#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_Chromosome_hg18	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_End_position_hg18	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_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_deletion_substructures	i_domain	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_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
CYBB	1536	genome.wustl.edu	37	X	37665662	37665662	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chrX:37665662G>A	ENST00000378588.4	+	11	1404	c.1337G>A	c.(1336-1338)cGg>cAg	p.R446Q	CYBB_ENST00000545017.1_Missense_Mutation_p.R414Q|CYBB_ENST00000536160.1_Missense_Mutation_p.R179Q|TM4SF2_ENST00000465127.1_Intron	NM_000397.3	NP_000388.2	P04839	CY24B_HUMAN	cytochrome b-245, beta polypeptide	446					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)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|respiratory burst (GO:0045730)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagocytic vesicle membrane (GO:0030670)|rough endoplasmic reticulum (GO:0005791)	flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|superoxide-generating NADPH oxidase activity (GO:0016175)|voltage-gated ion channel activity (GO:0005244)	p.R446Q(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|prostate(2)|skin(2)	32					Dextromethorphan(DB00514)	TGGCTGTGCCGGGACACACAT	0.488																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	X											131.0	110.0	117.0					X																	37665662		2202	4300	6502	37550606	SO:0001583	missense	0			X04011	CCDS14242.1	Xp21.1	2014-09-17	2008-07-29		ENSG00000165168	ENSG00000165168		"""Cytochrome b genes"""	2578	protein-coding gene	gene with protein product		300481	"""chronic granulomatous disease"""	CGD			Standard	NM_000397		Approved	GP91-PHOX, NOX2	uc004ddr.2	P04839	OTTHUMG00000033175	ENST00000378588.4:c.1337G>A	X.37:g.37665662G>A	ENSP00000367851:p.Arg446Gln	1460	0.14	2		NA	NA	NA	37550606	408	60.98	644	A8K138|Q2PP16	Missense_Mutation	SNP	HMMPfam_FAD_binding_8,HMMPfam_NAD_binding_6,HMMPfam_Ferric_reduct,superfamily_Riboflavin synthase domain-like,superfamily_Ferredoxin reductase-like C-terminal NADP-linked domain	p.R446Q	ENST00000378588.4	37	c.1337	CCDS14242.1	X	.	.	.	.	.	.	.	.	.	.	G	27.6	4.844486	0.91197	.	.	ENSG00000165168	ENST00000378588;ENST00000545017;ENST00000536160	D;D;D	0.97455	-4.39;-4.39;-4.39	5.63	5.63	0.86233	Ferric reductase, NAD binding (1);	0.174489	0.49305	D	0.000141	D	0.98251	0.9421	H	0.94698	3.57	0.35259	D	0.77943	D;P	0.57899	0.981;0.895	P;B	0.48901	0.594;0.355	D	0.99979	1.2410	10	0.72032	D	0.01	.	18.6209	0.91321	0.0:0.0:1.0:0.0	.	414;446	F5GWD2;P04839	.;CY24B_HUMAN	Q	446;414;179	ENSP00000367851:R446Q;ENSP00000441896:R414Q;ENSP00000441958:R179Q	ENSP00000367851:R446Q	R	+	2	0	CYBB	37550606	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	5.003000	0.63959	2.341000	0.79615	0.513000	0.50165	CGG	-	HMMPfam_NAD_binding_6,superfamily_Ferredoxin reductase-like C-terminal NADP-linked domain		0.488	CYBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CYBB	protein_coding	OTTHUMT00000080881.1	G			37550606	+1	no_errors	NM_000397.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
C1orf168	199920	genome.wustl.edu	37	1	57254703	57254703	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr1:57254703C>T	ENST00000343433.6	-	3	942	c.862G>A	c.(862-864)Gtg>Atg	p.V288M	C1orf168_ENST00000484327.1_5'UTR	NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	288								p.V288M(1)		NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|skin(6)|stomach(1)|urinary_tract(2)	46						TGGAGGTTCACGATGGGAGGT	0.577																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	1											148.0	135.0	139.0					1																	57254703		2203	4300	6503	57027291	SO:0001583	missense	0			BX648439	CCDS30729.1	1p32.2	2011-02-22			ENSG00000187889	ENSG00000187889			27295	protein-coding gene	gene with protein product						14702039	Standard	NM_001004303		Approved	RP4-758N20.2, FLJ43208	uc001cym.4	Q5VWT5	OTTHUMG00000008281	ENST00000343433.6:c.862G>A	1.37:g.57254703C>T	ENSP00000345972:p.Val288Met	1447	0.34	5		NA	NA	NA	57027291	661	31.58	306	Q63HM3|Q6ZUY6	Missense_Mutation	SNP	superfamily_SH3-domain	p.V288M	ENST00000343433.6	37	c.862	CCDS30729.1	1	.	.	.	.	.	.	.	.	.	.	c	13.01	2.109771	0.37242	.	.	ENSG00000187889	ENST00000343433	T	0.47177	0.85	5.4	4.49	0.54785	.	0.113633	0.38663	N	0.001607	T	0.55016	0.1894	L	0.34521	1.04	0.26250	N	0.978747	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.47394	-0.9121	10	0.62326	D	0.03	-7.1295	10.1701	0.42904	0.0:0.9108:0.0:0.0892	.	288;288	Q5VWT5-2;Q5VWT5	.;CA168_HUMAN	M	288	ENSP00000345972:V288M	ENSP00000345972:V288M	V	-	1	0	C1orf168	57027291	0.954000	0.32549	0.800000	0.32199	0.037000	0.13140	2.300000	0.43620	1.531000	0.49152	-0.119000	0.15052	GTG	-	NULL		0.577	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C1orf168	protein_coding	OTTHUMT00000022751.2	C	NM_001004303		57027291	-1	no_errors	NM_001004303.4	genbank	human	validated	54_36p	missense	SNP	0.410	T
PAPPA2	60676	genome.wustl.edu	37	1	176759024	176759024	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr1:176759024C>T	ENST00000367662.3	+	18	5959	c.4795C>T	c.(4795-4797)Cct>Tct	p.P1599S		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1599	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.P1599S(1)		NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						TGAGCCACCCCCTCCTGTGTT	0.478																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	1											126.0	127.0	126.0					1																	176759024		2012	4168	6180	175025647	SO:0001583	missense	0			BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"""placenta-specific 3"""	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.4795C>T	1.37:g.176759024C>T	ENSP00000356634:p.Pro1599Ser	1924	0.05	1		NA	NA	NA	175025647	1086	32.48	523	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	"HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_Notch,HMMSmart_SM00004,superfamily_Notch domain,PatternScan_N6_MTASE,PatternScan_ZINC_PROTEASE,HMMSmart_SM00560,HMMPfam_Peptidase_M43,superfamily_Concanavalin A-like lectins/glucanases,superfamily_Complement control module/SCR domain,superfamily_Metalloproteases (""zincins"") catalytic domain"	p.P1599S	ENST00000367662.3	37	c.4795	CCDS41438.1	1	.	.	.	.	.	.	.	.	.	.	C	9.066	0.995683	0.19043	.	.	ENSG00000116183	ENST00000367662	T	0.01963	4.53	5.51	0.234	0.15390	Complement control module (1);Sushi/SCR/CCP (2);	0.186704	0.45867	N	0.000321	T	0.01489	0.0048	N	0.20530	0.585	0.53005	D	0.999968	B	0.20368	0.044	B	0.20767	0.031	T	0.56715	-0.7933	10	0.34782	T	0.22	-5.1636	4.5672	0.12193	0.0:0.2664:0.3064:0.4272	.	1599	Q9BXP8	PAPP2_HUMAN	S	1599	ENSP00000356634:P1599S	ENSP00000356634:P1599S	P	+	1	0	PAPPA2	175025647	0.036000	0.19791	0.732000	0.30844	0.778000	0.44026	-0.006000	0.12833	0.062000	0.16340	-0.484000	0.04775	CCT	-	HMMSmart_SM00032,superfamily_Complement control module/SCR domain		0.478	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PAPPA2	protein_coding	OTTHUMT00000084763.1	C			175025647	+1	no_errors	NM_020318.2	genbank	human	validated	54_36p	missense	SNP	0.691	T
