	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	6.544	0.468685	0.12461	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985;ENST00000538206	D;D;D	0.96491	-4.02;-4.03;-4.02	3.54	3.54	0.40534	.	0.395517	0.21765	U	0.069442	D	0.92750	0.7695	L	0.48642	1.525	0.39161	D	0.962412	B;B;B	0.16396	0.002;0.017;0.01	B;B;B	0.12156	0.003;0.007;0.003	D	0.89436	0.3720	10	0.12430	T	0.62	.	12.6296	0.56649	0.0:1.0:0.0:0.0	.	3302;3302;3302	P21817-3;P21817-2;P21817	.;.;RYR1_HUMAN	Q	3302;3302;3302;222	ENSP00000352608:P3302Q;ENSP00000347667:P3302Q;ENSP00000354254:P3302Q	ENSP00000347667:P3302Q	P	+	2	0	RYR1	43700058	0.007000	0.16637	0.557000	0.28306	0.405000	0.30901	1.104000	0.31074	1.826000	0.53198	0.205000	0.17691	CCA		0.652	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			
SLC25A2	83884	broad.mit.edu;ucsc.edu	37	5	140682821	140682821	+	Missense_Mutation	SNP	T	T	G			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr5:140682821T>G	ENST00000239451.4	-	1	791	c.612A>C	c.(610-612)aaA>aaC	p.K204N		NM_031947.2	NP_114153.1	Q9BXI2	ORNT2_HUMAN	solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 2	204					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|urea cycle (GO:0000050)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.K204N(1)		breast(3)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(500;0.000249)|Lung NSC(810;0.0011)|Ovarian(839;0.00556)|Breast(839;0.0173)|all_hematologic(541;0.152)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.00204)	L-Ornithine(DB00129)	CTAGTTCATCTTTTGATCTCC	0.438																																																	1	Substitution - Missense(1)	kidney(1)											109.0	109.0	109.0					5																	140682821		2203	4300	6503	SO:0001583	missense	83884			AF332005	CCDS4258.1	5q31.3	2013-05-22			ENSG00000120329	ENSG00000120329		"""Solute carriers"""	22921	protein-coding gene	gene with protein product		608157				11004451	Standard	NM_031947		Approved	ORNT2	uc003ljf.3	Q9BXI2	OTTHUMG00000129604	ENST00000239451.4:c.612A>C	5.37:g.140682821T>G	ENSP00000239451:p.Lys204Asn	Somatic		WXS	Illumina GAIIx	Phase_I	Q496C1|Q6XUI0|Q8NFZ2	Missense_Mutation	SNP	ENST00000239451.4	37	CCDS4258.1	.	.	.	.	.	.	.	.	.	.	T	13.72	2.320553	0.41096	.	.	ENSG00000120329	ENST00000239451	T	0.78003	-1.14	3.78	2.64	0.31445	Mitochondrial carrier domain (2);	0.105430	0.64402	D	0.000006	T	0.68577	0.3016	L	0.58302	1.8	0.58432	D	0.999998	P	0.45672	0.864	B	0.40165	0.321	T	0.65105	-0.6249	10	0.42905	T	0.14	-22.3666	5.4373	0.16488	0.0:0.1807:0.0:0.8193	.	204	Q9BXI2	ORNT2_HUMAN	N	204	ENSP00000239451:K204N	ENSP00000239451:K204N	K	-	3	2	SLC25A2	140663005	1.000000	0.71417	0.999000	0.59377	0.915000	0.54546	1.211000	0.32382	0.826000	0.34661	0.528000	0.53228	AAA		0.438	SLC25A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251799.2		NM_031947	
STEAP3	55240	hgsc.bcm.edu	37	2	120003082	120003090	+	In_Frame_Del	DEL	GAGATGGAC	GAGATGGAC	-	rs149645383|rs202057547	byFrequency	TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	GAGATGGAC	GAGATGGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr2:120003082_120003090delGAGATGGAC	ENST00000354888.5	+	3	514_522	c.10_18delGAGATGGAC	c.