#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_EVS_AA	i_EVS_All	i_EVS_EA	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_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	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_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	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_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
ACTR2	10097	genome.wustl.edu	37	2	65455000	65455000	+	5'UTR	SNP	G	G	A			TCGA-AN-A0XT-01A-11D-A10G-09	TCGA-AN-A0XT-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	353d9161-95fd-4bec-abb7-859d9ee19785	447c5906-5e0a-48f1-acaf-80ea46081efd	g.chr2:65455000G>A	ENST00000260641.5	+	0	114				ACTR2_ENST00000377982.4_5'UTR|ACTR2_ENST00000542850.1_5'UTR|ACTR2_ENST00000476840.1_3'UTR	NM_005722.3	NP_005713.1	P61160	ARP2_HUMAN	ARP2 actin-related protein 2 homolog (yeast)						Arp2/3 complex-mediated actin nucleation (GO:0034314)|asymmetric cell division (GO:0008356)|cellular component movement (GO:0006928)|cilium assembly (GO:0042384)|cytoplasmic transport (GO:0016482)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|meiotic chromosome movement towards spindle pole (GO:0016344)|meiotic cytokinesis (GO:0033206)|spindle localization (GO:0051653)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)	12						GGGCGGCGGTGGCTGTAGGTT	0.687																																						dbGAP											0													10.0	12.0	11.0					2																	65455000		2106	4119	6225	-	-	-	SO:0001623	5_prime_UTR_variant	0			AF006082	CCDS1881.1, CCDS46307.1	2p14	2008-05-20	2001-11-28		ENSG00000138071	ENSG00000138071			169	protein-coding gene	gene with protein product		604221	"""ARP2 (actin-related protein 2, yeast) homolog"""			9230079	Standard	NM_001005386		Approved	ARP2	uc002sdp.3	P61160	OTTHUMG00000129540	ENST00000260641.5:c.-44G>A	2.37:g.65455000G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RCP5|D6W5F4|E9PF41|O15142|Q96C82	RNA	SNP	-	NULL	ENST00000260641.5	37	NULL	CCDS1881.1	2																																																																																			ACTR2	-	-	ENSG00000138071		0.687	ACTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ACTR2	HGNC	protein_coding	OTTHUMT00000251730.1	78	0.00	0	G	NM_001005386		65455000	65455000	+1	no_errors	ENST00000471552	ensembl	human	known	69_37n	rna	39	26.42	14	SNP	0.004	A
ADAMTS17	170691	genome.wustl.edu	37	15	100649205	100649205	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0XT-01A-11D-A10G-09	TCGA-AN-A0XT-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	353d9161-95fd-4bec-abb7-859d9ee19785	447c5906-5e0a-48f1-acaf-80ea46081efd	g.chr15:100649205C>T	ENST00000268070.4	-	14	2110	c.2005G>A	c.(2005-2007)Ggc>Agc	p.G669S		NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	669	Cys-rich.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		TGGCACTTGCCGTGCACGCAG	0.632																																						dbGAP											0													87.0	76.0	80.0					15																	100649205		2203	4300	6503	-	-	-	SO:0001583	missense	0			AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17109	protein-coding gene	gene with protein product		607511	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"""			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.2005G>A	15.37:g.100649205C>T	ENSP00000268070:p.Gly669Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	Q2I7G4|Q6ZN75	Missense_Mutation	SNP	pfam_Thrombospondin_1_rpt,pfam_Peptidase_M12B,pfam_Peptidase_M12B_N,pfam_ADAM_spacer1,pfam_PLAC,superfamily_Thrombospondin_1_rpt,smart_ADAM_Cys-rich,smart_Thrombospondin_1_rpt,pfscan_PLAC,pfscan_Thrombospondin_1_rpt,pfscan_Peptidase_M12B,prints_Peptidase_M12B_ADAM-TS	p.G669S	ENST00000268070.4	37	c.2005	CCDS10383.1	15	.	.	.	.	.	.	.	.	.	.	C	29.7	5.026514	0.93518	.	.	ENSG00000140470	ENST00000268070;ENST00000378898	T	0.63580	-0.05	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	D	0.86024	0.5834	H	0.96208	3.785	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.90694	0.4615	10	0.87932	D	0	.	17.6076	0.88042	0.0:1.0:0.0:0.0	.	426;669	Q8TE56-2;Q8TE56	.;ATS17_HUMAN	S	669;426	ENSP00000268070:G669S	ENSP00000268070:G669S	G	-	1	0	ADAMTS17	98466728	1.000000	0.71417	0.994000	0.49952	0.964000	0.63967	6.342000	0.72982	2.397000	0.81536	0.655000	0.94253	GGC	ADAMTS17	-	prints_Peptidase_M12B_ADAM-TS	ENSG00000140470		0.632	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ADAMTS17	HGNC	protein_coding	OTTHUMT00000313595.1	74	0.00	0	C	NM_139057		100649205	100649205	-1	no_errors	ENST00000268070	ensembl	human	known	69_37n	missense	30	37.50	18	SNP	1.000	T
