#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
AP1G2	8906	genome.wustl.edu	37	14	24032653	24032654	+	Frame_Shift_Ins	INS	-	-	C	rs572740402		TCGA-A8-A08X-01A-21W-A019-09	TCGA-A8-A08X-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	67c7d350-5c82-49b0-a7eb-6ca829ffcbc9	263fb74b-c2f8-4ad7-8b3e-0e02749d167e	g.chr14:24032653_24032654insC	ENST00000308724.5	-	13	2100_2101	c.1345_1346insG	c.(1345-1347)gccfs	p.A449fs	AP1G2_ENST00000556277.1_5'Flank|RP11-66N24.4_ENST00000553985.1_RNA|AP1G2_ENST00000397120.3_Frame_Shift_Ins_p.A449fs|RP11-66N24.3_ENST00000555968.1_RNA	NM_003917.2	NP_003908.1	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2 subunit	449					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	28	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)		TAGCTCCTGGGCCCCCCCAATC	0.609											OREG0022605	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											0										12,4252		0,12,2120						4.7	1.0			57	10,8244		0,10,4117	no	frameshift	AP1G2	NM_003917.2		0,22,6237	A1A1,A1R,RR		0.1212,0.2814,0.1757				22,12496				-	-	-	SO:0001589	frameshift_variant	0			AB015318	CCDS9602.1	14q11.2	2008-07-03			ENSG00000213983	ENSG00000213983			556	protein-coding gene	gene with protein product		603534				9733768, 9762922	Standard	XM_005268167		Approved	G2AD	uc001wkl.2	O75843	OTTHUMG00000028760	ENST00000308724.5:c.1346dupG	14.37:g.24032660_24032660dupC	ENSP00000312442:p.Ala449fs	Somatic	768	WXS	Illumina GAIIx	Phase_IV	D3DS51|O75504	Frame_Shift_Ins	INS	pfam_Clathrin/coatomer_adapt-like_N,pfam_Clathrin_a/b/g-adaptin_app_Ig,superfamily_ARM-type_fold,superfamily_Coatomer/clathrin_app_Ig-like,smart_Clathrin_a/b/g-adaptin_app_Ig,pirsf_AP1_complex_gsu,pfscan_Clathrin_g-adaptin_app	p.A449fs	ENST00000308724.5	37	c.1346_1345	CCDS9602.1	14																																																																																			AP1G2	-	pfam_Clathrin/coatomer_adapt-like_N,superfamily_ARM-type_fold,pirsf_AP1_complex_gsu	ENSG00000213983		0.609	AP1G2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	AP1G2	HGNC	protein_coding	OTTHUMT00000071812.4	44	0.00	0	-	NM_003917		24032653	24032654	-1	no_errors	ENST00000308724	ensembl	human	known	69_37n	frame_shift_ins	53	10.17	6	INS	1.000:0.996	C
DLC1	10395	genome.wustl.edu	37	8	12957977	12957977	+	Silent	SNP	G	G	A			TCGA-A8-A08X-01A-21W-A019-09	TCGA-A8-A08X-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	67c7d350-5c82-49b0-a7eb-6ca829ffcbc9	263fb74b-c2f8-4ad7-8b3e-0e02749d167e	g.chr8:12957977G>A	ENST00000276297.4	-	9	2278	c.1869C>T	c.(1867-1869)agC>agT	p.S623S	DLC1_ENST00000358919.2_Silent_p.S186S|DLC1_ENST00000512044.2_Silent_p.S220S|DLC1_ENST00000520226.1_Silent_p.S112S	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	623					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						AGGAGCAAACGCTGATGACGG	0.632																																						dbGAP											0													63.0	65.0	64.0					8																	12957977		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	2897	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 12"""	604258	"""deleted in liver cancer 1"""			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1869C>T	8.37:g.12957977G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	pfam_START_lipid-bd,pfam_RhoGAP_dom,pfam_SAM_2,superfamily_Rho_GTPase_activation_prot,smart_RhoGAP_dom,smart_START_lipid-bd,pfscan_START_lipid-bd,pfscan_RhoGAP_dom	p.S623	ENST00000276297.4	37	c.1869	CCDS5989.1	8																																																																																			DLC1	-	NULL	ENSG00000164741		0.632	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	DLC1	HGNC	protein_coding	OTTHUMT00000207632.2	69	0.00	0	G	NM_182643, NM_006094		12957977	12957977	-1	no_errors	ENST00000276297	ensembl	human	known	69_37n	silent	47	18.97	11	SNP	0.998	A
COX6C	1345	genome.wustl.edu	37	8	100899792	100899792	+	Missense_Mutation	SNP	C	C	A			TCGA-A8-A08X-01A-21W-A019-09	TCGA-A8-A08X-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	67c7d350-5c82-49b0-a7eb-6ca829ffcbc9	263fb74b-c2f8-4ad7-8b3e-0e02749d167e	g.chr8:100899792C>A	ENST00000520468.2	-	3	623	c.169G>T	c.