(10-18)gagatggacdel	p.EMD4del	STEAP3_ENST00000393108.2_In_Frame_Del_p.EMD4del|STEAP3_ENST00000393106.2_In_Frame_Del_p.EMD4del|STEAP3_ENST00000409811.1_In_Frame_Del_p.EMD4del|STEAP3_ENST00000450943.2_In_Frame_Del_p.EMD4del|STEAP3-AS1_ENST00000454260.1_RNA|STEAP3_ENST00000393107.2_In_Frame_Del_p.EMD4del|STEAP3_ENST00000425223.2_In_Frame_Del_p.EMD4del|STEAP3_ENST00000393110.2_In_Frame_Del_p.EMD14del	NM_182915.2	NP_878919.2	Q658P3	STEA3_HUMAN	STEAP family member 3, metalloreductase	4					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cellular iron ion homeostasis (GO:0006879)|copper ion import (GO:0015677)|exosomal secretion (GO:1990182)|ferric iron import into cell (GO:0097461)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902167)|protein secretion (GO:0009306)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	17						AATGCCAGAAGAGATGGACAAGCCACTGA	0.579																																																	0																																										SO:0001651	inframe_deletion	55240			AY029585	CCDS2125.1, CCDS42738.1	2q14.2	2011-09-30	2011-09-30		ENSG00000115107	ENSG00000115107			24592	protein-coding gene	gene with protein product		609671				12606722	Standard	NM_182915		Approved	TSAP6, dudlin-2, STMP3	uc002tlr.3	Q658P3	OTTHUMG00000131402	ENST00000354888.5:c.10_18delGAGATGGAC	2.37:g.120003082_120003090delGAGATGGAC	ENSP00000346961:p.Glu4_Asp6del	Somatic		WXS	Illumina HiSeq	Phase_I	A8K6E3|Q4VBR2|Q4ZG36|Q53SQ8|Q7Z389|Q86SF6|Q8NEW6|Q8TDP3|Q8TF03|Q9NVB5	In_Frame_Del	DEL	ENST00000354888.5	37	CCDS2125.1																																																																																				0.579	STEAP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254193.1		NM_018234	
TBC1D16	125058	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	77926601	77926601	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr17:77926601C>G	ENST00000310924.2	-	4	911	c.796G>C	c.(796-798)Gac>Cac	p.D266H	TBC1D16_ENST00000570373.1_5'Flank|TBC1D16_ENST00000340848.7_5'Flank|TBC1D16_ENST00000572862.1_5'Flank|TBC1D16_ENST00000576768.1_5'Flank	NM_001271844.1|NM_001271845.1|NM_019020.2	NP_001258773.1|NP_001258774.1|NP_061893.2	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16	266							Rab GTPase activator activity (GO:0005097)	p.D266H(1)		NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(3)	28	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			AGGCCGGCGTCGGAGCTGGAC	0.672																																					Ovarian(14;397 562 4850 31922 49378)												1	Substitution - Missense(1)	kidney(1)											25.0	29.0	28.0					17																	77926601		2198	4283	6481	SO:0001583	missense	125058			AL157485	CCDS11766.1, CCDS62351.1, CCDS62352.1, CCDS62353.1	17q25.3	2013-07-10				ENSG00000167291			28356	protein-coding gene	gene with protein product						23019362	Standard	NM_019020		Approved	MGC25062, FLJ20748	uc002jxj.4	Q8TBP0		ENST00000310924.2:c.796G>C	17.37:g.77926601C>G	ENSP00000309794:p.Asp266His	Somatic		WXS	Illumina HiSeq	Phase_I	B9A6L7|I3L1E0|I3L4U2|Q8N3Z4|Q96DH7	Missense_Mutation	SNP	ENST00000310924.2	37	CCDS11766.1	.	.	.	.	.	.	.	.	.	.	C	14.86	2.660024	0.47572	.	.	ENSG00000167291	ENST00000310924	T	0.11604	2.76	5.3	3.28	0.37604	.	1.018550	0.07807	N	0.957539	T	0.21550	0.0519	L	0.51422	1.61	0.80722	D	1	D	0.71674	0.998	P	0.56700	0.804	T	0.01940	-1.1243	10	0.46703	T	0.11	-38.1723	9.4216	0.38555	0.0:0.7744:0.0:0.2256	.	266	Q8TBP0	TBC16_HUMAN	H	266	ENSP00000309794:D266H	ENSP00000309794:D266H	D	-	1	0	TBC1D16	75541196	1.000000	0.71417	0.042000	0.18584	0.044000	0.14063	4.649000	0.61433	1.227000	0.43598	0.655000	0.94253	GAC		0.672	TBC1D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437145.1		NM_019020	