COL6A2	1292	genome.wustl.edu	37	21	47549113	47549113	+	Intron	SNP	C	C	T			TCGA-AN-A0XT-01A-11D-A10G-09	TCGA-AN-A0XT-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	353d9161-95fd-4bec-abb7-859d9ee19785	447c5906-5e0a-48f1-acaf-80ea46081efd	g.chr21:47549113C>T	ENST00000300527.4	+	27	2565				COL6A2_ENST00000310645.5_3'UTR|COL6A2_ENST00000357838.4_Missense_Mutation_p.A822V|COL6A2_ENST00000409416.1_3'UTR|COL6A2_ENST00000397763.1_Missense_Mutation_p.A822V	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		CTTGCAGATGCACCGTGGCCT	0.667																																						dbGAP											0													51.0	56.0	55.0					21																	47549113		2203	4297	6500	-	-	-	SO:0001627	intron_variant	0			M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2461+2658C>T	21.37:g.47549113C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	pfam_VWF_A,pfam_Collagen,smart_VWF_A,pfscan_VWF_A	p.A822V	ENST00000300527.4	37	c.2465	CCDS13728.1	21	.	.	.	.	.	.	.	.	.	.	C	8.807	0.934209	0.18206	.	.	ENSG00000142173	ENST00000357838;ENST00000397763	D;D	0.89415	-2.51;-2.51	4.26	2.39	0.29439	.	.	.	.	.	T	0.78755	0.4333	.	.	.	0.80722	D	1	B	0.21905	0.062	B	0.25759	0.063	T	0.63005	-0.6733	8	0.17369	T	0.5	.	4.6223	0.12461	0.3015:0.1763:0.5222:0.0	.	822	P12110-2	.	V	822	ENSP00000350497:A822V;ENSP00000380870:A822V	ENSP00000350497:A822V	A	+	2	0	COL6A2	46373541	0.232000	0.23762	0.500000	0.27589	0.927000	0.56198	0.358000	0.20216	0.240000	0.21263	-0.499000	0.04595	GCA	COL6A2	-	NULL	ENSG00000142173		0.667	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL6A2	HGNC	protein_coding	OTTHUMT00000206971.1	18	0.00	0	C			47549113	47549113	+1	no_errors	ENST00000357838	ensembl	human	known	69_37n	missense	16	38.46	10	SNP	0.193	T
DHDH	27294	genome.wustl.edu	37	19	49438313	49438313	+	Silent	SNP	C	C	T			TCGA-AN-A0XT-01A-11D-A10G-09	TCGA-AN-A0XT-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	353d9161-95fd-4bec-abb7-859d9ee19785	447c5906-5e0a-48f1-acaf-80ea46081efd	g.chr19:49438313C>T	ENST00000221403.2	+	2	187	c.147C>T	c.(145-147)caC>caT	p.H49H	DHDH_ENST00000522614.1_Silent_p.H49H|DHDH_ENST00000523250.1_Silent_p.H49H	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	49					carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		CACAGAAACACGACATCCCCA	0.672																																						dbGAP											0													35.0	29.0	31.0					19																	49438313		2201	4295	6496	-	-	-	SO:0001819	synonymous_variant	0			AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.147C>T	19.37:g.49438313C>T		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	pfam_Oxidoreductase_N	p.H49	ENST00000221403.2	37	c.147	CCDS12741.1	19																																																																																			DHDH	-	pfam_Oxidoreductase_N	ENSG00000104808		0.672	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DHDH	HGNC	protein_coding	OTTHUMT00000381477.1	44	0.00	0	C	NM_014475		49438313	49438313	+1	no_errors	ENST00000221403	ensembl	human	known	69_37n	silent	21	46.15	18	SNP	0.108	T
AGO3	192669	genome.wustl.edu	37	1	36509128	36509128	+	Silent	SNP	C	C	T			TCGA-AN-A0XT-01A-11D-A10G-09	TCGA-AN-A0XT-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	353d9161-95fd-4bec-abb7-859d9ee19785	447c5906-5e0a-48f1-acaf-80ea46081efd	g.chr1:36509128C>T	ENST00000373191.4	+	17	2602	c.2253C>T	c.(2251-2253)ctC>ctT	p.L751L	AGO3_ENST00000471099.1_3'UTR|AGO3_ENST00000246314.6_Silent_p.L517L	NM_024852.3	NP_079128.2	Q9H9G7	AGO3_HUMAN	argonaute RISC catalytic component 3	751	Piwi. {ECO:0000255|HAMAP-Rule:MF_03032}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of stem cell proliferation (GO:0072091)	cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)										ATTTTTACCTCTGTAGCCATG	0.363																																						dbGAP											0													119.0	110.0	113.0					1																	36509128		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB046787	CCDS399.1, CCDS400.1	1p34	2013-06-03	2013-02-15	2013-02-15	ENSG00000126070	ENSG00000126070		"""Argonaute/PIWI family"""	18421	protein-coding gene	gene with protein product	"""argonaute 3"""	607355	"""eukaryotic translation initiation factor 2C, 3"""	EIF2C3		12906857	Standard	NM_024852		Approved	hAGO3, FLJ12765	uc001bzp.3	Q9H9G7	OTTHUMG00000184172	ENST00000373191.4:c.2253C>T	1.37:g.36509128C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B1ALI0|Q5TA55|Q9H1U6	Silent	SNP	pfam_Piwi,pfam_PAZ,pfam_DUF1785,superfamily_RNaseH-like_dom,superfamily_PAZ,smart_PAZ,smart_Piwi,pfscan_PAZ,pfscan_Piwi	p.L751	ENST00000373191.4	37	c.2253	CCDS399.1	1																																																																																			EIF2C3	-	pfam_Piwi,superfamily_RNaseH-like_dom,smart_Piwi,pfscan_Piwi	ENSG00000126070		0.363	AGO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	EIF2C3	HGNC	protein_coding	OTTHUMT00000019831.4	168	0.00	0	C	NM_024852		36509128	36509128	+1	no_errors	ENST00000373191	ensembl	human	known	69_37n	silent	119	43.87	93	SNP	1.000	T
