#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
ACY3	91703	genome.wustl.edu	37	11	67414330	67414331	+	Frame_Shift_Ins	INS	-	-	G	rs151057744	byFrequency	TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr11:67414330_67414331insG	ENST00000255082.3	-	3	354_355	c.184_185insC	c.(184-186)cgcfs	p.R62fs	ACY3_ENST00000529256.1_5'UTR	NM_080658.1	NP_542389.1	Q96HD9	ACY3_HUMAN	aspartoacylase (aminocyclase) 3	62	Hydrolytic domain. {ECO:0000250}.				viral process (GO:0016032)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aminoacylase activity (GO:0004046)|hydrolase activity, acting on ester bonds (GO:0016788)|metal ion binding (GO:0046872)			endometrium(1)|lung(5)|prostate(2)	8					L-Aspartic Acid(DB00128)	CACGTAGCGGCGGCAGCCGGAT	0.663																																					GBM(56;346 1011 27014 29495 46841)	dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			BC008689	CCDS8175.1	11q13.2	2014-08-08			ENSG00000132744	ENSG00000132744			24104	protein-coding gene	gene with protein product		614413				14656720	Standard	NM_080658		Approved	HCBP1, MGC9740, ACY-3	uc001omq.3	Q96HD9	OTTHUMG00000167283	ENST00000255082.3:c.185dupC	11.37:g.67414332_67414332dupG	ENSP00000255082:p.Arg62fs	Somatic		WXS	Illumina GAIIx	Phase_IV		Frame_Shift_Ins	INS	pfam_Aste_AspA,pirsf_Aspartoacylase	p.R62fs	ENST00000255082.3	37	c.185_184	CCDS8175.1	11																																																																																			ACY3	-	pfam_Aste_AspA,pirsf_Aspartoacylase	ENSG00000132744		0.663	ACY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ACY3	HGNC	protein_coding	OTTHUMT00000394002.1	17	0.00	0	-	NM_080658		67414330	67414331	-1	no_errors	ENST00000255082	ensembl	human	known	69_37n	frame_shift_ins	5	28.57	2	INS	0.864:0.864	G
ADAM10	102	genome.wustl.edu	37	15	58974428	58974428	+	Missense_Mutation	SNP	C	C	G			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr15:58974428C>G	ENST00000260408.3	-	3	735	c.292G>C	c.(292-294)Gat>Cat	p.D98H	ADAM10_ENST00000396140.2_Intron|ADAM10_ENST00000561288.1_Intron|ADAM10_ENST00000558733.1_5'UTR|ADAM10_ENST00000402627.1_Intron	NM_001110.2	NP_001101.1	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10	98					cell death (GO:0008219)|cell-cell signaling (GO:0007267)|collagen catabolic process (GO:0030574)|constitutive protein ectodomain proteolysis (GO:0051089)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|negative regulation of cell adhesion (GO:0007162)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of T cell chemotaxis (GO:0010820)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|tetraspanin-enriched microdomain (GO:0097197)	endopeptidase activity (GO:0004175)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)	p.D98H(1)		breast(1)|endometrium(1)|kidney(5)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)	27				GBM - Glioblastoma multiforme(80;0.202)		TGAGAGGTATCATAATCAAGT	0.323																																						dbGAP											1	Substitution - Missense(1)	breast(1)											90.0	90.0	90.0					15																	58974428		2192	4287	6479	-	-	-	SO:0001583	missense	0			AF009615	CCDS10167.1	15q2	2006-09-25	2005-08-18		ENSG00000137845	ENSG00000137845		"""ADAM metallopeptidase