(169-171)Gat>Tat	p.D57Y	COX6C_ENST00000520271.1_Missense_Mutation_p.D57Y|COX6C_ENST00000518171.1_Missense_Mutation_p.D57Y|COX6C_ENST00000517682.2_Missense_Mutation_p.D57Y|COX6C_ENST00000522940.1_Missense_Mutation_p.D57Y|COX6C_ENST00000523016.1_Missense_Mutation_p.D57Y|COX6C_ENST00000297564.2_Missense_Mutation_p.D57Y|COX6C_ENST00000524245.1_Missense_Mutation_p.D57Y	NM_004374.3	NP_004365.1	P09669	COX6C_HUMAN	cytochrome c oxidase subunit VIc	57					cellular metabolic process (GO:0044237)|generation of precursor metabolites and energy (GO:0006091)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)		HMGA2/COX6C(2)	liver(1)|lung(2)	3			all cancers(13;8.32e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			TTCATGACATCGTAGTTTCTG	0.343			T	HMGA2	uterine leiomyoma																																NSCLC(46;1123 1136 1705 23767 45086)	dbGAP		Dom	yes		8	8q22-q23	1345	cytochrome c oxidase subunit VIc		M	0													57.0	59.0	58.0					8																	100899792		2203	4298	6501	-	-	-	SO:0001583	missense	0			X13238	CCDS6284.1	8q22.2	2011-07-04			ENSG00000164919	ENSG00000164919	1.9.3.1	"""Mitochondrial respiratory chain complex / Complex IV"""	2285	protein-coding gene	gene with protein product		124090				10072584	Standard	NM_004374		Approved		uc003yiy.2	P09669	OTTHUMG00000164703	ENST00000520468.2:c.169G>T	8.37:g.100899792C>A	ENSP00000428895:p.Asp57Tyr	Somatic		WXS	Illumina GAIIx	Phase_IV	B2R4D7	Missense_Mutation	SNP	pfam_Cyt_c_oxidase_su6c,superfamily_Cyt_c_oxidase_su6c	p.D57Y	ENST00000520468.2	37	c.169	CCDS6284.1	8	.	.	.	.	.	.	.	.	.	.	C	13.06	2.125246	0.37533	.	.	ENSG00000164919	ENST00000520468;ENST00000297564;ENST00000520271;ENST00000517682;ENST00000524245;ENST00000522940;ENST00000518171;ENST00000523016	.	.	.	5.57	4.7	0.59300	.	0.000000	0.85682	D	0.000000	T	0.78672	0.4320	.	.	.	0.53688	D	0.999976	D	0.89917	1.0	D	0.87578	0.998	T	0.81311	-0.0990	8	0.87932	D	0	.	11.9291	0.52837	0.0:0.9178:0.0:0.0822	.	57	P09669	COX6C_HUMAN	Y	57	.	ENSP00000297564:D57Y	D	-	1	0	COX6C	100968968	1.000000	0.71417	1.000000	0.80357	0.001000	0.01503	4.014000	0.57145	1.365000	0.46057	-0.657000	0.03884	GAT	COX6C	-	pfam_Cyt_c_oxidase_su6c,superfamily_Cyt_c_oxidase_su6c	ENSG00000164919		0.343	COX6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COX6C	HGNC	protein_coding	OTTHUMT00000379834.3	95	0.00	0	C	NM_004374		100899792	100899792	-1	no_errors	ENST00000297564	ensembl	human	known	69_37n	missense	168	10.16	19	SNP	1.000	A
FCRL1	115350	genome.wustl.edu	37	1	157773658	157773658	+	Missense_Mutation	SNP	C	C	T			TCGA-A8-A08X-01A-21W-A019-09	TCGA-A8-A08X-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	67c7d350-5c82-49b0-a7eb-6ca829ffcbc9	263fb74b-c2f8-4ad7-8b3e-0e02749d167e	g.chr1:157773658C>T	ENST00000368176.3	-	3	363	c.296G>A	c.(295-297)aGg>aAg	p.R99K	FCRL1_ENST00000489998.1_5'UTR|FCRL1_ENST00000358292.3_Missense_Mutation_p.R99K|FCRL1_ENST00000491942.1_Missense_Mutation_p.R99K	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	99	Ig-like C2-type 1.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6)	42	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			CTGGGATCTCCTGCTCCTCAA	0.547																																					GBM(54;482 1003 11223 30131 35730)	dbGAP											0													117.0	98.0	105.0					1																	157773658		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC033690	CCDS1170.1, CCDS53382.1, CCDS53383.1	1q21-q22	2013-01-14			ENSG00000163534	ENSG00000163534		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18509	protein-coding gene	gene with protein product		606508				11493702, 11929751	Standard	NM_052938		Approved	FCRH1, IRTA5, IFGP1, CD307a	uc001frg.3	Q96LA6	OTTHUMG00000019398	ENST00000368176.3:c.296G>A	1.37:g.157773658C>T	ENSP00000357158:p.Arg99Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Missense_Mutation	SNP	pfam_Ig_I-set,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like	p.R99K	ENST00000368176.3	37	c.296	CCDS1170.1	1	.	.	.	.	.	.	.	.	.	.	C	5.817	0.334978	0.11013	.	.	ENSG00000163534	ENST00000358292;ENST00000368176;ENST00000491942	T;T;T	0.11277	2.79;2.79;2.79	4.55	-9.11	0.00711	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	4.466460	0.01291	N	0.010029	T	0.01592	0.0051	L	0.43923	1.385	0.09310	N	1	B;B;B	0.14805	0.007;0.004;0.011	B;B;B	0.16722	0.009;0.016;0.016	T	0.32268	-0.9913	10	0.14252	T	0.57	.	4.1991	0.10457	0.1348:0.0876:0.408:0.3696	.	99;99;99	Q96LA6-3;Q96LA6-2;Q96LA6	.;.;FCRL1_HUMAN	K	99	ENSP00000351039:R99K;ENSP00000357158:R99K;ENSP00000418130:R99K	ENSP00000351039:R99K	R	-	2	0	FCRL1	156040282	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.927000	0.00049	-4.282000	0.00059	-1.094000	0.02160	AGG	FCRL1	-	smart_Ig_sub,pfscan_Ig-like	ENSG00000163534		0.547	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	FCRL1	HGNC	protein_coding	OTTHUMT00000051401.1	168	0.00	0	C	NM_052938		157773658	157773658	-1	no_errors	ENST00000368176	ensembl	human	known	69_37n	missense	166	27.51	63	SNP	0.000	T