FAM179A	165186	genome.wustl.edu	37	2	29259479	29259479	+	Missense_Mutation	SNP	G	G	A	rs535137926		TCGA-AN-A0XT-01A-11D-A10G-09	TCGA-AN-A0XT-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	353d9161-95fd-4bec-abb7-859d9ee19785	447c5906-5e0a-48f1-acaf-80ea46081efd	g.chr2:29259479G>A	ENST00000379558.4	+	18	2842	c.2491G>A	c.(2491-2493)Gcc>Acc	p.A831T	FAM179A_ENST00000465300.1_3'UTR|FAM179A_ENST00000403861.2_Missense_Mutation_p.A776T	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	831										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GGAGTCCTTCGCCAAGATGAT	0.498													g|||	1	0.000199681	0.0	0.0014	5008	,	,		19733	0.0		0.0	False		,,,				2504	0.0					dbGAP											0													125.0	105.0	111.0					2																	29259479		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.2491G>A	2.37:g.29259479G>A	ENSP00000368876:p.Ala831Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6ZUF5	Missense_Mutation	SNP	pfam_CLASP_N_dom,superfamily_ARM-type_fold	p.A831T	ENST00000379558.4	37	c.2491	CCDS1769.2	2	.	.	.	.	.	.	.	.	.	.	g	6.373	0.436969	0.12104	.	.	ENSG00000189350	ENST00000379558;ENST00000403861	T;T	0.14144	2.53;2.53	6.04	1.22	0.21188	Armadillo-like helical (1);Armadillo-type fold (1);	0.266535	0.32802	N	0.005625	T	0.08044	0.0201	L	0.50333	1.59	0.09310	N	1	B;B;P	0.36249	0.179;0.034;0.545	B;B;B	0.22386	0.024;0.003;0.039	T	0.34403	-0.9830	10	0.13853	T	0.58	.	6.7617	0.23544	0.1701:0.0:0.6081:0.2218	.	776;831;129	F8W8E4;Q6ZUX3;Q6ZUX3-3	.;F179A_HUMAN;.	T	831;776	ENSP00000368876:A831T;ENSP00000384699:A776T	ENSP00000368876:A831T	A	+	1	0	FAM179A	29112983	0.000000	0.05858	0.439000	0.26833	0.203000	0.24098	0.488000	0.22371	0.461000	0.27071	-0.217000	0.12591	GCC	FAM179A	-	superfamily_ARM-type_fold	ENSG00000189350		0.498	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	FAM179A	HGNC	protein_coding	OTTHUMT00000317848.4	166	0.00	0	G	NM_199280		29259479	29259479	+1	no_errors	ENST00000379558	ensembl	human	known	69_37n	missense	91	29.46	38	SNP	0.007	A
HTR5A	3361	genome.wustl.edu	37	7	154862859	154862859	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0XT-01A-11D-A10G-09	TCGA-AN-A0XT-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	353d9161-95fd-4bec-abb7-859d9ee19785	447c5906-5e0a-48f1-acaf-80ea46081efd	g.chr7:154862859G>A	ENST00000287907.2	+	1	826	c.250G>A	c.(250-252)Gtc>Atc	p.V84I	HTR5A-AS1_ENST00000543018.1_Missense_Mutation_p.T52M|HTR5A-AS1_ENST00000395731.2_Missense_Mutation_p.T52M|HTR5A-AS1_ENST00000493904.1_5'UTR	NM_024012.3	NP_076917.1	P47898	5HT5A_HUMAN	5-hydroxytryptamine (serotonin) receptor 5A, G protein-coupled	84					cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hippocampus development (GO:0021766)|response to estradiol (GO:0032355)|serotonin receptor signaling pathway (GO:0007210)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	serotonin receptor activity (GO:0004993)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(3)|stomach(1)	48	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0238)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)	Asenapine(DB06216)|Loxapine(DB00408)|Olanzapine(DB00334)	ATCCATGGCCGTCTCGGATGT	0.687																																						dbGAP											0													68.0	49.0	56.0					7																	154862859		2203	4299	6502	-	-	-	SO:0001583	missense	0				CCDS5936.1	7q36.1	2012-08-08	2012-02-03		ENSG00000157219	ENSG00000157219		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5300	protein-coding gene	gene with protein product		601305	"""5-hydroxytryptamine (serotonin) receptor 5A"""			7988681	Standard	NM_024012		Approved	5-HT5A	uc003wlu.2	P47898	OTTHUMG00000151327	ENST00000287907.2:c.250G>A	7.37:g.154862859G>A	ENSP00000287907:p.Val84Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	Q2M2D2	Missense_Mutation	SNP	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_7TM_GPCR_Rhodpsn,prints_5HT5A_rcpt,prints_5HT_rcpt	p.V84I	ENST00000287907.2	37	c.250	CCDS5936.1	7	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.46|11.46	1.645361|1.645361	0.29246|0.29246	.|.	.|.	ENSG00000220575|ENSG00000157219	ENST00000395731;ENST00000543018|ENST00000287907	.|T	.|0.37058	.|1.22	4.52|4.52	0.761|0.761	0.18448|0.18448	.|GPCR, rhodopsin-like superfamily (1);	.|0.051628	.|0.85682	.|N	.|0.000000	T|T	0.21631|0.21631	0.0521|0.0521	N|N	0.25426|0.25426	0.745|0.745	0.09310|0.09310	N|N	0.999998|0.999998	B|B	0.02656|0.06786	0.0|0.001	B|B	0.04013|0.11329	0.001|0.006	T|T	0.23048|0.23048	-1.0199|-1.0199	8|10	0.87932|0.18710	D|T	0|0.47	.