NAV1	89796	genome.wustl.edu	37	1	201777192	201777192	+	Missense_Mutation	SNP	C	C	G			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr1:201777192C>G	ENST00000367296.4	+	18	4180	c.3760C>G	c.(3760-3762)Ccc>Gcc	p.P1254A	MIR1231_ENST00000408101.1_RNA|NAV1_ENST00000367297.4_Missense_Mutation_p.P1246A|NAV1_ENST00000367302.1_Missense_Mutation_p.P1207A|IPO9-AS1_ENST00000413035.1_RNA|NAV1_ENST00000295624.6_Missense_Mutation_p.P1251A|NAV1_ENST00000367300.3_Missense_Mutation_p.P1194A|NAV1_ENST00000367295.1_Missense_Mutation_p.P860A	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	1254					microtubule bundle formation (GO:0001578)|neuron migration (GO:0001764)	cytoplasm (GO:0005737)|microtubule (GO:0005874)		p.P1251A(1)		breast(5)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(29)|ovary(4)|prostate(3)|skin(1)|stomach(2)	70						CCCCTCATCCCCCAAACTACA	0.517																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	1											135.0	134.0	134.0					1																	201777192		2203	4300	6503	200043815	SO:0001583	missense	0			AF086348	CCDS1414.1, CCDS1414.2, CCDS53456.1	1q32.3	2008-07-18			ENSG00000134369	ENSG00000134369			15989	protein-coding gene	gene with protein product	"""neuron navigator-1"", ""pore membrane and/or filament interacting like protein 3"""	611628				12079279, 12062803	Standard	NM_020443		Approved	FLJ12560, FLJ14203, KIAA1151, MGC14961, POMFIL3, steerin-1, DKFZp781D0314	uc001gwu.3	Q8NEY1	OTTHUMG00000035766	ENST00000367296.4:c.3760C>G	1.37:g.201777192C>G	ENSP00000356265:p.Pro1254Ala	1948	0.00	0		NA	NA	NA	200043815	728	31.71	339	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Missense_Mutation	SNP	HMMSmart_AAA,PatternScan_PPASE,superfamily_SSF52540	p.P1251A	ENST00000367296.4	37	c.3751	CCDS1414.2	1	.	.	.	.	.	.	.	.	.	.	c	20.5	4.005888	0.74932	.	.	ENSG00000134369	ENST00000367302;ENST00000367296;ENST00000295624;ENST00000367297;ENST00000367300;ENST00000367295	D;D;D;D;D;D	0.94000	-3.33;-3.33;-3.33;-3.33;-3.33;-3.33	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	D	0.96741	0.8936	M	0.76838	2.35	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	D	0.97130	0.9817	10	0.87932	D	0	-35.5464	18.8431	0.92192	0.0:1.0:0.0:0.0	.	860;1251	Q8NEY1-5;Q8NEY1-3	.;.	A	1207;1254;1251;1246;1194;860	ENSP00000356271:P1207A;ENSP00000356265:P1254A;ENSP00000295624:P1251A;ENSP00000356266:P1246A;ENSP00000356269:P1194A;ENSP00000356264:P860A	ENSP00000295624:P1251A	P	+	1	0	NAV1	200043815	1.000000	0.71417	1.000000	0.80357	0.256000	0.26092	7.809000	0.86057	2.538000	0.85594	0.552000	0.68991	CCC	-	NULL		0.517	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NAV1	protein_coding	OTTHUMT00000087013.1	C	NM_020443		200043815	+1	no_errors	NM_020443.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	G
ABCG8	64241	genome.wustl.edu	37	2	44079555	44079555	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr2:44079555G>A	ENST00000272286.2	+	5	714	c.624G>A	c.(622-624)atG>atA	p.M208I		NM_022437.2	NP_071882.1	Q9H221	ABCG8_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 8	208	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|phospholipid transport (GO:0015914)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein heterodimerization activity (GO:0046982)|sterol transporter activity (GO:0015248)	p.M208I(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(21)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	TGGGCAACATGTACGTGCGGG	0.672																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	2											35.0	39.0	37.0					2																	44079555		2203	4300	6503	43933059	SO:0001583	missense	0			AF320294	CCDS1815.1	2p21	2012-03-14	2008-07-31		ENSG00000143921	ENSG00000143921		"""ATP binding cassette transporters / subfamily G"""	13887	protein-coding gene	gene with protein product	"""gallbladder disease 4"", ""sterolin 2"""	605460	"""ATP-binding cassette, sub-family G (WHITE), member 8 (sterolin 2)"""			11099417, 17626266	Standard	NM_022437		Approved	GBD4	uc002rtq.3	Q9H221	OTTHUMG00000128756	ENST00000272286.2:c.624G>A	2.37:g.44079555G>A	ENSP00000272286:p.Met208Ile	1027	0.00	0		NA	NA	NA	43933059	620	37.06	365	Q53QN8	Missense_Mutation	SNP	HMMPfam_ABC_tran,HMMPfam_ABC2_membrane,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.M208I	ENST00000272286.2	37	c.624	CCDS1815.1	2	.	.	.	.	.	.	.	.	.	.	G	5.439	0.266079	0.10294	.	.	ENSG00000143921	ENST00000272286	T	0.41400	1.0	5.11	-3.24	0.05094	ABC transporter-like (2);	1.890310	0.02274	N	0.068726	T	0.18551	0.0445	N	0.04508	-0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.06552	-1.0820	10	0.36615	T	0.2	.	1.5089	0.02492	0.2018:0.3547:0.2333:0.2102	.	208;208	Q9H221-2;Q9H221	.;ABCG8_HUMAN	I	208	ENSP00000272286:M208I	ENSP00000272286:M208I	M	+	3	0	ABCG8	43933059	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.298000	0.08265	-0.815000	0.04346	0.561000	0.74099	ATG	-	HMMPfam_ABC_tran,superfamily_P-loop containing nucleoside triphosphate hydrolases		0.672	ABCG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ABCG8	protein_coding	OTTHUMT00000250671.1	G	NM_022437		43933059	+1	no_errors	NM_022437.2	genbank	human	reviewed	54_36p	missense	SNP	0.069	A