FNDC3A	22862	genome.wustl.edu	37	13	49712942	49712945	+	Splice_Site	DEL	GTAA	GTAA	-			TCGA-A8-A08X-01A-21W-A019-09	TCGA-A8-A08X-10A-01W-A021-09	GTAA	GTAA					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	67c7d350-5c82-49b0-a7eb-6ca829ffcbc9	263fb74b-c2f8-4ad7-8b3e-0e02749d167e	g.chr13:49712942_49712945delGTAA	ENST00000492622.2	+	7	1124		c.e7+1		FNDC3A_ENST00000398316.3_Splice_Site|FNDC3A_ENST00000541916.1_Splice_Site	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A						fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		CAAACCAGTGGTAAGTATCTTATG	0.221																																						dbGAP											0																																										-	-	-	SO:0001630	splice_region_variant	0			AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531		"""Fibronectin type III domain containing"""	20296	protein-coding gene	gene with protein product		615794	"""fibronectin type III domain containing 3"""	FNDC3			Standard	NM_001079673		Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.819+1GTAA>-	13.37:g.49712942_49712945delGTAA		Somatic		WXS	Illumina GAIIx	Phase_IV	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Splice_Site	DEL	-	e6+1	ENST00000492622.2	37	c.819+1_819+1	CCDS41886.1	13																																																																																			FNDC3A	-	-	ENSG00000102531		0.221	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	FNDC3A	HGNC	protein_coding	OTTHUMT00000354845.2	97	0.00	0	GTAA	NM_014923	Intron	49712942	49712945	+1	no_errors	ENST00000492622	ensembl	human	known	69_37n	splice_site_del	48	15.79	9	DEL	1.000:1.000:1.000:1.000	-
IL12RB1	3594	genome.wustl.edu	37	19	18186597	18186597	+	Missense_Mutation	SNP	G	G	A			TCGA-A8-A08X-01A-21W-A019-09	TCGA-A8-A08X-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	67c7d350-5c82-49b0-a7eb-6ca829ffcbc9	263fb74b-c2f8-4ad7-8b3e-0e02749d167e	g.chr19:18186597G>A	ENST00000600835.2	-	8	960	c.662C>T	c.(661-663)tCc>tTc	p.S221F	IL12RB1_ENST00000593993.2_Missense_Mutation_p.S221F|IL12RB1_ENST00000322153.7_Missense_Mutation_p.S221F			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	221	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						CTTGCTCCAGGAACTTCCTTG	0.597																																						dbGAP											0													64.0	64.0	64.0					19																	18186597		2203	4300	6503	-	-	-	SO:0001583	missense	0			U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.662C>T	19.37:g.18186597G>A	ENSP00000470788:p.Ser221Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Missense_Mutation	SNP	pfam_Fibronectin_type3,superfamily_Fibronectin_type3,smart_Fibronectin_type3,pfscan_Fibronectin_type3	p.S221F	ENST00000600835.2	37	c.662	CCDS54232.1	19	.	.	.	.	.	.	.	.	.	.	G	0.145	-1.097326	0.01843	.	.	ENSG00000096996	ENST00000430026;ENST00000322153	T;T	0.58506	0.33;0.33	4.49	0.91	0.19337	Immunoglobulin-like fold (1);	1.357460	0.05115	N	0.489595	T	0.33411	0.0862	N	0.08118	0	0.21290	N	0.999734	P;P;P	0.44380	0.834;0.654;0.744	B;B;B	0.42282	0.382;0.153;0.212	T	0.18903	-1.0322	10	0.11485	T	0.65	-4.9808	3.0519	0.06172	0.2464:0.0:0.4831:0.2705	.	221;221;221	P42701-2;P42701-3;P42701	.;.;I12R1_HUMAN	F	221	ENSP00000403103:S221F;ENSP00000314425:S221F	ENSP00000314425:S221F	S	-	2	0	IL12RB1	18047597	0.978000	0.34361	0.772000	0.31596	0.074000	0.17049	0.794000	0.26958	0.351000	0.24027	0.543000	0.68304	TCC	IL12RB1	-	superfamily_Fibronectin_type3	ENSG00000096996		0.597	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	IL12RB1	HGNC	protein_coding	OTTHUMT00000466525.3	33	0.00	0	G			18186597	18186597	-1	no_errors	ENST00000430026	ensembl	human	known	69_37n	missense	28	28.21	11	SNP	0.627	A
MAN2A1	4124	genome.wustl.edu	37	5	109091135	109091135	+	Silent	SNP	T	T	C			TCGA-A8-A08X-01A-21W-A019-09	TCGA-A8-A08X-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	67c7d350-5c82-49b0-a7eb-6ca829ffcbc9	263fb74b-c2f8-4ad7-8b3e-0e02749d167e	g.chr5:109091135T>C	ENST00000261483.4	+	5	1865	c.813T>C	c.(811-813)caT>caC	p.H271H		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	271					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		TTGAAGGACATCAGTGGCTGG	0.368																																						dbGAP											0													120.0	119.0	119.0					5																	109091135		2202	4300	6502	-	-	-	SO:0001819	synonymous_variant	0				CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"""golgi integral membrane protein 7"""	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.813T>C	5.37:g.109091135T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	Q16767	Silent	SNP	pfam_Glyco_hydro_38_core,pfam_Glyco_hydro_38_C,pfam_Glyco_hydro_38_cen_dom,superfamily_Glyco_hydro-type_carb-bd,superfamily_Glyco_hydro/deAcase_b/a-brl,smart_Glyco_hydro_38_cen_dom	p.H271	ENST00000261483.4	37	c.813	CCDS34209.1	5																																																																																			MAN2A1	-	pfam_Glyco_hydro_38_core,superfamily_Glyco_hydro/deAcase_b/a-brl	ENSG00000112893		0.368	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MAN2A1	HGNC	protein_coding	OTTHUMT00000370680.1	275	0.00	0	T			109091135	109091135	+1	no_errors	ENST00000261483	ensembl	human	known	69_37n	silent	125	21.88	35	SNP	1.000	C