|.	10.0867|10.0867	0.42423|0.42423	0.6454:0.0:0.3546:0.0|0.6454:0.0:0.3546:0.0	.|.	52|84	B7Z8E6|P47898	.|5HT5A_HUMAN	M|I	52|84	.|ENSP00000287907:V84I	ENSP00000379080:T52M|ENSP00000287907:V84I	T|V	-|+	2|1	0|0	AC093726.4|HTR5A	154493792|154493792	0.993000|0.993000	0.37304|0.37304	0.992000|0.992000	0.48379|0.48379	0.972000|0.972000	0.66771|0.66771	0.515000|0.515000	0.22801|0.22801	-0.273000|-0.273000	0.09246|0.09246	-0.360000|-0.360000	0.07572|0.07572	ACG|GTC	HTR5A	-	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_7TM_GPCR_Rhodpsn	ENSG00000157219		0.687	HTR5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HTR5A	HGNC	protein_coding	OTTHUMT00000322240.1	67	0.00	0	G	NM_024012		154862859	154862859	+1	no_errors	ENST00000287907	ensembl	human	known	69_37n	missense	26	53.57	30	SNP	1.000	A
LMBR1	64327	genome.wustl.edu	37	7	156619309	156619309	+	Silent	SNP	G	G	A			TCGA-AN-A0XT-01A-11D-A10G-09	TCGA-AN-A0XT-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	353d9161-95fd-4bec-abb7-859d9ee19785	447c5906-5e0a-48f1-acaf-80ea46081efd	g.chr7:156619309G>A	ENST00000353442.5	-	4	545	c.309C>T	c.(307-309)tcC>tcT	p.S103S	LMBR1_ENST00000540390.1_Silent_p.S82S|LMBR1_ENST00000354505.4_Silent_p.S103S	NM_022458.3	NP_071903.2	Q8WVP7	LMBR1_HUMAN	limb development membrane protein 1	103					embryonic digit morphogenesis (GO:0042733)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	18	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		CATGAATCAGGGAGCCATTTA	0.323																																						dbGAP											0													49.0	46.0	47.0					7																	156619309		2202	4296	6498	-	-	-	SO:0001819	synonymous_variant	0			AF107454	CCDS5945.1	7q36.3	2013-08-05	2013-08-05	2005-07-25	ENSG00000105983	ENSG00000105983			13243	protein-coding gene	gene with protein product		605522	"""chromosome 7 open reading frame 2"", ""limb region 1 homolog (mouse)"""	C7orf2		10329000, 11090342	Standard	NM_022458		Approved	ACHP, FLJ11665, ZRS	uc003wmw.4	Q8WVP7	OTTHUMG00000151510	ENST00000353442.5:c.309C>T	7.37:g.156619309G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A4D242|Q8N3E3|Q96QZ5|Q9H5N0|Q9HAG9|Q9UDN5|Q9Y6U2	Silent	SNP	pfam_LMBR1-like_membr_prot,prints_Lipcalin_1_rcpt	p.S103	ENST00000353442.5	37	c.309	CCDS5945.1	7																																																																																			LMBR1	-	pfam_LMBR1-like_membr_prot	ENSG00000105983		0.323	LMBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LMBR1	HGNC	protein_coding	OTTHUMT00000347939.3	116	0.00	0	G	NM_022458		156619309	156619309	-1	no_errors	ENST00000354505	ensembl	human	known	69_37n	silent	85	34.35	45	SNP	1.000	A
LPAR6	10161	genome.wustl.edu	37	13	48986180	48986180	+	Missense_Mutation	SNP	A	A	G			TCGA-AN-A0XT-01A-11D-A10G-09	TCGA-AN-A0XT-10A-01D-A10G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	353d9161-95fd-4bec-abb7-859d9ee19785	447c5906-5e0a-48f1-acaf-80ea46081efd	g.chr13:48986180A>G	ENST00000378434.4	-	7	2004	c.380T>C	c.(379-381)cTa>cCa	p.L127P	LPAR6_ENST00000345941.2_Missense_Mutation_p.L127P|RB1_ENST00000267163.4_Intron	NM_005767.5	NP_005758.2	P43657	LPAR6_HUMAN	lysophosphatidic acid receptor 6	127						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.0?(15)|p.?(4)		NS(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	14						TTTGGTTCTTAGAGTCTTTGA	0.418																																						dbGAP											19	Whole gene deletion(15)|Unknown(4)	bone(10)|breast(4)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)											38.0	38.0	38.0					13																	48986180		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF000546	CCDS9410.1	13q14	2012-08-08	2009-06-23	2009-06-23	ENSG00000139679	ENSG00000139679		"""GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"""	15520	protein-coding gene	gene with protein product		609239	"""purinergic receptor P2Y, G-protein coupled, 5"""	P2RY5		11004484, 9755289, 19386608	Standard	NM_005767		Approved	P2Y5	uc010acu.3	P43657	OTTHUMG00000016895	ENST00000378434.4:c.380T>C	13.37:g.48986180A>G	ENSP00000367691:p.Leu127Pro	Somatic		WXS	Illumina GAIIx	Phase_IV	A4FTW9|B3KVF2|F2YGU4|O15133|Q3KPF5|Q53FA0|Q5VW44|Q7Z3S0|Q7Z3S6	Missense_Mutation	SNP	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_P2Y5_purnocptor,prints_7TM_GPCR_Rhodpsn,prints_P2_purnocptor	p.L127P	ENST00000378434.4	37	c.380	CCDS9410.1	13	.	.	.	.	.	.	.	.	.	.	A	20.2	3.956092	0.73902	.	.	ENSG00000139679	ENST00000378434;ENST00000345941	T;T	0.73047	-0.71;-0.71	6.06	6.06	0.98353	GPCR, rhodopsin-like superfamily (1);	0.232564	0.35585	N	0.003120	T	0.80270	0.4592	L	0.52905	1.665	0.80722	D	1	D	0.60575	0.988	D	0.65874	0.939	T	0.78448	-0.2200	10	0.36615	T	0.2	.	16.6093	0.84858	1.0:0.0:0.0:0.0	.	127	P43657	LPAR6_HUMAN	P	127	ENSP00000367691:L127P;ENSP00000344353:L127P	ENSP00000344353:L127P	L	-	2	0	LPAR6	47884181	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.962000	0.93254	2.324000	0.78689	0.533000	0.62120	CTA	LPAR6	-	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam	ENSG00000139679		0.418	LPAR6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	LPAR6	HGNC	protein_coding	OTTHUMT00000276280.2	67	0.00	0	A	NM_005767		48986180	48986180	-1	no_errors	ENST00000345941	ensembl	human	known	69_37n	missense	18	58.14	25	SNP	0.985	G