IL1R1	3554	genome.wustl.edu	37	2	102793205	102793205	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr2:102793205G>A	ENST00000410023.1	+	12	2014	c.1696G>A	c.(1696-1698)Gtg>Atg	p.V566M	IL1R1_ENST00000409929.1_Missense_Mutation_p.V535M|AC007271.3_ENST00000428188.1_RNA|IL1R1_ENST00000233946.3_Missense_Mutation_p.V566M|IL1R1_ENST00000409589.1_Intron|IL1R1_ENST00000424272.1_3'UTR			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I	566					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|interleukin-1-mediated signaling pathway (GO:0070498)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)|platelet-derived growth factor receptor binding (GO:0005161)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)	p.V566M(2)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(2)|skin(3)	19					Anakinra(DB00026)	AGAGGCTCACGTGCCTCTCGG	0.522																																						dbGAP											2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	2											80.0	81.0	81.0					2																	102793205		2202	4300	6502	102159637	SO:0001583	missense	0			M27492	CCDS2055.1, CCDS74547.1	2q12	2013-01-29			ENSG00000115594	ENSG00000115594		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5993	protein-coding gene	gene with protein product		147810		IL1R, IL1RA		1833184, 10191101	Standard	XM_005263929		Approved	D2S1473, CD121A	uc002tbr.3	P14778	OTTHUMG00000130783	ENST00000410023.1:c.1696G>A	2.37:g.102793205G>A	ENSP00000386380:p.Val566Met	1704	0.06	1		NA	NA	NA	102159637	985	32.67	478	Q587I7	Missense_Mutation	SNP	HMMPfam_TIR,HMMSmart_SM00255,superfamily_Toll/Interleukin receptor TIR domain,HMMSmart_SM00409,HMMPfam_ig,superfamily_Immunoglobulin	p.V566M	ENST00000410023.1	37	c.1696	CCDS2055.1	2	.	.	.	.	.	.	.	.	.	.	G	9.782	1.175469	0.21704	.	.	ENSG00000115594	ENST00000409929;ENST00000410023;ENST00000233946	T;T;T	0.02345	4.33;4.35;4.35	5.52	-4.89	0.03103	.	3.314520	0.00520	N	0.000189	T	0.02807	0.0084	L	0.44542	1.39	0.09310	N	1	B;B	0.19073	0.033;0.009	B;B	0.08055	0.003;0.003	T	0.43065	-0.9414	10	0.49607	T	0.09	.	1.2151	0.01913	0.3211:0.2862:0.2584:0.1343	.	535;566	B8ZZW4;P14778	.;IL1R1_HUMAN	M	535;566;566	ENSP00000386776:V535M;ENSP00000386380:V566M;ENSP00000233946:V566M	ENSP00000233946:V566M	V	+	1	0	IL1R1	102159637	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	-0.679000	0.05203	-0.923000	0.03785	-1.289000	0.01358	GTG	-	NULL		0.522	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IL1R1	protein_coding	OTTHUMT00000253299.1	G			102159637	+1	no_errors	NM_000877.2	genbank	human	reviewed	54_36p	missense	SNP	0.000	A
LRP1B	53353	genome.wustl.edu	37	2	141083356	141083356	+	Silent	SNP	T	T	C			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr2:141083356T>C	ENST00000389484.3	-	80	13286	c.12315A>G	c.(12313-12315)tcA>tcG	p.S4105S		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4105					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.S4105S(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CAGAGACTACTGAATTAGAGC	0.363										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)	dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	2											111.0	100.0	103.0					2																	141083356		2203	4300	6503	140799826	SO:0001819	synonymous_variant	0			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.12315A>G	2.37:g.141083356T>C		1711	0.12	2		NA	NA	NA	140799826	1223	28.69	492	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	HMMPfam_Ldl_recept_b,HMMSmart_LY,PatternScan_ASX_HYDROXYL,HMMPfam_NHL,HMMSmart_EGF_CA,HMMPfam_Ldl_recept_a,HMMSmart_LDLa,PatternScan_LDLRA_1,superfamily_LDL_rcpt_classA_cys-rich,HMMPfam_EGF,HMMSmart_EGF,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,HMMPfam_EGF_2,PatternScan_EGF_CA,superfamily_SSF57196,superfamily_SSF63825	p.S4105	ENST00000389484.3	37	c.12315	CCDS2182.1	2	.	.	.	.	.	.	.	.	.	.	T	0.080	-1.186285	0.01620	.	.	ENSG00000168702	ENST00000437977	.	.	.	5.13	-2.66	0.06077	.	.	.	.	.	T	0.28433	0.0703	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.33369	-0.9871	4	.	.	.	.	6.8077	0.23786	0.3477:0.0:0.3577:0.2946	.	.	.	.	R	337	.	.	Q	-	2	0	LRP1B	140799826	0.884000	0.30299	0.000000	0.03702	0.007000	0.05969	-0.107000	0.10873	-0.337000	0.08426	-0.438000	0.05819	CAG	-	HMMPfam_Ldl_recept_b,HMMSmart_LY,superfamily_SSF63825		0.363	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LRP1B	protein_coding	OTTHUMT00000254736.2	T	NM_018557		140799826	-1	no_errors	NM_018557.2	genbank	human	validated	54_36p	silent	SNP	0.934	C
UGT1A10	54575	genome.wustl.edu	37	2	234545658	234545658	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr2:234545658C>T	ENST00000344644.5	+	1	559	c.490C>T	c.(490-492)Ccc>Tcc	p.P164S	UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000373445.1_Missense_Mutation_p.P164S	NM_019075.2	NP_061948.1	Q9HAW8	UD110_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A10	164					cellular glucuronidation (GO:0052695)|flavone metabolic process (GO:0051552)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)	p.P164S(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(2)|skin(3)	32		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0334)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;1.96e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000468)|Lung(119;0.00381)|LUSC - Lung squamous cell carcinoma(224;0.008)	Acetaminophen(DB00316)|Etodolac(DB00749)|Losartan(DB00678)|Mycophenolate mofetil(DB00688)|Valproic Acid(DB00313)	TTTCTCCCTCCCCTCTGTGGT	0.433																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	2											138.0	144.0	142.0					2																	234545658		2203	4300	6503	234210397	SO:0001583	missense	0			U39550	CCDS33403.1	2q37	2010-03-05	2005-07-20		ENSG00000242515	ENSG00000242515		"""UDP glucuronosyltransferases"""	12531	other	complex locus constituent		606435	"""UDP glycosyltransferase 1 family, polypeptide A10"""			9295054, 9325166	Standard	NM_019075		Approved	UGT1J		Q9HAW8	OTTHUMG00000059121	ENST00000344644.5:c.490C>T	2.37:g.234545658C>T	ENSP00000343838:p.Pro164Ser	420	0.24	1		NA	NA	NA	234210397	400	30.56	176	O00474|Q6NT91|Q7Z6H8	Missense_Mutation	SNP	HMMPfam_UDPGT,PatternScan_UDPGT,superfamily_UDP-Glycosyltransferase/glycogen phosphorylase	p.P164S	ENST00000344644.5	37	c.490	CCDS33403.1	2	.	.	.	.	.	.	.	.	.	.	C	16.11	3.029325	0.54790	.	.	ENSG00000242515	ENST00000344644;ENST00000373445	T;T	0.74002	-0.8;-0.8	3.52	3.52	0.40303	.	.	.	.	.	D	0.89136	0.6629	M	0.93375	3.41	0.40420	D	0.979832	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92840	0.6288	9	0.87932	D	0	.	15.6441	0.77033	0.0:1.0:0.0:0.0	.	164;164	Q9HAW8;Q7Z6H8	UD110_HUMAN;.	S	164	ENSP00000343838:P164S;ENSP00000362544:P164S	ENSP00000343838:P164S	P	+	1	0	UGT1A10	234210397	1.000000	0.71417	0.583000	0.28640	0.551000	0.35334	7.548000	0.82154	1.997000	0.58415	0.405000	0.27470	CCC	-	HMMPfam_UDPGT,superfamily_UDP-Glycosyltransferase/glycogen phosphorylase		0.433	UGT1A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	UGT1A10	protein_coding	OTTHUMT00000130986.1	C	NM_019075		234210397	+1	no_errors	NM_019075.2	genbank	human	reviewed	54_36p	missense	SNP	0.874	T