PDS5B	23047	genome.wustl.edu	37	13	33233398	33233398	+	Missense_Mutation	SNP	A	A	T			TCGA-A8-A08X-01A-21W-A019-09	TCGA-A8-A08X-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	67c7d350-5c82-49b0-a7eb-6ca829ffcbc9	263fb74b-c2f8-4ad7-8b3e-0e02749d167e	g.chr13:33233398A>T	ENST00000315596.10	+	6	791	c.605A>T	c.(604-606)aAt>aTt	p.N202I		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	202					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		GTTTTAGTAAATCTGGTACCT	0.373																																						dbGAP											0													186.0	164.0	171.0					13																	33233398		1858	4097	5955	-	-	-	SO:0001583	missense	0			AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"""androgen-induced proliferation inhibitor"""	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.605A>T	13.37:g.33233398A>T	ENSP00000313851:p.Asn202Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Missense_Mutation	SNP	superfamily_ARM-type_fold	p.N202I	ENST00000315596.10	37	c.605	CCDS41878.1	13	.	.	.	.	.	.	.	.	.	.	A	26.3	4.722474	0.89298	.	.	ENSG00000083642	ENST00000315596;ENST00000421084	.	.	.	5.77	5.77	0.91146	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.76506	0.3997	M	0.72118	2.19	0.80722	D	1	D;P	0.69078	0.997;0.946	D;P	0.65874	0.939;0.595	T	0.74633	-0.3600	9	0.31617	T	0.26	-0.4042	16.3948	0.83586	1.0:0.0:0.0:0.0	.	202;202	Q9NTI5;Q9NTI5-3	PDS5B_HUMAN;.	I	202	.	ENSP00000313851:N202I	N	+	2	0	PDS5B	32131398	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.165000	0.94761	2.326000	0.78906	0.533000	0.62120	AAT	PDS5B	-	superfamily_ARM-type_fold	ENSG00000083642		0.373	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	PDS5B	HGNC	protein_coding	OTTHUMT00000044428.3	222	0.00	0	A	NM_015032		33233398	33233398	+1	no_errors	ENST00000315596	ensembl	human	known	69_37n	missense	164	24.42	53	SNP	1.000	T
PLEKHS1	79949	genome.wustl.edu	37	10	115540376	115540376	+	Missense_Mutation	SNP	A	A	G			TCGA-A8-A08X-01A-21W-A019-09	TCGA-A8-A08X-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	67c7d350-5c82-49b0-a7eb-6ca829ffcbc9	263fb74b-c2f8-4ad7-8b3e-0e02749d167e	g.chr10:115540376A>G	ENST00000354462.3	+	6	591	c.433A>G	c.(433-435)Atc>Gtc	p.I145V	PLEKHS1_ENST00000369309.1_Missense_Mutation_p.I229V|PLEKHS1_ENST00000361048.1_3'UTR|PLEKHS1_ENST00000369312.4_Missense_Mutation_p.I313V			Q5SXH7	PKHS1_HUMAN	pleckstrin homology domain containing, family S member 1	409																	AAAGCTTACCATCGGCAGGAT	0.403																																						dbGAP											0													116.0	110.0	112.0					10																	115540376		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK027190	CCDS7583.1, CCDS53580.1, CCDS53581.1	10q26.11	2013-01-11	2012-05-31	2012-05-31	ENSG00000148735	ENSG00000148735		"""Pleckstrin homology (PH) domain containing"""	26285	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 81"""	C10orf81		12477932	Standard	NM_024889		Approved	FLJ23537, bA211N11.2	uc001lat.2	Q5SXH7	OTTHUMG00000019074	ENST00000354462.3:c.433A>G	10.37:g.115540376A>G	ENSP00000346451:p.Ile145Val	Somatic		WXS	Illumina GAIIx	Phase_IV	A8KA02|B3KX00|B6EDE1|Q5SXH8|Q5SXI0|Q6ZQR5|Q8NE42|Q9H5D9	Missense_Mutation	SNP	NULL	p.I313V	ENST00000354462.3	37	c.937		10	.	.	.	.	.	.	.	.	.	.	A	14.74	2.625811	0.46840	.	.	ENSG00000148735	ENST00000369312;ENST00000369309;ENST00000354462	T;T;T	0.30448	1.53;1.53;1.53	5.49	4.35	0.52113	.	.	.	.	.	T	0.32852	0.0843	L	0.48362	1.52	0.27591	N	0.949266	P;P	0.46784	0.884;0.884	P;P	0.47162	0.54;0.54	T	0.12708	-1.0537	9	0.51188	T	0.08	.	8.4327	0.32769	0.9114:0.0:0.0886:0.0	.	409;395	Q5SXH7;Q5SXH7-2	CJ081_HUMAN;.	V	313;229;145	ENSP00000358318:I313V;ENSP00000358315:I229V;ENSP00000346451:I145V	ENSP00000346451:I145V	I	+	1	0	C10orf81	115530366	0.976000	0.34144	0.980000	0.43619	0.444000	0.32077	1.815000	0.38981	1.033000	0.39918	0.533000	0.62120	ATC	PLEKHS1	-	NULL	ENSG00000148735		0.403	PLEKHS1-002	KNOWN	basic	protein_coding	PLEKHS1	HGNC	protein_coding	OTTHUMT00000050431.2	133	0.00	0	A	NM_024889		115540376	115540376	+1	no_errors	ENST00000369312	ensembl	human	known	69_37n	missense	140	14.63	24	SNP	0.994	G
PLXNA3	55558	genome.wustl.edu	37	X	153688564	153688565	+	Frame_Shift_Ins	INS	-	-	G	rs375310385		TCGA-A8-A08X-01A-21W-A019-09	TCGA-A8-A08X-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	67c7d350-5c82-49b0-a7eb-6ca829ffcbc9	263fb74b-c2f8-4ad7-8b3e-0e02749d167e	g.chrX:153688564_153688565insG	ENST00000369682.3	+	2	216_217	c.41_42insG	c.(40-45)gtggggfs	p.VG14fs		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	14					axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)	p.A17fs*39(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TTCCTTGCCGTGGGGGGGGCCC	0.683																																						dbGAP											1	Insertion - Frameshift(1)	ovary(1)																																								-	-	-	SO:0001589	frameshift_variant	0			X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"""Plexins"""	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.49dupG	X.37:g.153688572_153688572dupG	ENSP00000358696:p.Val14fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5HY36	Frame_Shift_Ins	INS	pfam_Plexin_cytoplasmic_RasGAP_dom,pfam_Semaphorin/CD100_Ag,pfam_IPT_TIG_rcpt,pfam_Plexin_repeat,superfamily_Semaphorin/CD100_Ag,superfamily_Rho_GTPase_activation_prot,superfamily_Ig_E-set,superfamily_Plexin-like_fold,smart_Semaphorin/CD100_Ag,smart_Plexin-like,smart_IPT_TIG_rcpt,pfscan_Semaphorin/CD100_Ag	p.A17fs	ENST00000369682.3	37	c.41_42	CCDS14752.1	X																																																																																			PLXNA3	-	pfscan_Semaphorin/CD100_Ag	ENSG00000130827		0.683	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLXNA3	HGNC	protein_coding	OTTHUMT00000081634.1	16	0.00	0	-	NM_017514		153688564	153688565	+1	no_errors	ENST00000369682	ensembl	human	known	69_37n	frame_shift_ins	6	33.33	3	INS	0.001:0.006	G