FOXP1	27086	genome.wustl.edu	37	3	71591235	71591235	+	Intron	SNP	C	C	G			TCGA-AN-A0XT-01A-11D-A10G-09	TCGA-AN-A0XT-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	353d9161-95fd-4bec-abb7-859d9ee19785	447c5906-5e0a-48f1-acaf-80ea46081efd	g.chr3:71591235C>G	ENST00000318789.4	-	2	229				FOXP1_ENST00000318779.3_Intron|FOXP1_ENST00000493089.1_Intron|MIR1284_ENST00000408337.1_RNA|FOXP1_ENST00000475937.1_Intron	NM_001244810.1|NM_001244813.1|NM_032682.5	NP_001231739.1|NP_001231742.1|NP_116071.2	Q9H334	FOXP1_HUMAN	forkhead box P1						negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		GCTTATATATCAAAATCATGA	0.308			T	PAX5	ALL																																	dbGAP		Dom	yes		3	3p14.1	27086	forkhead box P1		L	0													20.0	19.0	19.0					3																	71591235		1565	3580	5145	-	-	-	SO:0001627	intron_variant	0			AF146696	CCDS2914.1, CCDS33785.1, CCDS58837.1, CCDS58838.1, CCDS58839.1, CCDS74963.1, CCDS74964.1	3p14.1	2008-07-18			ENSG00000114861	ENSG00000114861		"""Forkhead boxes"""	3823	protein-coding gene	gene with protein product	"""fork head-related protein like B"", ""glutamine-rich factor 1"", ""PAX5/FOXP1 fusion protein"""	605515				8265594, 11751404	Standard	NM_032682		Approved	QRF1, 12CC4, HSPC215, hFKH1B	uc003doj.3	Q9H334	OTTHUMG00000158803	ENST00000318789.4:c.296+39464G>C	3.37:g.71591235C>G		Somatic		WXS	Illumina GAIIx	Phase_IV	A3QVP8|B3KV70|G5E9V8|Q8NAN6|Q9BSG9|Q9H332|Q9H333|Q9P0R1	RNA	SNP	-	NULL	ENST00000318789.4	37	NULL	CCDS2914.1	3																																																																																			MIR1284	-	-	ENSG00000221264		0.308	FOXP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	MIR1284	HGNC	protein_coding	OTTHUMT00000352250.1	29	0.00	0	C	NM_032682		71591235	71591235	-1	no_errors	ENST00000408337	ensembl	human	known	69_37n	rna	25	35.90	14	SNP	1.000	G
PCSK5	5125	genome.wustl.edu	37	9	78790207	78790207	+	Intron	SNP	C	C	A	rs55947300|rs10124596|rs71372053	byFrequency	TCGA-AN-A0XT-01A-11D-A10G-09	TCGA-AN-A0XT-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	353d9161-95fd-4bec-abb7-859d9ee19785	447c5906-5e0a-48f1-acaf-80ea46081efd	g.chr9:78790207C>A	ENST00000545128.1	+	14	2438				PCSK5_ENST00000376767.3_Silent_p.R688R|PCSK5_ENST00000376752.4_Intron	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						cgaatcgaatcgaatagaata	0.343																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0				CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.1900+162C>A	9.37:g.78790207C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	F5H2G7|Q13527|Q96EP4	Silent	SNP	pfam_Peptidase_S8/S53,pfam_PrprotnconvertsP,superfamily_Peptidase_S8/S53,superfamily_Galactose-bd-like,superfamily_Prot_inh_propept,prints_Peptidase_S8_subtilisin-rel	p.R688	ENST00000545128.1	37	c.2062	CCDS55320.1	9	.	.	.	.	.	.	.	.	.	.	N	0.971	-0.700223	0.03279	.	.	ENSG00000099139	ENST00000396108	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	1.4193	0.02309	0.3429:0.3282:0.0:0.3289	rs10124596	.	.	.	X	686	.	ENSP00000379415:S686X	S	+	2	0	PCSK5	77980027	0.000000	0.05858	0.006000	0.13384	0.010000	0.07245	-3.492000	0.00453	-2.375000	0.00598	-2.399000	0.00225	TCG	PCSK5	-	NULL	ENSG00000099139		0.343	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	PCSK5	HGNC	protein_coding		10	0.00	0	C			78790207	78790207	+1	no_errors	ENST00000376767	ensembl	human	known	69_37n	silent	13	31.58	6	SNP	0.000	A