domain containing"", ""CD molecules"""	188	protein-coding gene	gene with protein product		602192	"""a disintegrin and metalloproteinase domain 10"""			9344679, 9441766	Standard	XM_005254117		Approved	kuz, MADM, HsT18717, CD156c	uc002afd.1	O14672	OTTHUMG00000132633	ENST00000260408.3:c.292G>C	15.37:g.58974428C>G	ENSP00000260408:p.Asp98His	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DU28|Q10742|Q92650	Missense_Mutation	SNP	pfam_Blood-coag_inhib_Disintegrin,pfam_Peptidase_M12B_N,pfam_Peptidase_M12B,superfamily_Blood-coag_inhib_Disintegrin,smart_Blood-coag_inhib_Disintegrin,pfscan_Blood-coag_inhib_Disintegrin,pfscan_Peptidase_M12B	p.D98H	ENST00000260408.3	37	c.292	CCDS10167.1	15	.	.	.	.	.	.	.	.	.	.	C	25.4	4.631588	0.87660	.	.	ENSG00000137845	ENST00000260408;ENST00000439637	T;T	0.06142	3.34;3.34	5.38	5.38	0.77491	Peptidase M12B, propeptide (1);	0.000000	0.85682	D	0.000000	T	0.31231	0.0790	M	0.87381	2.88	0.80722	D	1	D;D	0.69078	0.997;0.988	D;D	0.69479	0.964;0.948	T	0.12993	-1.0526	10	0.72032	D	0.01	-23.8602	19.1258	0.93384	0.0:1.0:0.0:0.0	.	98;98	A0AV88;O14672	.;ADA10_HUMAN	H	98	ENSP00000260408:D98H;ENSP00000391930:D98H	ENSP00000260408:D98H	D	-	1	0	ADAM10	56761720	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.412000	0.80091	2.519000	0.84933	0.591000	0.81541	GAT	ADAM10	-	pfam_Peptidase_M12B_N	ENSG00000137845		0.323	ADAM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ADAM10	HGNC	protein_coding	OTTHUMT00000255880.2	122	0.00	0	C	NM_001110		58974428	58974428	-1	no_errors	ENST00000260408	ensembl	human	known	69_37n	missense	53	10.17	6	SNP	1.000	G
AMN1	196394	genome.wustl.edu	37	12	31862280	31862280	+	Silent	SNP	G	G	A			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr12:31862280G>A	ENST00000281471.6	-	2	283	c.118C>T	c.(118-120)Ctg>Ttg	p.L40L	AMN1_ENST00000541931.1_Intron|AMN1_ENST00000537562.1_Silent_p.L22L|AMN1_ENST00000536761.1_Silent_p.L22L|AMN1_ENST00000542781.1_Intron|AMN1_ENST00000541541.1_5'UTR	NM_001113402.1|NM_001278411.1|NM_001278412.1	NP_001106873.1|NP_001265340.1|NP_001265341.1	Q8IY45	AMN1_HUMAN	antagonist of mitotic exit network 1 homolog (S. cerevisiae)	40								p.L40L(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)|urinary_tract(1)	7	all_cancers(9;7.41e-12)|all_epithelial(9;1.18e-11)|all_lung(12;1.14e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.162)		OV - Ovarian serous cystadenocarcinoma(6;0.0014)			ATTTTAATCAGTCTGTCTTTT	0.318																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											194.0	176.0	182.0					12																	31862280		1842	4091	5933	-	-	-	SO:0001819	synonymous_variant	0				CCDS44858.1, CCDS61089.1	12p11.21	2010-07-19			ENSG00000151743	ENSG00000151743			27281	protein-coding gene	gene with protein product							Standard	NM_001113402		Approved		uc001rkq.4	Q8IY45	OTTHUMG00000169192	ENST00000281471.6:c.118C>T	12.37:g.31862280G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z7J3|Q6NVU4|Q86X98	Silent	SNP	smart_Leu-rich_rpt_Cys-con_subtyp	p.L40	ENST00000281471.6	37	c.118	CCDS44858.1	12																																																																																			AMN1	-	NULL	ENSG00000151743		0.318	AMN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AMN1	HGNC	protein_coding	OTTHUMT00000402807.2	345	0.00	0	G	NR_004854		31862280	31862280	-1	no_errors	ENST00000281471	ensembl	human	known	69_37n	silent	273	11.90	37	SNP	0.983	A