POLE2	5427	genome.wustl.edu	37	14	50122403	50122403	+	Missense_Mutation	SNP	C	C	T			TCGA-A8-A08X-01A-21W-A019-09	TCGA-A8-A08X-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	67c7d350-5c82-49b0-a7eb-6ca829ffcbc9	263fb74b-c2f8-4ad7-8b3e-0e02749d167e	g.chr14:50122403C>T	ENST00000216367.5	-	11	1013	c.914G>A	c.(913-915)cGc>cAc	p.R305H	POLE2_ENST00000554396.1_Missense_Mutation_p.R305H|POLE2_ENST00000556584.1_5'UTR|POLE2_ENST00000539565.2_Missense_Mutation_p.R279H	NM_002692.3	NP_002683.2	P56282	DPOE2_HUMAN	polymerase (DNA directed), epsilon 2, accessory subunit	305					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	epsilon DNA polymerase complex (GO:0008622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	10	all_epithelial(31;0.0021)|Breast(41;0.0124)				Cladribine(DB00242)	AAACATTATGCGAAGTTTTTC	0.313																																						dbGAP											0													178.0	187.0	184.0					14																	50122403		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF025840	CCDS32073.1, CCDS55914.1, CCDS55915.1	14q21-q22	2012-05-18	2012-05-18		ENSG00000100479	ENSG00000100479		"""DNA polymerases"""	9178	protein-coding gene	gene with protein product	"""DNA polymerase epsilon subunit B"""	602670	"""polymerase (DNA directed), epsilon 2 (p59 subunit)"""			9405441, 9443964	Standard	NM_002692		Approved	DPE2	uc001wwu.3	P56282	OTTHUMG00000170813	ENST00000216367.5:c.914G>A	14.37:g.50122403C>T	ENSP00000216367:p.Arg305His	Somatic		WXS	Illumina GAIIx	Phase_IV	A0AV55|A4FU92|A4LBB7|A6NH58|B4DDE6|O43560	Missense_Mutation	SNP	pfam_DNA_pol_alpha/epsilon_bsu,pfam_DNA_pol_e_bsu_N,pirsf_DNA_pol_e_bsu	p.R305H	ENST00000216367.5	37	c.914	CCDS32073.1	14	.	.	.	.	.	.	.	.	.	.	C	9.949	1.219629	0.22373	.	.	ENSG00000100479	ENST00000216367;ENST00000539565;ENST00000554396	T;T;T	0.32988	1.43;1.43;1.43	5.71	3.2	0.36748	DNA polymerase alpha/epsilon, subunit B (1);	0.185748	0.56097	N	0.000024	T	0.20210	0.0486	L	0.33710	1.025	0.24812	N	0.992634	B;B;B	0.12630	0.002;0.006;0.001	B;B;B	0.13407	0.009;0.006;0.006	T	0.22521	-1.0214	10	0.20046	T	0.44	-5.8472	8.4911	0.33100	0.0:0.2494:0.0:0.7506	.	305;279;305	A4FU92;B4DDE6;P56282	.;.;DPOE2_HUMAN	H	305;279;305	ENSP00000216367:R305H;ENSP00000446313:R279H;ENSP00000451621:R305H	ENSP00000216367:R305H	R	-	2	0	POLE2	49192153	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	2.208000	0.42797	0.366000	0.24427	0.491000	0.48974	CGC	POLE2	-	pfam_DNA_pol_alpha/epsilon_bsu,pirsf_DNA_pol_e_bsu	ENSG00000100479		0.313	POLE2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	POLE2	HGNC	protein_coding	OTTHUMT00000410512.1	455	0.00	0	C	NM_002692		50122403	50122403	-1	no_errors	ENST00000216367	ensembl	human	known	69_37n	missense	281	14.85	49	SNP	0.996	T
SERPINE1	5054	genome.wustl.edu	37	7	100776989	100776989	+	Silent	SNP	G	G	A			TCGA-A8-A08X-01A-21W-A019-09	TCGA-A8-A08X-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	67c7d350-5c82-49b0-a7eb-6ca829ffcbc9	263fb74b-c2f8-4ad7-8b3e-0e02749d167e	g.chr7:100776989G>A	ENST00000223095.4	+	5	871	c.714G>A	c.(712-714)acG>acA	p.T238T	SERPINE1_ENST00000445463.2_Silent_p.T223T	NM_000602.4	NP_000593.1	P05121	PAI1_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1	238					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to lipopolysaccharide (GO:0071222)|chronological cell aging (GO:0001300)|defense response to Gram-negative bacterium (GO:0050829)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|gene expression (GO:0010467)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell-matrix adhesion (GO:2000098)|negative regulation of vascular wound healing (GO:0061044)|negative regulation of wound healing (GO:0061045)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of leukotriene production involved in inflammatory response (GO:0035491)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of receptor activity (GO:0010469)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)	20	Lung NSC(181;0.136)|all_lung(186;0.182)				Alteplase(DB00009)|Anistreplase(DB00029)|Drotrecogin alfa(DB00055)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)	AGTTCACCACGCCCGATGGCC	