POLR2F	5435	genome.wustl.edu	37	22	38349806	38349806	+	Missense_Mutation	SNP	C	C	A			TCGA-AN-A0XT-01A-11D-A10G-09	TCGA-AN-A0XT-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	353d9161-95fd-4bec-abb7-859d9ee19785	447c5906-5e0a-48f1-acaf-80ea46081efd	g.chr22:38349806C>A	ENST00000442738.2	+	1	137	c.12C>A	c.(10-12)aaC>aaA	p.N4K	C22orf23_ENST00000249079.2_5'Flank|POLR2F_ENST00000488684.1_Missense_Mutation_p.N4K|RP5-1039K5.17_ENST00000609976.1_RNA|POLR2F_ENST00000606538.1_Missense_Mutation_p.N4K|POLR2F_ENST00000405557.1_Missense_Mutation_p.N4K|C22orf23_ENST00000403026.1_5'Flank|POLR2F_ENST00000460648.1_Missense_Mutation_p.N4K|POLR2F_ENST00000470701.1_5'UTR|POLR2F_ENST00000407936.1_Missense_Mutation_p.N4K|C22orf23_ENST00000403305.1_5'Flank	NM_021974.3	NP_068809.1	P61218	RPAB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide F	4					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of type I interferon production (GO:0032481)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase II, core complex (GO:0005665)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(1)|urinary_tract(2)	3	Melanoma(58;0.045)					TGTCAGACAACGAGGACAAGT	0.672																																						dbGAP											0													59.0	45.0	50.0					22																	38349806		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS13963.1	22q13.1	2013-01-21			ENSG00000100142	ENSG00000100142		"""RNA polymerase subunits"""	9193	protein-coding gene	gene with protein product	"""DNA directed RNA polymerase II 14.4 kda polypeptide"""	604414				8786150	Standard	XR_112241		Approved	RPB6, HRBP14.4	uc010gxi.3	P61218	OTTHUMG00000151160	ENST00000442738.2:c.12C>A	22.37:g.38349806C>A	ENSP00000403852:p.Asn4Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	P41584|Q6IAY3	Missense_Mutation	SNP	pfam_RNA_poly_omega/K/RPABC2,superfamily_RNA_poly_omega/K/RPABC2	p.N4K	ENST00000442738.2	37	c.12	CCDS13963.1	22	.	.	.	.	.	.	.	.	.	.	C	20.4	3.980661	0.74474	.	.	ENSG00000100142	ENST00000442738;ENST00000407936;ENST00000405557	.	.	.	5.19	1.96	0.26148	RNA polymerase subunit, RPB6/omega (1);	0.000000	0.85682	D	0.000000	T	0.59729	0.2215	L	0.36672	1.1	0.80722	D	1	D	0.53745	0.962	P	0.60012	0.867	T	0.55927	-0.8063	9	0.45353	T	0.12	.	10.4221	0.44356	0.0:0.787:0.0:0.213	.	4	P61218	RPAB2_HUMAN	K	4	.	ENSP00000384112:N4K	N	+	3	2	POLR2F	36679752	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.225000	0.42954	0.290000	0.22444	0.655000	0.94253	AAC	POLR2F	-	superfamily_RNA_poly_omega/K/RPABC2	ENSG00000100142		0.672	POLR2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	POLR2F	HGNC	protein_coding	OTTHUMT00000321570.1	84	0.00	0	C	NM_021974		38349806	38349806	+1	no_errors	ENST00000442738	ensembl	human	known	69_37n	missense	26	54.39	31	SNP	1.000	A
RPL4	6124	genome.wustl.edu	37	15	66795050	66795050	+	Silent	SNP	G	G	A	rs201003794		TCGA-AN-A0XT-01A-11D-A10G-09	TCGA-AN-A0XT-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	353d9161-95fd-4bec-abb7-859d9ee19785	447c5906-5e0a-48f1-acaf-80ea46081efd	g.chr15:66795050G>A	ENST00000307961.6	-	4	413	c.321C>T	c.(319-321)acC>acT	p.T107T	ZWILCH_ENST00000565627.1_5'Flank|SNORD18A_ENST00000363753.1_RNA|SNORD16_ENST00000362803.1_RNA|SNORD18C_ENST00000362704.1_RNA|ZWILCH_ENST00000535141.2_5'Flank|SNORD18B_ENST00000365659.1_RNA|RPL4_ENST00000568588.1_Silent_p.T13T|ZWILCH_ENST00000307897.5_5'Flank|ZWILCH_ENST00000446801.2_5'Flank|RPL4_ENST00000564517.1_5'Flank	NM_000968.3	NP_000959.2	P36578	RL4_HUMAN	ribosomal protein L4	107					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|stomach(1)|urinary_tract(1)	17						AACGGCGCCAGGTTTTGGTTG	0.453																																						dbGAP											0													118.0	108.0	112.0					15																	66795050		2201	4299	6500	-	-	-	SO:0001819	synonymous_variant	0			AB007167	CCDS10218.1	15q22	2011-04-06			ENSG00000174444	ENSG00000174444		"""L ribosomal proteins"""	10353	protein-coding gene	gene with protein product	"""60S ribosomal protein L4"""	180479				9582194, 8268230	Standard	NM_000968		Approved	L4	uc002apv.3	P36578	OTTHUMG00000133193	ENST00000307961.6:c.321C>T	15.37:g.66795050G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K502|P39029|Q4VBR0|Q969Z9	Silent	SNP	pfam_Ribosomal_L4/L1e,superfamily_Ribosomal_L4_dom	p.T107	ENST00000307961.6	37	c.321	CCDS10218.1	15																																																																																			RPL4	-	pfam_Ribosomal_L4/L1e,superfamily_Ribosomal_L4_dom	ENSG00000174444		0.453	RPL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RPL4	HGNC	protein_coding	OTTHUMT00000256903.2	229	0.00	0	G	NM_000968		66795050	66795050	-1	no_errors	ENST00000307961	ensembl	human	known	69_37n	silent	185	38.13	114	SNP	0.939	A