TTN	7273	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	179664360	179664360	+	Silent	SNP	C	C	T			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr2:179664360C>T	ENST00000591111.1	-	6	992	c.768G>A	c.(766-768)agG>agA	p.R256R	TTN_ENST00000360870.5_Silent_p.R256R|TTN_ENST00000359218.5_Silent_p.R256R|TTN_ENST00000460472.2_Silent_p.R256R|TTN_ENST00000342175.6_Silent_p.R256R|TTN_ENST00000589042.1_Silent_p.R256R|TTN_ENST00000342992.6_Silent_p.R256R			Q8WZ42	TITIN_HUMAN	titin	0	ZIS1.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R256R(6)|p.R256_K260>K(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCGGAGGAATCCTGGGAGGTG	0.532																																																	7	Substitution - coding silent(6)|Complex - deletion inframe(1)	kidney(6)|ovary(1)											121.0	114.0	116.0					2																	179664360		2203	4300	6503	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.768G>A	2.37:g.179664360C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.532	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1		NM_133378	
USH2A	7399	hgsc.bcm.edu	37	1	215813937	215813938	+	Frame_Shift_Ins	INS	-	-	A			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr1:215813937_215813938insA	ENST00000307340.3	-	68	15316_15317	c.14930_14931insT	c.(14929-14931)ttgfs	p.L4977fs	USH2A_ENST00000366943.2_Frame_Shift_Ins_p.L4977fs	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4977					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.L4977F(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GGGTGGTGTCCAAGCCGCTGTA	0.55										HNSCC(13;0.011)																																							1	Substitution - Missense(1)	lung(1)																																								SO:0001589	frameshift_variant	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.14931dupT	1.37:g.215813939_215813939dupA	ENSP00000305941:p.Leu4977fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VVM9|Q6S362|Q9NS27	Frame_Shift_Ins	INS	ENST00000307340.3	37	CCDS31025.1																																																																																				0.550	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1		NM_007123	
VHL	7428	hgsc.bcm.edu	37	3	10188262	10188262	+	Missense_Mutation	SNP	A	A	T	rs119103278|rs397516442		TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr3:10188262A>T	ENST00000256474.2	+	2	1245	c.405A>T	c.(403-405)ttA>ttT	p.L135F	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	135	Involved in binding to CCT complex.		L -> F (in hemangioblastoma). {ECO:0000269|PubMed:8069849}.		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.L135fs*24(3)|p.V137fs*7(3)|p.L135F(1)|p.?fs(1)|p.N131fs*7(1)|p.L135fs*7(1)|p.E134fs*7(1)|p.L135fs*9(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)		AAACTGAATTATTTGTGCCAT	0.433		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"""	12	Deletion - Frameshift(6)|Insertion - Frameshift(5)|Substitution - Missense(1)	kidney(11)|soft_tissue(1)											214.0	199.0	204.0					3																	10188262		2203	4300	6503	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.405A>T	3.37:g.10188262A>T	ENSP00000256474:p.Leu135Phe	Somatic		WXS	Illumina HiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	A	19.78	3.891757	0.72524	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99806	-6.84	5.07	-2.96	0.05547	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.254096	0.33290	N	0.005074	D	0.98400	0.9468	L	0.43152	1.355	0.58432	D	0.999998	P	0.44776	0.843	B	0.42851	0.4	D	0.94170	0.7422	10	0.72032	D	0.01	-2.9719	3.6055	0.08041	0.2483:0.1432:0.4687:0.1398	.	