ARHGAP17	55114	genome.wustl.edu	37	16	24971256	24971256	+	Silent	SNP	C	C	G	rs201422543		TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr16:24971256C>G	ENST00000289968.6	-	8	687	c.618G>C	c.(616-618)ggG>ggC	p.G206G	ARHGAP17_ENST00000575975.1_5'UTR|ARHGAP17_ENST00000303665.5_Silent_p.G206G|ARHGAP17_ENST00000441763.2_Silent_p.G206G	NM_001006634.1	NP_001006635.1	Q68EM7	RHG17_HUMAN	Rho GTPase activating protein 17	206	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)	p.G206G(2)		breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|urinary_tract(2)	30				GBM - Glioblastoma multiforme(48;0.0407)		TGCCATACTCCCCTTCTTTGG	0.358																																						dbGAP											2	Substitution - coding silent(2)	breast(2)											121.0	120.0	120.0					16																	24971256		2197	4300	6497	-	-	-	SO:0001819	synonymous_variant	0			AJ306731	CCDS32408.1, CCDS32409.1	16p12.2-p12.1	2011-06-29				ENSG00000140750		"""Rho GTPase activating proteins"""	18239	protein-coding gene	gene with protein product		608293				10967100, 11431473	Standard	XM_005255413		Approved	RICH1, FLJ10308, NADRIN, FLJ13219, WBP15	uc002dnb.3	Q68EM7		ENST00000289968.6:c.618G>C	16.37:g.24971256C>G		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K6M6|Q6ZUS4|Q7Z2F2|Q8NDG2|Q96KS2|Q96KS3|Q96SS8|Q9BVF6|Q9H8U5|Q9NW54	Silent	SNP	pfam_BAR_dom,pfam_RhoGAP_dom,superfamily_Rho_GTPase_activation_prot,smart_BAR_dom,smart_RhoGAP_dom,pfscan_BAR_dom,pfscan_RhoGAP_dom	p.G206	ENST00000289968.6	37	c.618	CCDS32409.1	16																																																																																			ARHGAP17	-	pfam_BAR_dom,smart_BAR_dom,pfscan_BAR_dom	ENSG00000140750		0.358	ARHGAP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARHGAP17	HGNC	protein_coding	OTTHUMT00000436548.3	349	0.57	2	C	NM_018054		24971256	24971256	-1	no_errors	ENST00000289968	ensembl	human	known	69_37n	silent	163	26.58	59	SNP	1.000	G
ATP2B3	492	genome.wustl.edu	37	X	152822475	152822475	+	Silent	SNP	C	C	T			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chrX:152822475C>T	ENST00000349466.2	+	15	2753	c.2427C>T	c.(2425-2427)ttC>ttT	p.F809F	ATP2B3_ENST00000460549.1_3'UTR|ATP2B3_ENST00000393842.1_Silent_p.F795F|ATP2B3_ENST00000359149.3_Silent_p.F809F|ATP2B3_ENST00000263519.4_Silent_p.F809F|ATP2B3_ENST00000370186.1_Silent_p.F795F|ATP2B3_ENST00000370181.2_Silent_p.F795F			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	809					blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)	p.F809F(3)|p.F795F(1)		NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					ACGTGGGCTTCGCCATGGTAA	0.627													C|||	1	0.000264901	0.0	0.0	3775	,	,		12974	0.0		0.0	False		,,,				2504	0.001					dbGAP											4	Substitution - coding silent(4)	breast(4)																																								-	-	-	SO:0001819	synonymous_variant	0			U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	3.6.3.8	"""ATPases / P-type"""	816	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 