0.542																																						dbGAP											0													187.0	156.0	166.0					7																	100776989		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			M16006	CCDS5711.1	7q22.1	2014-02-18	2005-08-18		ENSG00000106366	ENSG00000106366		"""Serine (or cysteine) peptidase inhibitors"""	8583	protein-coding gene	gene with protein product	"""plasminogen activator inhibitor, type I"""	173360	"""serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1"""	PLANH1, PAI1		3097076, 2891140, 24172014	Standard	NM_000602		Approved	PAI	uc003uxt.4	P05121	OTTHUMG00000157107	ENST00000223095.4:c.714G>A	7.37:g.100776989G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z4S0|F8WD53	Silent	SNP	pfam_Sepin_dom,superfamily_Sepin_dom,smart_Sepin_dom	p.T238	ENST00000223095.4	37	c.714	CCDS5711.1	7																																																																																			SERPINE1	-	pfam_Sepin_dom,superfamily_Sepin_dom,smart_Sepin_dom	ENSG00000106366		0.542	SERPINE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SERPINE1	HGNC	protein_coding	OTTHUMT00000347458.1	143	0.00	0	G	NM_000602		100776989	100776989	+1	no_errors	ENST00000223095	ensembl	human	known	69_37n	silent	232	10.77	28	SNP	0.706	A
STAP1	26228	genome.wustl.edu	37	4	68449419	68449419	+	Splice_Site	SNP	G	G	C			TCGA-A8-A08X-01A-21W-A019-09	TCGA-A8-A08X-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	67c7d350-5c82-49b0-a7eb-6ca829ffcbc9	263fb74b-c2f8-4ad7-8b3e-0e02749d167e	g.chr4:68449419G>C	ENST00000265404.2	+	6	740	c.658G>C	c.(658-660)Gac>Cac	p.D220H	STAP1_ENST00000396225.1_Splice_Site_p.D220H	NM_012108.2	NP_036240.1	Q9ULZ2	STAP1_HUMAN	signal transducing adaptor family member 1	220	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)				NS(1)|large_intestine(1)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	12						GCAGGAGATAGAGTATGTTTA	0.408																																						dbGAP											0													53.0	53.0	53.0					4																	68449419		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0			AB023483	CCDS3515.1	4q13.2	2013-02-14	2007-08-09		ENSG00000035720	ENSG00000035720		"""SH2 domain containing"""	24133	protein-coding gene	gene with protein product	"""BCR downstream signaling 1"""	604298				10518561, 10679268	Standard	NM_012108		Approved	STAP-1, BRDG1	uc003hde.4	Q9ULZ2	OTTHUMG00000129304	ENST00000265404.2:c.659+1G>C	4.37:g.68449419G>C		Somatic		WXS	Illumina GAIIx	Phase_IV	B2R980	Missense_Mutation	SNP	pfam_SH2,smart_Pleckstrin_homology,smart_SH2,pfscan_Pleckstrin_homology,pfscan_SH2	p.D220H	ENST00000265404.2	37	c.658	CCDS3515.1	4	.	.	.	.	.	.	.	.	.	.	G	11.93	1.787095	0.31593	.	.	ENSG00000035720	ENST00000265404;ENST00000396225	T;T	0.44881	0.91;0.91	5.73	5.73	0.89815	SH2 motif (4);	0.341186	0.30602	N	0.009263	T	0.37839	0.1018	L	0.46741	1.465	0.36789	D	0.884742	B	0.13594	0.008	B	0.16289	0.015	T	0.29912	-0.9996	10	0.25106	T	0.35	-15.1224	15.3949	0.74784	0.0:0.0:1.0:0.0	.	220	Q9ULZ2	STAP1_HUMAN	H	220	ENSP00000265404:D220H;ENSP00000379527:D220H	ENSP00000265404:D220H	D	+	1	0	STAP1	68132014	0.999000	0.42202	1.000000	0.80357	0.811000	0.45836	2.875000	0.48491	2.699000	0.92147	0.655000	0.94253	GAC	STAP1	-	pfam_SH2,smart_SH2,pfscan_SH2	ENSG00000035720		0.408	STAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	STAP1	HGNC	protein_coding	OTTHUMT00000251434.1	59	0.00	0	G	NM_012108	Missense_Mutation	68449419	68449419	+1	no_errors	ENST00000265404	ensembl	human	known	69_37n	missense	20	28.57	8	SNP	1.000	C
SVIL	6840	genome.wustl.edu	37	10	29813441	29813441	+	Missense_Mutation	SNP	C	C	T			TCGA-A8-A08X-01A-21W-A019-09	TCGA-A8-A08X-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	67c7d350-5c82-49b0-a7eb-6ca829ffcbc9	263fb74b-c2f8-4ad7-8b3e-0e02749d167e	g.chr10:29813441C>T	ENST00000355867.4	-	14	3298	c.2546G>A	c.(2545-2547)cGc>cAc	p.R849H	SVIL_ENST00000535393.1_5'Flank|SVIL_ENST00000375398.2_Missense_Mutation_p.R849H|SVIL_ENST00000375400.3_Missense_Mutation_p.R423H	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	849					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				AGTTTGATAGCGAGCGTTCAT	0.478																																						dbGAP											0													167.0	154.0	159.0					10																	29813441		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.2546G>A	10.37:g.29813441C>T	ENSP00000348128:p.Arg849His	Somatic		WXS	Illumina GAIIx	Phase_IV	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	pfam_Gelsolin_dom,pfam_Villin_headpiece,superfamily_Villin_headpiece,smart_Gelsolin,smart_Villin_headpiece,pfscan_Villin_headpiece,prints_Gelsolin	p.R849H	ENST00000355867.4	37	c.2546	CCDS7164.1	10	.	.	.	.	.	.	.	.	.	.	C	32	5.120604	0.94385	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867	T;T;T	0.63255	-0.03;-0.03;-0.03	5.82	5.82	0.92795	.	0.050626	0.85682	D	0.000000	T	0.80341	0.4605	M	0.75264	2.295	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.994	T	0.78871	-0.2033	9	.	.	.	-18.0089	20.093	0.97828	0.0:1.0:0.0:0.0	.	423;849	O95425-2;O95425	.;SVIL_HUMAN	H	423;849;849	ENSP00000364549:R423H;ENSP00000364547:R849H;ENSP00000348128:R849H	.	R	-	2	0	SVIL	29853447	1.000000	0.71417	0.992000	0.48379	0.711000	0.40976	7.395000	0.79876	2.756000	0.94617	0.561000	0.74099	CGC	SVIL	-	NULL	ENSG00000197321		0.478	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SVIL	HGNC	protein_coding	OTTHUMT00000047395.1	147	0.00	0	C			29813441	29813441	-1	no_errors	ENST00000355867	ensembl	human	known	69_37n	missense	166	19.81	41	SNP	1.000	T