135	P40337	VHL_HUMAN	F	135;53	ENSP00000256474:L135F	ENSP00000256474:L135F	L	+	3	2	VHL	10163262	0.927000	0.31430	0.316000	0.25252	0.888000	0.51559	-0.134000	0.10436	-0.460000	0.07003	0.460000	0.39030	TTA		0.433	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
VPS54	51542	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	64160992	64160992	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr2:64160992T>C	ENST00000272322.4	-	12	1708	c.1554A>G	c.(1552-1554)atA>atG	p.I518M	VPS54_ENST00000409558.4_Missense_Mutation_p.I506M|VPS54_ENST00000354504.3_Missense_Mutation_p.I365M			Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 homolog (S. cerevisiae)	518					growth (GO:0040007)|homeostasis of number of cells within a tissue (GO:0048873)|musculoskeletal movement (GO:0050881)|neurofilament cytoskeleton organization (GO:0060052)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)		p.I518M(1)		endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	27						ATGCATCACTTATAAACATGC	0.423																																																	1	Substitution - Missense(1)	kidney(1)											169.0	138.0	148.0					2																	64160992		2203	4300	6503	SO:0001583	missense	51542			AF102177	CCDS33208.1, CCDS46302.1	2p15-p14	2014-06-13	2006-12-19		ENSG00000143952	ENSG00000143952			18652	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 164"""	614633	"""vacuolar protein sorting 54 (yeast)"""			12039048	Standard	NM_016516		Approved	HCC8, PPP1R164	uc002scq.3	Q9P1Q0	OTTHUMG00000152627	ENST00000272322.4:c.1554A>G	2.37:g.64160992T>C	ENSP00000272322:p.Ile518Met	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VIR5|Q86YF7|Q8N6G3|Q9NPV0|Q9NT07|Q9NUJ0	Missense_Mutation	SNP	ENST00000272322.4	37	CCDS33208.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.327728	0.41197	.	.	ENSG00000143952	ENST00000354504;ENST00000272322;ENST00000409558;ENST00000483277;ENST00000394400	T;T;T	0.36878	1.23;1.32;1.32	4.97	2.49	0.30216	.	0.000000	0.85682	D	0.000000	T	0.36331	0.0963	L	0.59436	1.845	0.53005	D	0.999968	P;P;P	0.46512	0.879;0.808;0.879	B;B;P	0.46253	0.441;0.312;0.509	T	0.16808	-1.0390	10	0.45353	T	0.12	.	8.5152	0.33242	0.1123:0.0:0.2064:0.6813	.	365;518;506	Q9P1Q0-3;Q9P1Q0;Q9P1Q0-4	.;VPS54_HUMAN;.	M	365;518;506;506;518	ENSP00000346499:I365M;ENSP00000272322:I518M;ENSP00000386980:I506M	ENSP00000272322:I518M	I	-	3	3	VPS54	64014496	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.425000	0.34859	1.990000	0.58119	0.460000	0.39030	ATA		0.423	VPS54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327062.2		NM_016516	