FAM19A4	151647	genome.wustl.edu	37	3	68802037	68802037	+	Missense_Mutation	SNP	C	C	T	rs148065010		TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr3:68802037C>T	ENST00000295569.7	-	4	755	c.263G>A	c.(262-264)cGg>cAg	p.R88Q		NM_001005527.2|NM_182522.4	NP_001005527.1|NP_872328.1	Q96LR4	F19A4_HUMAN	family with sequence similarity 19 (chemokine (C-C motif)-like), member A4	88						extracellular region (GO:0005576)		p.R88Q(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(5)|skin(2)	10		Lung NSC(201;0.0198)		BRCA - Breast invasive adenocarcinoma(55;1.38e-05)|Epithelial(33;0.000124)|LUSC - Lung squamous cell carcinoma(21;0.0248)|KIRC - Kidney renal clear cell carcinoma(39;0.0729)|Kidney(39;0.0904)		AGGTTGAGCCCGAGTTGTGCC	0.522																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	3						C	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	88.0	80.0	82.0		263,263	4.6	1.0	3	dbSNP_134	82	0,8600		0,0,4300	no	missense,missense	FAM19A4	NM_001005527.1,NM_182522.3	43,43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	88/141,88/141	68802037	1,13005	2203	4300	6503	68884727	SO:0001583	missense	0			AY325117	CCDS2907.1	3p14.1	2014-08-14			ENSG00000163377	ENSG00000163377			21591	protein-coding gene	gene with protein product						15028294, 25109685	Standard	NM_182522		Approved	TAFA-4	uc021xah.1	Q96LR4	OTTHUMG00000158744	ENST00000295569.7:c.263G>A	3.37:g.68802037C>T	ENSP00000295569:p.Arg88Gln	1486	0.00	0		NA	NA	NA	68884727	911	32.42	438	A8MVT2	Missense_Mutation	SNP	NULL	p.R88Q	ENST00000295569.7	37	c.263	CCDS2907.1	3	.	.	.	.	.	.	.	.	.	.	C	19.23	3.786908	0.70337	2.27E-4	0.0	ENSG00000163377	ENST00000295569	.	.	.	5.46	4.58	0.56647	.	0.000000	0.85682	D	0.000000	T	0.69575	0.3126	M	0.72894	2.215	0.38512	D	0.948503	B	0.30605	0.287	B	0.42138	0.377	T	0.73987	-0.3809	9	0.66056	D	0.02	-17.9842	14.5115	0.67791	0.0:0.9286:0.0:0.0714	.	88	Q96LR4	F19A4_HUMAN	Q	88	.	ENSP00000295569:R88Q	R	-	2	0	FAM19A4	68884727	0.946000	0.32159	0.999000	0.59377	0.337000	0.28794	4.906000	0.63293	1.274000	0.44362	0.591000	0.81541	CGG	-	NULL		0.522	FAM19A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM19A4	protein_coding	OTTHUMT00000352002.1	C	NM_182522		68884727	-1	no_errors	NM_001005527.1	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
MGLL	11343	genome.wustl.edu	37	3	127414007	127414007	+	Silent	SNP	C	C	T			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr3:127414007C>T	ENST00000434178.2	-	7	1493	c.597G>A	c.(595-597)ctG>ctA	p.L199L	MGLL_ENST00000453507.2_Silent_p.L179L|MGLL_ENST00000398101.3_Silent_p.L173L|MGLL_ENST00000398104.1_Silent_p.L199L|MGLL_ENST00000265052.5_Silent_p.L209L|MGLL_ENST00000476682.1_5'UTR			Q99685	MGLL_HUMAN	monoglyceride lipase	199					acylglycerol acyl-chain remodeling (GO:0036155)|acylglycerol catabolic process (GO:0046464)|arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|fatty acid biosynthetic process (GO:0006633)|glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|long term synaptic depression (GO:0060292)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|regulation of endocannabinoid signaling pathway (GO:2000124)|regulation of inflammatory response (GO:0050727)|regulation of sensory perception of pain (GO:0051930)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acylglycerol lipase activity (GO:0047372)|lipid binding (GO:0008289)|lysophospholipase activity (GO:0004622)|protein homodimerization activity (GO:0042803)	p.L199L(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6						CCCGGCAGATCAGGGGGTCTG	0.592																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	3											42.0	47.0	45.0					3																	127414007		2021	4180	6201	128896697	SO:0001819	synonymous_variant	0			BC000551	CCDS43148.1, CCDS46902.1, CCDS58852.1	3p13-q13.33	2014-03-14			ENSG00000074416	ENSG00000074416	3.1.1.23		17038	protein-coding gene	gene with protein product		609699				9495531	Standard	NM_007283		Approved	HU-K5, MGL	uc003ejx.4	Q99685	OTTHUMG00000159641	ENST00000434178.2:c.597G>A	3.37:g.127414007C>T		768	0.00	0		NA	NA	NA	128896697	414	30.30	180	B3KRC2|B7Z9D1|Q6IBG9|Q96AA5	Silent	SNP	HMMPfam_Abhydrolase_1,PatternScan_LIPASE_SER,superfamily_SSF53474	p.L209	ENST00000434178.2	37	c.627	CCDS43148.1	3																																																																																			-	HMMPfam_Abhydrolase_1,superfamily_SSF53474		0.592	MGLL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MGLL	protein_coding	OTTHUMT00000356637.2	C	NM_007283		128896697	-1	no_errors	NM_007283.1	genbank	human	validated	54_36p	silent	SNP	0.991	T
PLRG1	5356	genome.wustl.edu	37	4	155458482	155458482	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr4:155458482C>T	ENST00000499023.2	-	14	1567	c.1441G>A	c.(1441-1443)Gaa>Aaa	p.E481K	PLRG1_ENST00000302078.5_Missense_Mutation_p.E472K|PLRG1_ENST00000393905.2_Missense_Mutation_p.E481K	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	481					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)	p.E481K(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				TTATCAGCTTCAGCTGTTAGT	0.408																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	4											110.0	108.0	108.0					4																	155458482		2203	4300	6503	155677932	SO:0001583	missense	0			AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"""WD repeat domain containing"""	9089	protein-coding gene	gene with protein product	"""transport and golgi organization 4 homolog (Drosophila)"""	605961	"""pleiotropic regulator 1 (PRL1, Arabidopsis homolog)"", ""pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"""				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.1441G>A	4.37:g.155458482C>T	ENSP00000424417:p.Glu481Lys	1182	0.34	4		NA	NA	NA	155677932	688	32.28	328	B3KMK4|Q3KQY5|Q8WUD8	Missense_Mutation	SNP	HMMSmart_SM00320,superfamily_WD40 repeat-like,PatternScan_WD_REPEATS_1,HMMPfam_WD40	p.E481K	ENST00000499023.2	37	c.1441	CCDS34083.1	4	.	