TET3	200424	genome.wustl.edu	37	2	74275539	74275539	+	Splice_Site	SNP	G	G	A			TCGA-A8-A08X-01A-21W-A019-09	TCGA-A8-A08X-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	67c7d350-5c82-49b0-a7eb-6ca829ffcbc9	263fb74b-c2f8-4ad7-8b3e-0e02749d167e	g.chr2:74275539G>A	ENST00000409262.3	+	1	2089		c.e1+1			NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3						DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)			NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GATTGCGTCGGTAAGTCCGCC	0.552																																						dbGAP											0													34.0	40.0	38.0					2																	74275539		1969	4151	6120	-	-	-	SO:0001630	splice_region_variant	0				CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"""tet oncogene family member 3"""			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.2089+1G>A	2.37:g.74275539G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NEI3|Q86Z24|Q8TBM9	Splice_Site	SNP	-	e1+1	ENST00000409262.3	37	c.2089+1	CCDS46339.1	2	.	.	.	.	.	.	.	.	.	.	G	25.9	4.680586	0.88542	.	.	ENSG00000187605	ENST00000409262;ENST00000233310	.	.	.	5.28	5.28	0.74379	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.8577	0.88771	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TET3	74129047	1.000000	0.71417	0.998000	0.56505	0.952000	0.60782	9.263000	0.95617	2.746000	0.94184	0.655000	0.94253	.	TET3	-	-	ENSG00000187605		0.552	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	TET3	HGNC	protein_coding	OTTHUMT00000328141.4	39	0.00	0	G		Intron	74275539	74275539	+1	no_errors	ENST00000409262	ensembl	human	known	69_37n	splice_site	40	13.04	6	SNP	1.000	A
TEX13B	56156	genome.wustl.edu	37	X	107224730	107224730	+	Silent	SNP	G	G	A			TCGA-A8-A08X-01A-21W-A019-09	TCGA-A8-A08X-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	67c7d350-5c82-49b0-a7eb-6ca829ffcbc9	263fb74b-c2f8-4ad7-8b3e-0e02749d167e	g.chrX:107224730G>A	ENST00000302917.1	-	3	611	c.519C>T	c.(517-519)gcC>gcT	p.A173A		NM_031273.2	NP_112563.1	Q9BXU2	TX13B_HUMAN	testis expressed 13B	173										breast(1)|endometrium(5)|large_intestine(4)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28						AATCCCCTCCGGCAGTGGCCA	0.607																																						dbGAP											0													70.0	81.0	77.0					X																	107224730		2192	4278	6470	-	-	-	SO:0001819	synonymous_variant	0			AF285598	CCDS14534.1	Xq23	2008-02-05	2007-03-13		ENSG00000170925	ENSG00000170925			11736	protein-coding gene	gene with protein product		300313	"""testis expressed sequence 13B"""			11279525	Standard	NM_031273		Approved	TSGA5, TGC3B	uc004enn.1	Q9BXU2	OTTHUMG00000022174	ENST00000302917.1:c.519C>T	X.37:g.107224730G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q5JYF6	Silent	SNP	NULL	p.A173	ENST00000302917.1	37	c.519	CCDS14534.1	X																																																																																			TEX13B	-	NULL	ENSG00000170925		0.607	TEX13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TEX13B	HGNC	protein_coding	OTTHUMT00000057857.1	128	0.00	0	G			107224730	107224730	-1	no_errors	ENST00000302917	ensembl	human	known	69_37n	silent	125	18.18	28	SNP	0.000	A
TP53	7157	genome.wustl.edu	37	17	7578403	7578403	+	Missense_Mutation	SNP	C	C	A			TCGA-A8-A08X-01A-21W-A019-09	TCGA-A8-A08X-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	67c7d350-5c82-49b0-a7eb-6ca829ffcbc9	263fb74b-c2f8-4ad7-8b3e-0e02749d167e	g.chr17:7578403C>A	ENST00000269305.4	-	5	716	c.527G>T	c.(526-528)tGc>tTc	p.C176F	TP53_ENST00000420246.2_Missense_Mutation_p.C176F|TP53_ENST00000445888.2_Missense_Mutation_p.C176F|TP53_ENST00000455263.2_Missense_Mutation_p.C176F|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000413465.2_Missense_Mutation_p.C176F|TP53_ENST00000359597.4_Missense_Mutation_p.C176F	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	176	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		C -> F (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:8829627, ECO:0000269|PubMed:9450901}.|C -> G (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in sporadic cancers; somatic mutation).|CP -> FS (in a sporadic cancer; somatic mutation).		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.C176F(129)|p.C176Y(63)|p.C83F(9)|p.C44F(9)|p.C176S(8)|p.0?