ZNF234	10780	broad.mit.edu;ucsc.edu	37	19	44660625	44660625	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr19:44660625G>C	ENST00000426739.2	+	6	714	c.456G>C	c.(454-456)gaG>gaC	p.E152D	ZNF234_ENST00000592437.1_Missense_Mutation_p.E152D	NM_006630.2	NP_006621.1	Q14588	ZN234_HUMAN	zinc finger protein 234	152					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E152D(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)	23		Prostate(69;0.0435)				AATGTGATGAGTACAAAAAAT	0.403																																																	1	Substitution - Missense(1)	kidney(1)											62.0	66.0	65.0					19																	44660625		2193	4292	6485	SO:0001583	missense	10780			X78927	CCDS46101.1	19q13	2013-01-08				ENSG00000263002		"""Zinc fingers, C2H2-type"", ""-"""	13027	protein-coding gene	gene with protein product		604750		ZNF269		7865130	Standard	NM_006630		Approved	HZF4	uc002oyl.4	Q14588		ENST00000426739.2:c.456G>C	19.37:g.44660625G>C	ENSP00000400878:p.Glu152Asp	Somatic		WXS	Illumina GAIIx	Phase_I	A8K1C8|Q96IR4|Q9NS45|Q9NYT7	Missense_Mutation	SNP	ENST00000426739.2	37	CCDS46101.1	.	.	.	.	.	.	.	.	.	.	G	9.120	1.008753	0.19199	.	.	ENSG00000167380	ENST00000426739	T	0.30448	1.53	3.65	-5.72	0.02406	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11153	0.0272	N	0.08118	0	0.09310	N	1	B	0.26512	0.151	B	0.25614	0.062	T	0.22941	-1.0202	9	0.46703	T	0.11	.	1.5839	0.02640	0.2075:0.1286:0.405:0.2588	.	152	Q14588	ZN234_HUMAN	D	152	ENSP00000400878:E152D	ENSP00000400878:E152D	E	+	3	2	ZNF226	49352465	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.802000	0.01741	-0.831000	0.04256	-0.302000	0.09304	GAG		0.403	ZNF234-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460586.2			
ATP4A	495	broad.mit.edu	37	19	36046428	36046428	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr19:36046428C>G	ENST00000262623.3	-	14	2099	c.2071G>C	c.(2071-2073)Gag>Cag	p.E691Q		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	691					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)	p.E691Q(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	CGCAGGGCCTCGACCAGTTCC	0.652																																																	1	Substitution - Missense(1)	kidney(1)											50.0	50.0	50.0					19																	36046428		2203	4300	6503	SO:0001583	missense	495				CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	3.6.3.10	"""ATPases / P-type"""	819	protein-coding gene	gene with protein product	"""gastric H,K-ATPase alpha subunit"", ""H(+)-K(+)-ATPase alpha subunit"", ""proton pump"""	137216				1330887	Standard	NM_000704		Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.2071G>C	19.37:g.36046428C>G	ENSP00000262623:p.Glu691Gln	Somatic		WXS	Illumina GAIIx	Phase_I	O00738	Missense_Mutation	SNP	ENST00000262623.3	37	CCDS12467.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.063056	0.76187	.	.	ENSG00000105675	ENST00000262623	D	0.93712	-3.27	4.87	4.87	0.63330	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.074209	0.51477	D	0.000091	D	0.92672	0.7671	N	0.13327	0.33	0.80722	D	1	D	0.53885	0.963	D	0.66084	0.941	D	0.93553	0.6888	10	0.54805	T	0.06	.	15.5367	0.76007	0.0:1.0:0.0:0.0	.	691	P20648	ATP4A_HUMAN	Q	691	ENSP00000262623:E691Q	ENSP00000262623:E691Q	E	-	1	0	ATP4A	40738268	1.000000	0.71417	0.974000	0.42286	0.702000	0.40608	7.443000	0.80521	2.537000	0.85549	0.462000	0.41574	GAG		0.652	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2		NM_000704	