.	.	.	.	.	.	.	.	.	C	35	5.560531	0.96527	.	.	ENSG00000171566	ENST00000499023;ENST00000393905;ENST00000302078	T;T;T	0.81078	-1.45;-1.45;-1.45	5.59	5.59	0.84812	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.176286	0.64402	D	0.000010	D	0.93171	0.7825	H	0.95187	3.635	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.81914	0.964;0.995	D	0.94538	0.7742	10	0.66056	D	0.02	-32.0772	19.5896	0.95503	0.0:1.0:0.0:0.0	.	472;481	O43660-2;O43660	.;PLRG1_HUMAN	K	481;481;472	ENSP00000424417:E481K;ENSP00000377483:E481K;ENSP00000303191:E472K	ENSP00000303191:E472K	E	-	1	0	PLRG1	155677932	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	7.818000	0.86416	2.632000	0.89209	0.585000	0.79938	GAA	-	HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40		0.408	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PLRG1	protein_coding	OTTHUMT00000364824.1	C	NM_002669		155677932	-1	no_errors	NM_002669.2	genbank	human	provisional	54_36p	missense	SNP	1.000	T
SLC26A2	1836	genome.wustl.edu	37	5	149357812	149357812	+	Silent	SNP	T	T	C			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr5:149357812T>C	ENST00000286298.4	+	2	865	c.597T>C	c.(595-597)aaT>aaC	p.N199N		NM_000112.3	NP_000103.2	P50443	S26A2_HUMAN	solute carrier family 26 (anion exchanger), member 2	199					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|ossification (GO:0001503)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)	p.N199N(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(1)|prostate(2)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			TGGTTTCAAATGGGAGCACAT	0.413																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	5											138.0	128.0	131.0					5																	149357812		2203	4300	6503	149338005	SO:0001819	synonymous_variant	0			U14528	CCDS4300.1	5q31-q34	2014-09-17	2013-07-18		ENSG00000155850	ENSG00000155850		"""Solute carriers"""	10994	protein-coding gene	gene with protein product		606718	"""solute carrier family 26 (sulfate transporter), member 2"""	DTD		7923357	Standard	NM_000112		Approved	DTDST	uc003lrh.3	P50443	OTTHUMG00000130054	ENST00000286298.4:c.597T>C	5.37:g.149357812T>C		1500	0.00	0		NA	NA	NA	149338005	675	30.98	303	A8K2U3|B2R6J1|Q6N051	Silent	SNP	HMMPfam_STAS,superfamily_STAS,HMMPfam_Sulfate_transp,PatternScan_SLC26A	p.N199	ENST00000286298.4	37	c.597	CCDS4300.1	5																																																																																			-	NULL		0.413	SLC26A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC26A2	protein_coding	OTTHUMT00000252333.2	T	NM_000112		149338005	+1	no_errors	NM_000112.3	genbank	human	reviewed	54_36p	silent	SNP	0.008	C
LRP4	4038	genome.wustl.edu	37	11	46905472	46905472	+	Silent	SNP	G	G	A			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr11:46905472G>A	ENST00000378623.1	-	19	2804	c.2562C>T	c.(2560-2562)atC>atT	p.I854I		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	854					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)	p.I854I(1)		breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		GGTTCTCCCAGATGAGTACTG	0.512																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	11											284.0	218.0	240.0					11																	46905472		2201	4299	6500	46862048	SO:0001819	synonymous_variant	0			AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.2562C>T	11.37:g.46905472G>A		1651	0.00	0		NA	NA	NA	46862048	826	29.57	348	B2RN39|Q4AC85|Q5KTZ5	Silent	SNP	HMMPfam_Ldl_recept_b,HMMSmart_SM00135,PatternScan_ASX_HYDROXYL,HMMSmart_SM00179,HMMPfam_Ldl_recept_a,HMMSmart_SM00192,PatternScan_LDLRA_1,superfamily_LDL receptor-like module,HMMPfam_EGF,HMMSmart_SM00181,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_EGF/Laminin,superfamily_YWTD domain	p.I854	ENST00000378623.1	37	c.2562	CCDS31478.1	11																																																																																			-	HMMPfam_Ldl_recept_b,HMMSmart_SM00135,superfamily_YWTD domain		0.512	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LRP4	protein_coding	OTTHUMT00000391133.1	G	NM_002334		46862048	-1	no_errors	NM_002334.2	genbank	human	validated	54_36p	silent	SNP	1.000	A
BICD1	636	genome.wustl.edu	37	12	32530523	32530523	+	Missense_Mutation	SNP	G	G	A	rs200603103		TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr12:32530523G>A	ENST00000281474.5	+	10	2993	c.2890G>A	c.(2890-2892)Gcc>Acc	p.A964T	BICD1_ENST00000548411.1_3'UTR	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	964					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)	p.A964T(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			CTCCCAGTGCGCCCCTCTCCA	0.547																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	12											172.0	144.0	154.0					12																	32530523		2203	4300	6503	32421790	SO:0001583	missense	0			U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"""Bicaudal D (Drosophila) homolog 1"""			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.2890G>A	12.37:g.32530523G>A	ENSP00000281474:p.Ala964Thr	758	0.26	2		NA	NA	NA	32421790	430	32.87	211	A8K2C3|F8W113|O43892|O43893	Missense_Mutation	SNP	HMMPfam_BicD	p.A964T	ENST00000281474.5	37	c.2890	CCDS8726.1	12	.	.	.	.	.	.	.	.	.	.	G	12.48	1.950156	0.34377	.	.	ENSG00000151746	ENST00000281474	T	0.48836	0.8	5.16	1.21	0.21127	.	0.717749	0.12085	N	0.500956	T	0.23886	0.0578	N	0.08118	0	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.04360	-1.0957	10	0.40728	T	0.16	.	5.0119	0.14317	0.2069:0.0:0.5391:0.254	.	964	Q96G01	BICD1_HUMAN	T	964	ENSP00000281474:A964T	ENSP00000281474:A964T	A	+	1	0	BICD1	32421790	1.000000	0.71417	0.601000	0.28877	0.974000	0.67602	2.240000	0.43088	-0.048000	0.13401	-0.225000	0.12378	GCC	-	NULL		0.547	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	BICD1	protein_coding	OTTHUMT00000403380.1	G	NM_001714		32421790	+1	no_errors	NM_001714.1	genbank	human	reviewed	54_36p	missense	SNP	0.995	A