3"", ""cilia and flagella associated protein 39"""	300014	"""spinocerebellar ataxia, X-linked 1"", ""cerebellar ataxia 2 (X-linked)"""	SCAX1, CLA2		8187550, 22912398	Standard	NM_021949		Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.2427C>T	X.37:g.152822475C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B7WNR8|B7WNY5|Q12995|Q16858	Silent	SNP	pfam_ATPase_P-typ_ATPase-assoc-dom,pfam_ATPase_P-typ_cation-transptr_C,pfam_ATP_Ca_trans_C,pfam_Dehalogen-like_hydro,pfam_ATPase_P-typ_cation-transptr_N,pfam_HAD-SF_hydro-like_3,superfamily_ATPase_cation_domN,superfamily_HAD-like_dom,smart_ATPase_P-typ_cation-transptr_N,prints_ATPase_P-typ_ion-transptr,tigrfam_ATPase_P-typ_Ca-transp_PMCA,tigrfam_ATPase_P-typ_ion-transptr	p.F809	ENST00000349466.2	37	c.2427	CCDS35440.1	X																																																																																			ATP2B3	-	pfam_HAD-SF_hydro-like_3,superfamily_HAD-like_dom,prints_ATPase_P-typ_ion-transptr,tigrfam_ATPase_P-typ_Ca-transp_PMCA,tigrfam_ATPase_P-typ_ion-transptr	ENSG00000067842		0.627	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	ATP2B3	HGNC	protein_coding	OTTHUMT00000060957.1	77	0.00	0	C	NM_021949		152822475	152822475	+1	no_errors	ENST00000263519	ensembl	human	known	69_37n	silent	13	35.00	7	SNP	0.601	T
BAI2	576	genome.wustl.edu	37	1	32208507	32208508	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr1:32208507_32208508insG	ENST00000373658.3	-	7	1524_1525	c.1183_1184insC	c.(1183-1185)cagfs	p.Q395fs	BAI2_ENST00000440175.2_Frame_Shift_Ins_p.Q37fs|BAI2_ENST00000398538.1_Frame_Shift_Ins_p.Q383fs|BAI2_ENST00000373655.2_Frame_Shift_Ins_p.Q395fs|BAI2_ENST00000257070.4_Frame_Shift_Ins_p.Q395fs|BAI2_ENST00000398542.1_Intron|BAI2_ENST00000398547.1_Frame_Shift_Ins_p.Q328fs|BAI2_ENST00000398556.3_Frame_Shift_Ins_p.Q343fs|BAI2_ENST00000527361.1_Frame_Shift_Ins_p.Q395fs	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	395	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.Q395fs*11(1)		breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		GCCGCCGTGCTGGGGGGGCACG	0.713																																						dbGAP											1	Insertion - Frameshift(1)	large_intestine(1)																																								-	-	-	SO:0001589	frameshift_variant	0			AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"""-"", ""GPCR / Class B : Orphans"""	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.1184dupC	1.37:g.32208514_32208514dupG	ENSP00000362762:p.Gln395fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Frame_Shift_Ins	INS	pfam_GPCR_2_secretin-like,pfam_DUF3497,pfam_Thrombospondin_1_rpt,pfam_GPS_dom,superfamily_Thrombospondin_1_rpt,smart_Thrombospondin_1_rpt,smart_GPCR_2_extracellular_dom,smart_GPS_dom,pfscan_GPS_dom,pfscan_Thrombospondin_1_rpt,pfscan_GPCR_2_extracellular_dom,pfscan_GPCR_2-like,prints_GPCR_2_brain-spec_angio_inhib,prints_GPCR_2_secretin-like	p.Q395fs	ENST00000373658.3	37	c.1184_1183	CCDS346.2	1																																																																																			BAI2	-	pfam_Thrombospondin_1_rpt,superfamily_Thrombospondin_1_rpt,smart_Thrombospondin_1_rpt,pfscan_Thrombospondin_1_rpt	ENSG00000121753		0.713	BAI2-015	KNOWN	basic|CCDS	protein_coding	BAI2	HGNC	protein_coding	OTTHUMT00000381838.1	25	0.00	0	-	NM_001703		32208507	32208508	-1	no_errors	ENST00000373658	ensembl	human	known	69_37n	frame_shift_ins	5	37.50	3	INS	1.000:1.000	G