ZNF473	25888	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	50549932	50549932	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr19:50549932G>C	ENST00000595661.1	+	6	2727	c.2232G>C	c.(2230-2232)gaG>gaC	p.E744D	ZNF473_ENST00000601364.1_Intron|CTD-2126E3.3_ENST00000599914.1_RNA|ZNF473_ENST00000445728.3_Missense_Mutation_p.E732D|CTD-2126E3.3_ENST00000599410.1_RNA|ZNF473_ENST00000270617.3_Missense_Mutation_p.E744D|ZNF473_ENST00000391821.2_Missense_Mutation_p.E744D			Q8WTR7	ZN473_HUMAN	zinc finger protein 473	744					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E744D(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00111)|OV - Ovarian serous cystadenocarcinoma(262;0.0058)		TGAGTGCTGAGCTTGTCCGCC	0.507											OREG0025632	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - Missense(1)	kidney(1)											77.0	81.0	79.0					19																	50549932		2203	4300	6503	SO:0001583	missense	25888			AB032967	CCDS33077.1	19q13.33	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	23239	protein-coding gene	gene with protein product						11782445	Standard	NM_015428		Approved	KIAA1141, DKFZP434N043, HZFP100	uc002prn.3	Q8WTR7		ENST00000595661.1:c.2232G>C	19.37:g.50549932G>C	ENSP00000472808:p.Glu744Asp	Somatic	970	WXS	Illumina HiSeq	Phase_I	A8K8T7|Q9ULS9|Q9Y4Q7	Missense_Mutation	SNP	ENST00000595661.1	37	CCDS33077.1	.	.	.	.	.	.	.	.	.	.	G	1.795	-0.478649	0.04414	.	.	ENSG00000142528	ENST00000270617;ENST00000391821;ENST00000445728	T;T;T	0.07567	3.18;3.18;3.18	4.23	-7.79	0.01218	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	1.268860	0.05944	N	0.637605	T	0.02888	0.0086	N	0.01464	-0.85	0.09310	N	1	B	0.17667	0.023	B	0.15870	0.014	T	0.48127	-0.9062	10	0.13853	T	0.58	-0.0183	14.9662	0.71196	0.1576:0.1076:0.7347:0.0	.	744	Q8WTR7	ZN473_HUMAN	D	744;744;732	ENSP00000270617:E744D;ENSP00000375697:E744D;ENSP00000388961:E732D	ENSP00000270617:E744D	E	+	3	2	ZNF473	55241744	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-6.149000	0.00078	-2.016000	0.00945	-0.355000	0.07637	GAG		0.507	ZNF473-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464833.1		XM_046390	
B4GALNT4	338707	broad.mit.edu	37	11	379656	379656	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr11:379656C>T	ENST00000329962.6	+	15	2443	c.2443C>T	c.(2443-2445)Cgc>Tgc	p.R815C		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	815					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)	p.R815C(1)		endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CCGGCCACTGCGCCTGGCCTG	0.721																																																	1	Substitution - Missense(1)	kidney(1)											5.0	6.0	6.0					11																	379656		1964	4044	6008	SO:0001583	missense	338707			AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"""Beta 4-glycosyltransferases"""	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.2443C>T	11.37:g.379656C>T	ENSP00000328277:p.Arg815Cys	Somatic		WXS	Illumina GAIIx	Phase_I	Q96LV2	Missense_Mutation	SNP	ENST00000329962.6	37	CCDS7694.1	.	.	.	.	.	.	.	.	.	.	c	18.90	3.721125	0.68959	.	.	ENSG00000182272	ENST00000329962	T	0.35236	1.32	3.61	3.61	0.41365	.	0.731881	0.12265	N	0.484332	T	0.30135	0.0755	L	0.29908	0.895	0.30602	N	0.760399	B	0.34226	0.443	B	0.37780	0.258	T	0.32295	-0.9912	10	0.62326	D	0.03	-6.1776	10.1094	0.42552	0.3363:0.6637:0.0:0.0	.	815	Q76KP1	B4GN4_HUMAN	C	815	ENSP00000328277:R815C	ENSP00000328277:R815C	R	+	1	0	B4GALNT4	369656	0.011000	0.17503	0.994000	0.49952	0.969000	0.65631	0.570000	0.23653	2.022000	0.59522	0.555000	0.69702	CGC		0.721	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2		NM_178537	