NOS1	4842	genome.wustl.edu	37	12	117669802	117669802	+	Missense_Mutation	SNP	C	C	T	rs372660293		TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr12:117669802C>T	ENST00000338101.4	-	22	3476	c.3472G>A	c.(3472-3474)Gag>Aag	p.E1158K	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Missense_Mutation_p.E1124K			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)	p.E1124K(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		TTCTCCTTCTCGCTGGTAGCT	0.592																																					Esophageal Squamous(162;1748 2599 51982 52956)	dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	12						C	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	0,4278		0,0,2139	48.0	54.0	52.0		3472,2362,2362,3370	4.4	0.9	12		52	1,8499		0,1,4249	no	missense,missense,missense,missense	NOS1	NM_001204218.1,NM_001204214.1,NM_001204213.1,NM_000620.4	56,56,56,56	0,1,6388	TT,TC,CC		0.0118,0.0,0.0078	benign,benign,benign,benign	1158/1469,788/1099,788/1099,1124/1435	117669802	1,12777	2139	4250	6389	116154185	SO:0001583	missense	0				CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.3472G>A	12.37:g.117669802C>T	ENSP00000337459:p.Glu1158Lys	1929	0.05	1		NA	NA	NA	116154185	735	33.45	370		Missense_Mutation	SNP	HMMPfam_NAD_binding_1,HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like,HMMPfam_FAD_binding_1,HMMPfam_NO_synthase,PatternScan_NOS,superfamily_Nitric oxide (NO) synthase oxygenase domain,HMMPfam_Flavodoxin_1,superfamily_Riboflavin synthase domain-like,superfamily_Flavoproteins,superfamily_Ferredoxin reductase-like C-terminal NADP-linked domain	p.E1124K	ENST00000338101.4	37	c.3370	CCDS55890.1	12	.	.	.	.	.	.	.	.	.	.	C	14.27	2.483927	0.44147	0.0	1.18E-4	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.70749	-0.51;-0.51	4.45	4.45	0.53987	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain-3 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.101978	0.64402	D	0.000003	T	0.63177	0.2489	L	0.41079	1.255	0.80722	D	1	B	0.27594	0.182	B	0.22753	0.041	T	0.63523	-0.6618	10	0.45353	T	0.12	-35.581	17.257	0.87060	0.0:1.0:0.0:0.0	.	1124	P29475	NOS1_HUMAN	K	1019;1124;1124;1158	ENSP00000320758:E1124K;ENSP00000337459:E1158K	ENSP00000320758:E1124K	E	-	1	0	NOS1	116154185	1.000000	0.71417	0.945000	0.38365	0.016000	0.09150	7.651000	0.83577	2.313000	0.78055	0.305000	0.20034	GAG	-	HMMPfam_FAD_binding_1,superfamily_Riboflavin synthase domain-like		0.592	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NOS1	protein_coding	OTTHUMT00000268053.1	C			116154185	-1	no_errors	NM_000620.2	genbank	human	validated	54_36p	missense	SNP	1.000	T
TTLL5	23093	genome.wustl.edu	37	14	76232532	76232532	+	Silent	SNP	A	A	G			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr14:76232532A>G	ENST00000298832.9	+	20	2041	c.1836A>G	c.(1834-1836)agA>agG	p.R612R	TTLL5_ENST00000555422.1_3'UTR|TTLL5_ENST00000557636.1_Silent_p.R626R|TTLL5_ENST00000556893.1_Silent_p.R163R|TTLL5_ENST00000554510.1_Silent_p.R121R	NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	612					fertilization (GO:0009566)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)	p.R612R(1)		NS(2)|breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(3)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	50				BRCA - Breast invasive adenocarcinoma(234;0.029)		GATTTCTTAGAGAAAATCAAG	0.398																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	14											64.0	62.0	63.0					14																	76232532		2203	4300	6503	75302285	SO:0001819	synonymous_variant	0			AF107885	CCDS32124.1	14q24.3	2014-09-09	2005-07-29	2005-07-29	ENSG00000119685	ENSG00000119685		"""Tubulin tyrosine ligase-like family"""	19963	protein-coding gene	gene with protein product		612268	"""KIAA0998"""	KIAA0998		15890843	Standard	NM_015072		Approved		uc001xrx.3	Q6EMB2	OTTHUMG00000171611	ENST00000298832.9:c.1836A>G	14.37:g.76232532A>G		936	0.11	1		NA	NA	NA	75302285	705	30.75	313	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Silent	SNP	HMMPfam_TTL,superfamily_Glutathione synthetase ATP-binding domain-like	p.R612	ENST00000298832.9	37	c.1836	CCDS32124.1	14																																																																																			-	NULL		0.398	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TTLL5	protein_coding	OTTHUMT00000414453.1	A	NM_015072		75302285	+1	no_errors	NM_015072.3	genbank	human	validated	54_36p	silent	SNP	0.056	G
RNF111	54778	genome.wustl.edu	37	15	59368279	59368279	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr15:59368279C>T	ENST00000557998.1	+	7	2100	c.1813C>T	c.(1813-1815)Cag>Tag	p.Q605*	RNF111_ENST00000434298.1_Nonsense_Mutation_p.Q605*|RNF111_ENST00000561186.1_Nonsense_Mutation_p.Q605*|RNF111_ENST00000559209.1_Nonsense_Mutation_p.Q605*|RNF111_ENST00000348370.4_Nonsense_Mutation_p.Q605*	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	605					gene expression (GO:0010467)|pattern specification process (GO:0007389)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.Q605*(1)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		CTTTGGCCATCAGGCCGCTGC	0.557																																					NSCLC(72;983 1365 10746 34387 47081)	dbGAP											1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	15											90.0	87.0	88.0					15																	59368279		2192	4291	6483	57155571	SO:0001587	stop_gained	0			AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"""RING-type (C3HC4) zinc fingers"""	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.1813C>T	15.37:g.59368279C>T	ENSP00000452732:p.Gln605*	941	0.00	0		NA	NA	NA	57155571	523	29.53	220	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Nonsense_Mutation	SNP	HMMSmart_SM00184,HMMPfam_zf-C3HC4,superfamily_RING/U-box	p.Q605*	ENST00000557998.1	37	c.1813	CCDS58366.1	15	.	.	.	.	.	.	.	.	.	.	C	43	10.212615	0.99360	.	.	ENSG00000157450	ENST00000348370;ENST00000434298	.	.	.	5.66	5.66	0.87406	.	0.111307	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-11.346	20.1225	0.97967	0.0:1.0:0.0:0.0	.	.	.	.	X	605	.	ENSP00000288199:Q605X	Q	+	1	0	RNF111	57155571	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.231000	0.78106	2.831000	0.97527	0.650000	0.86243	CAG	-	NULL		0.557	RNF111-003	KNOWN	basic|CCDS	protein_coding	RNF111	protein_coding	OTTHUMT00000416012.1	C	NM_017610		57155571	+1	no_errors	NM_017610.6	genbank	human	reviewed	54_36p	nonsense	SNP	1.000	T