SKIDA1	387640	genome.wustl.edu	37	10	21805480	21805480	+	Silent	SNP	T	T	C	rs201836118		TCGA-AN-A0XT-01A-11D-A10G-09	TCGA-AN-A0XT-10A-01D-A10G-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	353d9161-95fd-4bec-abb7-859d9ee19785	447c5906-5e0a-48f1-acaf-80ea46081efd	g.chr10:21805480T>C	ENST00000449193.2	-	4	3524	c.1272A>G	c.(1270-1272)gaA>gaG	p.E424E	SKIDA1_ENST00000444772.3_Silent_p.E345E|SKIDA1_ENST00000487107.1_5'Flank	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	343						nucleus (GO:0005634)											cctcctcctcttcctcctcct	0.632																																						dbGAP											0													5.0	6.0	6.0					10																	21805480		2001	4121	6122	-	-	-	SO:0001819	synonymous_variant	0			AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 140"""	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.1272A>G	10.37:g.21805480T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	B1ANA5|Q6ZMX4|Q8N3C3	Silent	SNP	pfam_Transform_Ski,superfamily_DNA-bd_dom_put	p.E424	ENST00000449193.2	37	c.1272	CCDS44363.1	10																																																																																			SKIDA1	-	NULL	ENSG00000180592		0.632	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SKIDA1	HGNC	protein_coding	OTTHUMT00000286950.2	20	0.00	0	T	NM_207371		21805480	21805480	-1	no_errors	ENST00000449193	ensembl	human	known	69_37n	silent	20	23.08	6	SNP	0.381	C
TMED4	222068	genome.wustl.edu	37	7	44621754	44621754	+	Silent	SNP	G	G	A			TCGA-AN-A0XT-01A-11D-A10G-09	TCGA-AN-A0XT-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	353d9161-95fd-4bec-abb7-859d9ee19785	447c5906-5e0a-48f1-acaf-80ea46081efd	g.chr7:44621754G>A	ENST00000457408.2	-	1	104	c.52C>T	c.(52-54)Ctg>Ttg	p.L18L	TMED4_ENST00000289577.5_Silent_p.L18L|TMED4_ENST00000481238.1_Silent_p.L18L|TMED4_ENST00000444131.2_5'UTR	NM_182547.2	NP_872353.2	Q7Z7H5	TMED4_HUMAN	transmembrane emp24 protein transport domain containing 4	18					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein transport (GO:0015031)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)	6						GCGAGAAGCAGCAGGGCCTGC	0.677																																						dbGAP											0													14.0	13.0	13.0					7																	44621754		2111	4077	6188	-	-	-	SO:0001819	synonymous_variant	0			BC035467	CCDS5493.1	7p13	2004-12-21			ENSG00000158604	ENSG00000158604			22301	protein-coding gene	gene with protein product		612038				12761501	Standard	NM_182547		Approved	HNLF	uc003tli.3	Q7Z7H5	OTTHUMG00000129210	ENST00000457408.2:c.52C>T	7.37:g.44621754G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A4D2K8|B4DFJ4|Q56VW3|Q7Z432|Q8N2P6	Silent	SNP	pfam_GOLD,pfscan_GOLD	p.L18	ENST00000457408.2	37	c.52	CCDS5493.1	7																																																																																			TMED4	-	NULL	ENSG00000158604		0.677	TMED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TMED4	HGNC	protein_coding	OTTHUMT00000251290.1	14	0.00	0	G	NM_182547		44621754	44621754	-1	no_errors	ENST00000457408	ensembl	human	known	69_37n	silent	11	31.25	5	SNP	0.418	A
TP53	7157	genome.wustl.edu	37	17	7578555	7578555	+	Splice_Site	SNP	C	C	T			TCGA-AN-A0XT-01A-11D-A10G-09	TCGA-AN-A0XT-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	353d9161-95fd-4bec-abb7-859d9ee19785	447c5906-5e0a-48f1-acaf-80ea46081efd	g.chr17:7578555C>T	ENST00000269305.4	-	5	565		c.e5-1		TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000413465.2_Splice_Site|TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(39)|p.0?(8)|p.V73fs*9(1)|p.Y126fs*11(1)|p.P13fs*18(1)|p.T125_Y126insX(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CAGGGGAGTACTGTAGGAAGA	0.552		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	dbGAP	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	51	Unknown(39)|Whole gene deletion(8)|Deletion - Frameshift(3)|Insertion - In frame(1)	ovary(9)|pancreas(6)|bone(5)|upper_aerodigestive_tract(4)|liver(4)|lung(4)|breast(4)|large_intestine(3)|central_nervous_system(3)|oesophagus(3)|haematopoietic_and_lymphoid_tissue(2)|stomach(1)|endometrium(1)|urinary_tract(1)|autonomic_ganglia(1)											42.0	42.0	42.0					17																	7578555		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.376-1G>A	17.37:g.7578555C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	SNP	-	e4-1	ENST00000269305.4	37	c.376-1	CCDS11118.1	17	.	.	.	.	.	.	.	.	.	.	C	17.60	3.431133	0.62844	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000514944;ENST00000508793;ENST00000503591	.	.	.	4.87	3.9	0.45041	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4246	0.50003	0.0:0.9094:0.0:0.0906	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7519280	1.000000	0.71417	0.999000	0.59377	0.918000	0.54935	7.639000	0.83342	1.359000	0.45940	0.655000	0.94253	.	TP53	-	-	ENSG00000141510		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TP53	HGNC	protein_coding	OTTHUMT00000367397.1	92	0.00	0	C	NM_000546	Intron	7578555	7578555	-1	no_errors	ENST00000269305	ensembl	human	known	69_37n	splice_site	10	76.74	33	SNP	1.000	T