KCNJ12	3768	broad.mit.edu	37	17	21319528	21319528	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr17:21319528G>A	ENST00000583088.1	+	3	1769	c.874G>A	c.(874-876)Gac>Aac	p.D292N	KCNJ12_ENST00000331718.5_Missense_Mutation_p.D292N	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	292					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)	p.D292N(1)		NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	GGAGACGGACGACTTTGAGAT	0.612										Prostate(3;0.18)																																							1	Substitution - Missense(1)	kidney(1)											96.0	88.0	91.0					17																	21319528		2203	4300	6503	SO:0001583	missense	3768			L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.874G>A	17.37:g.21319528G>A	ENSP00000463778:p.Asp292Asn	Somatic		WXS	Illumina GAIIx	Phase_I	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.454209	0.63290	.	.	ENSG00000184185	ENST00000331718	D	0.94793	-3.52	5.44	5.44	0.79542	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.047559	0.85682	D	0.000000	D	0.92535	0.7629	L	0.48877	1.53	0.80722	D	1	B	0.19583	0.037	B	0.15052	0.012	D	0.88881	0.3339	10	0.49607	T	0.09	.	19.2719	0.94013	0.0:0.0:1.0:0.0	.	292	Q14500	IRK12_HUMAN	N	292	ENSP00000328150:D292N	ENSP00000328150:D292N	D	+	1	0	KCNJ12	21260121	1.000000	0.71417	0.962000	0.40283	0.867000	0.49689	9.698000	0.98700	2.561000	0.86390	0.561000	0.74099	GAC		0.612	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2		NM_021012	
PROCR	10544	broad.mit.edu	37	20	33762727	33762727	+	Missense_Mutation	SNP	G	G	T	rs200377875		TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr20:33762727G>T	ENST00000216968.4	+	2	375	c.293G>T	c.(292-294)cGc>cTc	p.R98L	EDEM2_ENST00000540582.1_Intron	NM_006404.3	NP_006395.2	Q9UNN8	EPCR_HUMAN	protein C receptor, endothelial	98					antigen processing and presentation (GO:0019882)|blood coagulation (GO:0007596)|immune response (GO:0006955)|negative regulation of coagulation (GO:0050819)	cell surface (GO:0009986)|centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)	p.R98L(2)		breast(1)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10			BRCA - Breast invasive adenocarcinoma(18;0.0152)		Drotrecogin alfa(DB00055)	GGCCTCGTGCGCCTGGTGCAC	0.726																																																	2	Substitution - Missense(2)	prostate(1)|kidney(1)											20.0	17.0	18.0					20																	33762727		2194	4296	6490	SO:0001583	missense	10544			L35545	CCDS13248.1	20q11.2	2010-05-04	2010-05-04		ENSG00000101000	ENSG00000101000		"""CD molecules"""	9452	protein-coding gene	gene with protein product		600646				7929370, 10518938	Standard	NM_006404		Approved	EPCR, CCD41, CD201	uc002xbt.3	Q9UNN8	OTTHUMG00000032323	ENST00000216968.4:c.293G>T	20.37:g.33762727G>T	ENSP00000216968:p.Arg98Leu	Somatic		WXS	Illumina GAIIx	Phase_I	B2RC04|Q14218|Q6IB56|Q96CB3|Q9ULX1	Missense_Mutation	SNP	ENST00000216968.4	37	CCDS13248.1	.	.	.	.	.	.	.	.	.	.	g	26.5	4.741327	0.89573	.	.	ENSG00000101000	ENST00000374477;ENST00000216968	D	0.82984	-1.67	5.22	-10.4	0.00318	MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	1.402480	0.04770	N	0.427767	T	0.71837	0.3387	L	0.51422	1.61	0.09310	N	1	B	0.30179	0.271	B	0.28385	0.089	T	0.61227	-0.7105	10	0.56958	D	0.05	-6.7275	4.9914	0.14216	0.5133:0.0:0.1891:0.2976	.	98	Q9UNN8	EPCR_HUMAN	L	98	ENSP00000216968:R98L	ENSP00000216968:R98L	R	+	2	0	PROCR	33226388	0.000000	0.05858	0.002000	0.10522	0.952000	0.60782	-3.074000	0.00617	-2.082000	0.00868	0.556000	0.70494	CGC		0.726	PROCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078843.3			