CACNA1G	8913	genome.wustl.edu	37	17	48646555	48646555	+	Silent	SNP	T	T	C			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr17:48646555T>C	ENST00000359106.5	+	3	384	c.384T>C	c.(382-384)ttT>ttC	p.F128F	CACNA1G_ENST00000515165.1_Silent_p.F128F|CACNA1G_ENST00000514079.1_Silent_p.F128F|CACNA1G_ENST00000507609.1_Silent_p.F128F|CACNA1G_ENST00000513689.2_Silent_p.F128F|CACNA1G_ENST00000510115.1_Silent_p.F128F|CACNA1G_ENST00000515765.1_Silent_p.F128F|CACNA1G_ENST00000429973.2_Silent_p.F128F|CACNA1G_ENST00000354983.4_Silent_p.F128F|CACNA1G_ENST00000515411.1_Silent_p.F128F|CACNA1G_ENST00000514717.1_Silent_p.F128F|CACNA1G_ENST00000507896.1_Silent_p.F128F|CACNA1G_ENST00000358244.5_Silent_p.F128F|CACNA1G_ENST00000352832.5_Silent_p.F128F|CACNA1G_ENST00000513964.1_Silent_p.F128F|CACNA1G_ENST00000503485.1_Silent_p.F128F|CACNA1G_ENST00000416767.4_Silent_p.F128F|CACNA1G_ENST00000505165.1_Silent_p.F128F|CACNA1G_ENST00000507336.1_Silent_p.F128F|CACNA1G_ENST00000514181.1_Silent_p.F128F|CACNA1G_ENST00000502264.1_Silent_p.F128F|CACNA1G_ENST00000442258.2_Silent_p.F128F|CACNA1G_ENST00000507510.2_Silent_p.F128F|CACNA1G_ENST00000360761.4_Silent_p.F128F|CACNA1G_ENST00000512389.1_Silent_p.F128F|CACNA1G_ENST00000510366.1_Silent_p.F128F	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	128					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)	p.F128F(4)		breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	TTGCCTTCTTTGCCGTGGAGA	0.517																																						dbGAP											4	Substitution - coding silent(4)	breast(4)											140.0	131.0	134.0					17																	48646555		1986	4164	6150	-	-	-	SO:0001819	synonymous_variant	0			AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.384T>C	17.37:g.48646555T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Silent	SNP	pfam_Ion_trans_dom,pfam_PKD1_2_channel,prints_VDCC_T_a1su,prints_VDCCAlpha1	p.F128	ENST00000359106.5	37	c.384	CCDS45730.1	17																																																																																			CACNA1G	-	pfam_Ion_trans_dom	ENSG00000006283		0.517	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	CACNA1G	HGNC	protein_coding	OTTHUMT00000367895.1	401	0.00	0	T	NM_018896		48646555	48646555	+1	no_errors	ENST00000359106	ensembl	human	known	69_37n	silent	224	17.28	47	SNP	0.999	C
CCDC127	133957	genome.wustl.edu	37	5	216868	216868	+	Missense_Mutation	SNP	G	G	T	rs561280577		TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr5:216868G>T	ENST00000296824.3	-	2	229	c.97C>A	c.(97-99)Cca>Aca	p.P33T	SDHA_ENST00000264932.6_5'Flank|SDHA_ENST00000504309.1_5'Flank|SDHA_ENST00000510361.1_5'Flank|CTD-2083E4.4_ENST00000565521.1_RNA	NM_145265.2	NP_660308.1	Q96BQ5	CC127_HUMAN	coiled-coil domain containing 127	33										breast(1)|endometrium(4)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	12			all cancers(22;0.0236)|Lung(60;0.113)			CCCAGCATTGGAACCAACAGG	0.498																																						dbGAP											0													33.0	34.0	34.0					5																	216868		2201	4295	6496	-	-	-	SO:0001583	missense	0			AK098567	CCDS3852.1	5p15.33	2008-02-05			ENSG00000164366	ENSG00000164366			30520	protein-coding gene	gene with protein product						12477932	Standard	NM_145265		Approved	FLJ25701	uc003jam.1	Q96BQ5	OTTHUMG00000161586	ENST00000296824.3:c.97C>A	5.37:g.216868G>T	ENSP00000296824:p.Pro33Thr	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	NULL	p.P33T	ENST00000296824.3	37	c.97	CCDS3852.1	5	.	