PARP6	56965	genome.wustl.edu	37	15	72549766	72549766	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr15:72549766G>T	ENST00000569795.1	-	13	1609	c.922C>A	c.(922-924)Cgt>Agt	p.R308S	PARP6_ENST00000287196.9_Missense_Mutation_p.R308S|PARP6_ENST00000260376.7_Missense_Mutation_p.R308S|PARP6_ENST00000413097.2_5'UTR			Q2NL67	PARP6_HUMAN	poly (ADP-ribose) polymerase family, member 6	308							NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.R308S(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	18						CATAGTTCACGAGTACAGACA	0.527																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	15											129.0	137.0	134.0					15																	72549766		2056	4205	6261	70336820	SO:0001583	missense	0			AL390093	CCDS10241.2	15q22	2010-02-16			ENSG00000137817	ENSG00000137817		"""Poly (ADP-ribose) polymerases"""	26921	protein-coding gene	gene with protein product						15273990	Standard	XM_005254557		Approved	pART17	uc002auc.3	Q2NL67	OTTHUMG00000133443	ENST00000569795.1:c.922C>A	15.37:g.72549766G>T	ENSP00000456348:p.Arg308Ser	1316	0.75	10		NA	NA	NA	70336820	725	31.41	332	Q9H7C5|Q9H9X6|Q9HAF3|Q9NPS6|Q9UFG4	Missense_Mutation	SNP	HMMPfam_PARP,superfamily_ADP-ribosylation	p.R308S	ENST00000569795.1	37	c.922	CCDS10241.2	15	.	.	.	.	.	.	.	.	.	.	G	19.38	3.816504	0.70912	.	.	ENSG00000137817	ENST00000419739;ENST00000287196;ENST00000260376;ENST00000413097;ENST00000544520;ENST00000336471	.	.	.	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.74688	0.3749	L	0.54323	1.7	0.51012	D	0.999905	D;D;D	0.69078	0.981;0.995;0.997	P;D;P	0.70227	0.654;0.968;0.873	T	0.70916	-0.4742	9	0.30078	T	0.28	-43.6955	18.1578	0.89699	0.0:0.0:1.0:0.0	.	308;308;240	Q0VDG0;Q2NL67;A0PJ50	.;PARP6_HUMAN;.	S	308;308;308;153;153;308	.	ENSP00000260376:R308S	R	-	1	0	PARP6	70336820	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.230000	0.65321	2.533000	0.85409	0.650000	0.86243	CGT	-	NULL		0.527	PARP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PARP6	protein_coding	OTTHUMT00000257315.2	G	NM_020214		70336820	-1	no_errors	NM_020214.2	genbank	human	provisional	54_36p	missense	SNP	0.993	T
NAPA	8775	genome.wustl.edu	37	19	47995334	47995334	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr19:47995334C>T	ENST00000263354.3	-	8	903	c.604G>A	c.(604-606)Gcc>Acc	p.A202T	NAPA-AS1_ENST00000593284.1_RNA|NAPA-AS1_ENST00000594367.1_RNA|NAPA_ENST00000595227.1_Missense_Mutation_p.A163T	NM_003827.3	NP_003818.2	P54920	SNAA_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, alpha	202					apical protein localization (GO:0045176)|brain development (GO:0007420)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|neuron differentiation (GO:0030182)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of synaptic vesicle priming (GO:0010807)|SNARE complex disassembly (GO:0035494)|synaptic transmission, glutamatergic (GO:0035249)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)		p.A202T(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)	11		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000466)|all cancers(93;0.000739)|Epithelial(262;0.0168)|GBM - Glioblastoma multiforme(486;0.049)		TAGTCTTTGGCGCTGTACTTG	0.622																																					Ovarian(185;1135 2042 27703 31345 42493)	dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	19											206.0	166.0	180.0					19																	47995334		2203	4300	6503	52687146	SO:0001583	missense	0			U39412	CCDS12702.1	19q13.33	2012-08-16			ENSG00000105402	ENSG00000105402			7641	protein-coding gene	gene with protein product	"""alpha SNAP"""	603215				9269766	Standard	NM_003827		Approved		uc002pha.2	P54920		ENST00000263354.3:c.604G>A	19.37:g.47995334C>T	ENSP00000263354:p.Ala202Thr	1045	0.29	3		NA	NA	NA	52687146	566	26.64	207	A8K879|Q96IK3|Q9BVJ3	Missense_Mutation	SNP	HMMPfam_NSF,superfamily_TPR-like	p.A202T	ENST00000263354.3	37	c.604	CCDS12702.1	19	.	.	.	.	.	.	.	.	.	.	C	30	5.055522	0.93793	.	.	ENSG00000105402	ENST00000263354	T	0.34275	1.37	5.02	5.02	0.67125	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.56396	0.1982	M	0.88031	2.925	0.80722	D	1	D	0.59357	0.985	P	0.50082	0.63	T	0.66114	-0.6004	10	0.52906	T	0.07	-13.2717	17.2678	0.87092	0.0:1.0:0.0:0.0	.	202	P54920	SNAA_HUMAN	T	202	ENSP00000263354:A202T	ENSP00000263354:A202T	A	-	1	0	NAPA	52687146	1.000000	0.71417	1.000000	0.80357	0.767000	0.43475	7.350000	0.79385	2.616000	0.88540	0.511000	0.50034	GCC	-	superfamily_TPR-like		0.622	NAPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NAPA	protein_coding	OTTHUMT00000466048.2	C	NM_003827		52687146	-1	no_errors	NM_003827.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
KCNQ2	3785	genome.wustl.edu	37	20	62038564	62038564	+	Silent	SNP	G	G	T			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr20:62038564G>T	ENST00000359125.2	-	17	2226	c.2052C>A	c.(2050-2052)ggC>ggA	p.G684G	KCNQ2_ENST00000354587.3_Silent_p.G692G|KCNQ2_ENST00000370224.1_Silent_p.G692G|KCNQ2_ENST00000359689.1_Silent_p.G684G|KCNQ2_ENST00000360480.3_Silent_p.G656G|KCNQ2_ENST00000344462.4_Silent_p.G653G|KCNQ2_ENST00000357249.2_Silent_p.G666G	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	684					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.G684G(1)		biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	TGACAATGCAGCCGTGCCTGT	0.692																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	20											13.0	16.0	15.0					20																	62038564		2189	4282	6471	61509008	SO:0001819	synonymous_variant	0			AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.2052C>A	20.37:g.62038564G>T		163	0.00	0		NA	NA	NA	61509008	84	33.33	42	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Silent	SNP	HMMPfam_Ion_trans,HMMPfam_KCNQ_channel,superfamily_Voltage-gated potassium channels	p.G684	ENST00000359125.2	37	c.2052	CCDS13520.1	20																																																																																			-	NULL		0.692	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	KCNQ2	protein_coding	OTTHUMT00000080353.1	G	NM_172109		61509008	-1	no_errors	NM_172107.4	genbank	human	reviewed	54_36p	silent	SNP	1.000	T