SPNS3	201305	broad.mit.edu	37	17	4381896	4381896	+	Silent	SNP	G	G	C			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chr17:4381896G>C	ENST00000355530.2	+	9	1423	c.1143G>C	c.(1141-1143)ctG>ctC	p.L381L	SPNS3_ENST00000333476.2_Silent_p.L254L	NM_182538.4	NP_872344.3	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3 (Drosophila)	381					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)		p.L381L(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(6)|stomach(2)	28						AGCTGCTTCTGTCCTGCAACT	0.637																																																	1	Substitution - coding silent(1)	kidney(1)											65.0	49.0	54.0					17																	4381896		2201	4300	6501	SO:0001819	synonymous_variant	201305				CCDS11045.1	17p13.2	2014-08-12			ENSG00000182557	ENSG00000182557			28433	protein-coding gene	gene with protein product		611701					Standard	NM_182538		Approved	MGC29671	uc002fxt.3	Q6ZMD2	OTTHUMG00000177737	ENST00000355530.2:c.1143G>C	17.37:g.4381896G>C		Somatic		WXS	Illumina GAIIx	Phase_I	Q8IZ31	Silent	SNP	ENST00000355530.2	37	CCDS11045.1																																																																																				0.637	SPNS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438793.1		NM_182538	
GTPBP6	8225	broad.mit.edu	37	X	228267	228267	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4986-01A-01D-1462-08	TCGA-BP-4986-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4465171a-d048-4078-b1ae-021b2c635ff4	2ed78cfb-2ff0-4682-9c25-21174a4e4853	g.chrX:228267G>A	ENST00000326153.4	-	3	256	c.257C>T	c.(256-258)aCg>aTg	p.T86M				O43824	GTPB6_HUMAN	GTP binding protein 6 (putative)	315							GTP binding (GO:0005525)|metal ion binding (GO:0046872)	p.D85D(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(3)	7		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				GGCATCGCCCGTCAGTGCCTT	0.677													G|||	7	0.00139776	0.0053	0.0	5008	,	,		14084	0.0		0.0	False		,,,				2504	0.0																1	Substitution - coding silent(1)	kidney(1)							MET/THR	4,4400		0,4,2198	161.0	188.0	179.0		258	0.6	0.1	X		179	1,8581		0,1,4290	no	missense	GTPBP6	NM_012227.2	81	0,5,6488	AA,AG,GG		0.0117,0.0908,0.0385	probably-damaging	315/517	228267	5,12981	2202	4291	6493	SO:0001583	missense	0			Y14391	CCDS75943.1	Xp22.33 and Yp11.32	2010-07-28			ENSG00000178605	ENSG00000178605		"""Pseudoautosomal regions / PAR1"""	30189	protein-coding gene	gene with protein product	"""pseudoautosomal GTP binding protein-like"""	300124				9466997	Standard	XM_006724447		Approved	PGPL, FLJ20977	uc004cpe.1	O43824	OTTHUMG00000022694	ENST00000326153.4:c.257C>T	X.37:g.228267G>A	ENSP00000316598:p.Thr86Met	Somatic		WXS	Illumina GAIIx	Phase_I	Q53F77|Q5HYX8	Translation_Start_Site	SNP	ENST00000326153.4	37		9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	.	9.947	1.218972	0.22373	9.08E-4	1.17E-4	ENSG00000178605	ENST00000326153	T	0.21031	2.03	1.57	0.643	0.17770	GTP-binding domain, HSR1-related (1);	0.113505	0.64402	U	0.000013	T	0.23727	0.0574	.	.	.	0.48087	D	0.999587	D	0.89917	1.0	D	0.85130	0.997	T	0.41910	-0.9482	8	0.87932	D	0	-11.074	6.6438	0.22925	0.1722:0.0:0.8278:0.0	.	315	O43824	GTPB6_HUMAN	M	86	ENSP00000316598:T86M	ENSP00000316598:T86M	T	-	2	0	GTPBP6	168267	1.000000	0.71417	0.110000	0.21437	0.104000	0.19210	6.707000	0.74654	-0.138000	0.11434	0.100000	0.15512	ACG		0.677	GTPBP6-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			NM_012227	