TREM1	54210	genome.wustl.edu	37	6	41243863	41243863	+	Silent	SNP	C	C	T			TCGA-AN-A0XT-01A-11D-A10G-09	TCGA-AN-A0XT-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	353d9161-95fd-4bec-abb7-859d9ee19785	447c5906-5e0a-48f1-acaf-80ea46081efd	g.chr6:41243863C>T	ENST00000244709.4	-	4	768	c.705G>A	c.(703-705)taG>taA	p.*235*	TREM1_ENST00000589614.1_Intron|TREM1_ENST00000334475.6_3'UTR	NM_018643.3	NP_061113.1	Q9NP99	TREM1_HUMAN	triggering receptor expressed on myeloid cells 1	0					blood coagulation (GO:0007596)|chemokine metabolic process (GO:0050755)|cytokine secretion involved in immune response (GO:0002374)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|neutrophil mediated killing of gram-negative bacterium (GO:0070945)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			NS(1)|breast(2)|endometrium(2)|large_intestine(5)|lung(5)|skin(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					GTTCGTGGGCCTAGGGTACAA	0.527																																						dbGAP											0													148.0	126.0	133.0					6																	41243863		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF196329	CCDS4854.1, CCDS56427.1, CCDS59499.1	6p21.1	2013-01-11			ENSG00000124731	ENSG00000124731		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	17760	protein-coding gene	gene with protein product		605085				11922939, 10799849	Standard	NM_018643		Approved	TREM-1, CD354	uc003oqf.2	Q9NP99	OTTHUMG00000014674	ENST00000244709.4:c.705G>A	6.37:g.41243863C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B4DWG2|K7EJW1|Q53FL8|Q5T2C9|Q86YU1	Silent	SNP	pfam_Ig_V-set,smart_Ig_sub	p.*235	ENST00000244709.4	37	c.705	CCDS4854.1	6																																																																																			TREM1	-	NULL	ENSG00000124731		0.527	TREM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TREM1	HGNC	protein_coding	OTTHUMT00000040505.2	193	0.00	0	C	NM_018643		41243863	41243863	-1	no_errors	ENST00000244709	ensembl	human	known	69_37n	silent	120	32.58	58	SNP	0.022	T
TULP3	7289	genome.wustl.edu	37	12	3040249	3040249	+	Missense_Mutation	SNP	A	A	G			TCGA-AN-A0XT-01A-11D-A10G-09	TCGA-AN-A0XT-10A-01D-A10G-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	353d9161-95fd-4bec-abb7-859d9ee19785	447c5906-5e0a-48f1-acaf-80ea46081efd	g.chr12:3040249A>G	ENST00000448120.2	+	6	590	c.539A>G	c.(538-540)aAc>aGc	p.N180S	TULP3_ENST00000397132.2_Missense_Mutation_p.N180S|RNU7-166P_ENST00000459397.1_RNA	NM_003324.4	NP_003315.2	O75386	TULP3_HUMAN	tubby like protein 3	180				TSGSATAAQPADNL -> IPVLLLPPNQLITF (in Ref. 1; AAC95431). {ECO:0000305}.	anterior/posterior pattern specification (GO:0009952)|bone development (GO:0060348)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|central nervous system neuron differentiation (GO:0021953)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic neurocranium morphogenesis (GO:0048702)|G-protein coupled receptor signaling pathway (GO:0007186)|ganglion development (GO:0061548)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cilium (GO:0005929)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)			endometrium(1)|large_intestine(4)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			CCAGCTGATAACCTCCTGGGA	0.507																																						dbGAP											0													127.0	123.0	125.0					12																	3040249		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF045583	CCDS8519.1, CCDS53737.1	12p13	2014-02-21			ENSG00000078246	ENSG00000078246		"""Intraflagellar transport homologs"""	12425	protein-coding gene	gene with protein product		604730				9828123	Standard	NM_003324		Approved	TUBL3	uc001qlj.2	O75386	OTTHUMG00000168152	ENST00000448120.2:c.539A>G	12.37:g.3040249A>G	ENSP00000410051:p.Asn180Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	Missense_Mutation	SNP	pfam_Tubby_C,superfamily_Tubby_C-like,prints_Tubby_C,prints_Tubby_N	p.N180S	ENST00000448120.2	37	c.539	CCDS8519.1	12	.	.	.	.	.	.	.	.	.	.	A	8.476	0.858748	0.17178	.	.	ENSG00000078246	ENST00000228245;ENST00000542730;ENST00000448120;ENST00000397132	D;D	0.91945	-2.91;-2.94	5.58	-2.9	0.05648	Tubby, C-terminal (1);	1.237530	0.05148	N	0.495467	D	0.83566	0.5282	L	0.38175	1.15	0.09310	N	1	B;B;B	0.28933	0.021;0.021;0.228	B;B;B	0.24394	0.028;0.017;0.053	T	0.70407	-0.4880	10	0.07482	T	0.82	-2.351	6.2197	0.20675	0.3141:0.5181:0.0703:0.0975	.	37;180;180	B7Z1E7;O75386;F8WBZ9	.;TULP3_HUMAN;.	S	180;37;180;180	ENSP00000410051:N180S;ENSP00000380321:N180S	ENSP00000228245:N180S	N	+	2	0	TULP3	2910510	0.000000	0.05858	0.008000	0.14137	0.004000	0.04260	-0.196000	0.09532	-0.357000	0.08175	-0.250000	0.11733	AAC	TULP3	-	superfamily_Tubby_C-like	ENSG00000078246		0.507	TULP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	TULP3	HGNC	protein_coding	OTTHUMT00000398468.1	119	0.00	0	A	NM_003324		3040249	3040249	+1	no_errors	ENST00000228245	ensembl	human	known	69_37n	missense	90	45.78	76	SNP	0.000	G