(8)|p.C176_R181delCPHHER(3)|p.R174fs*24(3)|p.C44Y(3)|p.C83Y(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.C176fs*65(1)|p.C176_P177delCP(1)|p.V173fs*69(1)|p.C176fs*68(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.C176del(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.H178fs*3(1)|p.R174fs*3(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)	ATGGTGGGGGCAGCGCCTCAC	0.652		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"""	267	Substitution - Missense(224)|Deletion - Frameshift(18)|Deletion - In frame(13)|Whole gene deletion(8)|Complex - deletion inframe(3)|Insertion - Frameshift(1)	lung(42)|large_intestine(38)|upper_aerodigestive_tract(36)|oesophagus(26)|breast(26)|liver(20)|ovary(19)|haematopoietic_and_lymphoid_tissue(13)|stomach(10)|central_nervous_system(9)|bone(9)|urinary_tract(7)|genital_tract(2)|skin(2)|pancreas(2)|prostate(2)|adrenal_gland(1)|vulva(1)|biliary_tract(1)|endometrium(1)											49.0	49.0	49.0					17																	7578403		2203	4300	6503	-	-	-	SO:0001583	missense	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.527G>T	17.37:g.7578403C>A	ENSP00000269305:p.Cys176Phe	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	Missense_Mutation	SNP	pfam_p53_DNA-bd,pfam_p53_tetrameristn,pfam_p53_transactivation_domain,superfamily_p53-like_TF_DNA-bd,superfamily_p53_tetrameristn,prints_p53_tumour_suppressor	p.C176F	ENST00000269305.4	37	c.527	CCDS11118.1	17	.	.	.	.	.	.	.	.	.	.	C	23.6	4.433429	0.83776	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99982	-10.61;-10.61;-10.61;-10.61;-10.61;-10.61;-10.61;-10.61	5.59	4.61	0.57282	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.092184	0.85682	D	0.000000	D	0.99981	0.9994	M	0.92923	3.36	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.999;0.994;0.996;0.998;0.997;0.995;0.997	D	0.96187	0.9135	10	0.87932	D	0	-18.1821	13.8336	0.63395	0.1543:0.8457:0.0:0.0	.	137;176;176;83;176;176;176	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	F	176;176;176;176;176;176;165;83;44;83;44	ENSP00000410739:C176F;ENSP00000352610:C176F;ENSP00000269305:C176F;ENSP00000398846:C176F;ENSP00000391127:C176F;ENSP00000391478:C176F;ENSP00000425104:C44F;ENSP00000423862:C83F	ENSP00000269305:C176F	C	-	2	0	TP53	7519128	1.000000	0.71417	0.999000	0.59377	0.851000	0.48451	7.775000	0.85489	1.472000	0.48140	0.655000	0.94253	TGC	TP53	-	pfam_p53_DNA-bd,superfamily_p53-like_TF_DNA-bd,prints_p53_tumour_suppressor	ENSG00000141510		0.652	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TP53	HGNC	protein_coding	OTTHUMT00000367397.1	82	0.00	0	C	NM_000546		7578403	7578403	-1	no_errors	ENST00000269305	ensembl	human	known	69_37n	missense	72	33.33	36	SNP	1.000	A
VRTN	55237	genome.wustl.edu	37	14	74824804	74824804	+	Missense_Mutation	SNP	C	C	T			TCGA-A8-A08X-01A-21W-A019-09	TCGA-A8-A08X-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	67c7d350-5c82-49b0-a7eb-6ca829ffcbc9	263fb74b-c2f8-4ad7-8b3e-0e02749d167e	g.chr14:74824804C>T	ENST00000256362.4	+	2	1559	c.1318C>T	c.(1318-1320)Cgg>Tgg	p.R440W		NM_018228.2	NP_060698.2	Q9H8Y1	VRTN_HUMAN	vertebrae development associated	440					transposition, DNA-mediated (GO:0006313)		sequence-specific DNA binding (GO:0043565)|transposase activity (GO:0004803)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(15)|ovary(5)|prostate(2)|skin(1)|urinary_tract(1)	41						TTATAATTGGCGGCGAAAGGC	0.572																																						dbGAP											0													60.0	62.0	61.0					14																	74824804		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK001673	CCDS9830.1	14q24.2	2012-12-07	2012-12-07	2010-10-20	ENSG00000133980	ENSG00000133980			20223	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 115"", ""vertebrae development homolog (pig)"""	C14orf115		21232157	Standard	NM_018228		Approved	FLJ10811, vertnin	uc001xpw.4	Q9H8Y1	OTTHUMG00000171208	ENST00000256362.4:c.1318C>T	14.37:g.74824804C>T	ENSP00000256362:p.Arg440Trp	Somatic		WXS	Illumina GAIIx	Phase_IV	Q9NVC7	Missense_Mutation	SNP	pfam_Transposase_8	p.R440W	ENST00000256362.4	37	c.1318	CCDS9830.1	14	.	.	.	.	.	.	.	.	.	.	C	16.07	3.019527	0.54576	.	.	ENSG00000133980	ENST00000256362	T	0.62941	-0.01	4.5	2.57	0.30868	.	0.000000	0.64402	D	0.000001	T	0.66356	0.2781	L	0.32530	0.975	0.46096	D	0.998869	D	0.89917	1.0	D	0.67548	0.952	T	0.67007	-0.5779	10	0.87932	D	0	-7.042	11.4324	0.50050	0.4705:0.5295:0.0:0.0	.	440	Q9H8Y1	VRTN_HUMAN	W	440	ENSP00000256362:R440W	ENSP00000256362:R440W	R	+	1	2	VRTN	73894557	1.000000	0.71417	0.997000	0.53966	0.951000	0.60555	2.166000	0.42406	0.448000	0.26722	0.491000	0.48974	CGG	VRTN	-	NULL	ENSG00000133980		0.572	VRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VRTN	HGNC	protein_coding	OTTHUMT00000412339.1	62	0.00	0	C	NM_018228		74824804	74824804	+1	no_errors	ENST00000256362	ensembl	human	known	69_37n	missense	42	27.59	16	SNP	1.000	T