JAM2	58494	genome.wustl.edu	37	21	27066149	27066149	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr21:27066149G>A	ENST00000480456.1	+	4	873	c.323G>A	c.(322-324)cGt>cAt	p.R108H	JAM2_ENST00000400532.1_Missense_Mutation_p.R108H|JAM2_ENST00000425221.2_Missense_Mutation_p.R72H|JAM2_ENST00000312957.5_Missense_Mutation_p.R108H	NM_001270407.1|NM_021219.3	NP_001257336.1|NP_067042.1	P57087	JAM2_HUMAN	junctional adhesion molecule 2	108	Ig-like V-type.				blood coagulation (GO:0007596)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.R108H(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(1)|stomach(1)|urinary_tract(1)	19						GGGAAATATCGTTGTGAAGTT	0.403																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	21											176.0	181.0	180.0					21																	27066149		2013	4158	6171	25988020	SO:0001583	missense	0			AF255910	CCDS42911.1, CCDS58787.1, CCDS58788.1	21q21.2	2013-01-11			ENSG00000154721	ENSG00000154721		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	14686	protein-coding gene	gene with protein product		606870		C21orf43		10779521, 10945976	Standard	NM_021219		Approved	VE-JAM, JAM-B, JAMB, CD322	uc031rvc.1	P57087	OTTHUMG00000078441	ENST00000480456.1:c.323G>A	21.37:g.27066149G>A	ENSP00000420419:p.Arg108His	1121	0.09	1		NA	NA	NA	25988020	710	33.46	357	B2R6T9|B4DGT9|Q6UXG6|Q6YNC1	Missense_Mutation	SNP	HMMSmart_IGc2,HMMSmart_IG,HMMPfam_V-set,HMMPfam_ig,superfamily_SSF48726	p.R108H	ENST00000480456.1	37	c.323	CCDS42911.1	21	.	.	.	.	.	.	.	.	.	.	G	24.7	4.562852	0.86335	.	.	ENSG00000154721	ENST00000480456;ENST00000400533;ENST00000400532;ENST00000400537;ENST00000312957;ENST00000425221	T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15	5.56	5.56	0.83823	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.77565	0.4149	M	0.68952	2.095	0.54753	D	0.999985	D;D;D;D;D	0.89917	0.997;1.0;0.999;1.0;0.997	P;D;D;D;P	0.91635	0.864;0.973;0.932;0.999;0.898	T	0.76353	-0.2990	10	0.48119	T	0.1	.	16.5363	0.84373	0.0:0.0:1.0:0.0	.	72;108;108;108;108	B4DGT9;A8MQ45;A8MXS1;A8MTB0;P57087	.;.;.;.;JAM2_HUMAN	H	108;108;108;108;108;72	ENSP00000420419:R108H;ENSP00000383376:R108H;ENSP00000318416:R108H;ENSP00000392611:R72H	ENSP00000318416:R108H	R	+	2	0	JAM2	25988020	1.000000	0.71417	0.923000	0.36655	0.973000	0.67179	5.606000	0.67641	2.890000	0.99128	0.655000	0.94253	CGT	-	HMMSmart_IG,HMMPfam_V-set,superfamily_SSF48726		0.403	JAM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	JAM2	protein_coding	OTTHUMT00000171347.1	G			25988020	+1	no_errors	NM_021219.2	genbank	human	reviewed	54_36p	missense	SNP	0.994	A
CSMD1	64478	genome.wustl.edu	37	8	3000053	3000053	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	C	C	C	-	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr8:3000053delC	ENST00000520002.1	-	42	6733	c.6178delG	c.(6178-6180)gaafs	p.E2060fs	CSMD1_ENST00000602557.1_Frame_Shift_Del_p.E2060fs|CSMD1_ENST00000400186.3_Frame_Shift_Del_p.E2060fs|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000539096.1_Frame_Shift_Del_p.E2059fs|CSMD1_ENST00000537824.1_Frame_Shift_Del_p.E2059fs|CSMD1_ENST00000602723.1_Frame_Shift_Del_p.E2060fs|CSMD1_ENST00000542608.1_Frame_Shift_Del_p.E2059fs			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2060	CUB 12. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)		p.E1788fs*40(1)|p.E2059fs*40(1)		breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		ATGAGGGTTTCATGCGTTGTG	0.478																																						dbGAP											2	Deletion - Frameshift(2)	haematopoietic_and_lymphoid_tissue(2)	8											98.0	102.0	101.0					8																	3000053		1977	4163	6140	2987460	SO:0001589	frameshift_variant	0					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.6178delG	8.37:g.3000053delC	ENSP00000430733:p.Glu2060fs	709	0.00	0		NA	NA	NA	2987460	374	30.23	169	Q0H0J5|Q96QU9|Q96RM4	Frame_Shift_Del	DEL	HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_CUB,HMMSmart_SM00042,superfamily_Spermadhesin CUB domain,superfamily_Complement control module/SCR domain	p.N2061fs	ENST00000520002.1	37	c.6179		8																																																																																			-	NULL		0.478	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	CSMD1	protein_coding	OTTHUMT00000374500.2	C	NM_033225		2987460	-1	pseudogene:no_stop_codon:bad_bp_length_for_coding_region	NM_033225.4	genbank	human	validated	54_36p	frame_shift_del	DEL	0.975	-
WT1	7490	genome.wustl.edu	37	11	32417922	32417923	+	Frame_Shift_Ins	INS	-	-	TCGGGGCTAC			TCGA-AB-2905-03A-01D-0739-09	TCGA-AB-2905-11A-01D-0739-09	-	-	-	TCGGGGCTAC	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	ccdc0b99-43b9-465c-97cc-199fa22b7d06	d38f4cbf-101a-445d-adaf-b3803d5dcfc5	g.chr11:32417922_32417923insTCGGGGCTAC	ENST00000379079.2	-	7	766_767	c.493_494insGTAGCCCCGA	c.(493-495)actfs	p.T165fs	WT1_ENST00000530998.1_Frame_Shift_Ins_p.T148fs|WT1_ENST00000448076.3_Frame_Shift_Ins_p.T377fs|WT1_ENST00000332351.3_Frame_Shift_Ins_p.T377fs	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1	309					adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.T309fs*71(3)|p.T309fs*9(2)|p.T309fs*75(2)|p.L310fs*9(2)|p.L310fs*73(2)|p.T309fs*12(2)|p.R301fs*3(1)|p.A307fs*69(1)|p.P308fs*67(1)|p.A307fs*70(1)|p.T309fs*5(1)|p.T309fs*4(1)|p.?fs(1)|p.V300fs*6(1)|p.R301fs*73(1)|p.T309fs*74(1)|p.T309fs*73(1)|p.P308fs*9(1)|p.R302fs*12(1)|p.T309fs*11(1)	EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			CCGTACAAGAGTCGGGGCTACT	0.52			"""D, Mis, N, F, S"""	EWSR1	"""Wilms, desmoplastic small round cell tumor"""	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome																													dbGAP	yes	Rec	yes	"""Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"""	11	11p13	7490	Wilms tumour 1 gene		O	27	Insertion - Frameshift(12)|Deletion - Frameshift(8)|Complex - frameshift(7)	haematopoietic_and_lymphoid_tissue(24)|kidney(3)	11																																								32374499	SO:0001589	frameshift_variant	0	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"""Zinc fingers, C2H2-type"""	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000379079.2:c.484_493dupGTAGCCCCGA	11.37:g.32417923_32417932dupTCGGGGCTAC	ENSP00000368370:p.Thr165fs	NA	NA	NA		NA	NA	NA	32374498	NA	NA	NA	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Frame_Shift_Ins	INS	HMMPfam_WT1,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers	p.T377fs	ENST00000379079.2	37	c.1130_1129	CCDS55751.1	11																																																																																			-	HMMPfam_WT1		0.520	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	WT1	protein_coding	OTTHUMT00000095434.1	-	NM_000378		32374499	-1	no_errors	NM_024426.3	genbank	human	reviewed	54_36p	frame_shift_ins	INS	0.991:0.888	TCGGGGCTAC