.	.	.	.	.	.	.	.	.	G	27.5	4.833478	0.91036	.	.	ENSG00000164366	ENST00000296824;ENST00000441693	T;T	0.47869	0.83;0.83	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.65080	0.2657	L	0.59436	1.845	0.80722	D	1	D	0.76494	0.999	D	0.68039	0.955	T	0.66284	-0.5962	10	0.72032	D	0.01	-8.2589	17.2004	0.86904	0.0:0.0:1.0:0.0	.	33	Q96BQ5	CC127_HUMAN	T	33	ENSP00000296824:P33T;ENSP00000411206:P33T	ENSP00000296824:P33T	P	-	1	0	CCDC127	269868	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	8.715000	0.91416	2.736000	0.93811	0.650000	0.86243	CCA	CCDC127	-	NULL	ENSG00000164366		0.498	CCDC127-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CCDC127	HGNC	protein_coding	OTTHUMT00000365459.2	80	0.00	0	G	NM_145265		216868	216868	-1	no_errors	ENST00000296824	ensembl	human	known	69_37n	missense	22	12.00	3	SNP	1.000	T
CCDC136	64753	genome.wustl.edu	37	7	128446752	128446752	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr7:128446752G>A	ENST00000297788.4	+	9	1626	c.1259G>A	c.(1258-1260)tGc>tAc	p.C420Y	CCDC136_ENST00000464832.1_Intron|CCDC136_ENST00000487361.1_Missense_Mutation_p.C367Y|CCDC136_ENST00000378685.4_Intron	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	420						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.C420Y(2)|p.C536Y(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						GAGTTACTGTGCCGGCTGCAG	0.552																																						dbGAP											3	Substitution - Missense(3)	breast(3)											22.0	23.0	23.0					7																	128446752		1945	4133	6078	-	-	-	SO:0001583	missense	0				CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.1259G>A	7.37:g.128446752G>A	ENSP00000297788:p.Cys420Tyr	Somatic		WXS	Illumina GAIIx	Phase_IV	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Missense_Mutation	SNP	NULL	p.C420Y	ENST00000297788.4	37	c.1259	CCDS47704.1	7	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.35|17.35	3.367410|3.367410	0.61513|0.61513	.|.	.|.	ENSG00000128596|ENSG00000128596	ENST00000494552|ENST00000487361;ENST00000297788;ENST00000397697;ENST00000320524;ENST00000464672	.|T;T;T	.|0.63913	.|-0.07;-0.07;-0.07	5.62|5.62	2.61|2.61	0.31194|0.31194	.|.	.|0.546583	.|0.19524	.|N	.|0.112215	T|T	0.68952|0.68952	0.3057|0.3057	L|L	0.57536|0.57536	1.79|1.79	0.29087|0.29087	N|N	0.882329|0.882329	.|D;P;D	.|0.76494	.|0.997;0.926;0.999	.|D;P;D	.|0.85130	.|0.994;0.525;0.997	T|T	0.61192|0.61192	-0.7112|-0.7112	5|10	.|0.56958	.|D	.|0.05	-14.1711|-14.1711	3.1959|3.1959	0.06633|0.06633	0.0964:0.1886:0.5447:0.1703|0.0964:0.1886:0.5447:0.1703	.|.	.|420;367;420	.|Q96JN2-2;C9JE17;Q96JN2	.|.;.;CC136_HUMAN	T|Y	297|367;420;420;420;11	.|ENSP00000420509:C367Y;ENSP00000297788:C420Y;ENSP00000417991:C11Y	.|ENSP00000297788:C420Y	A|C	+|+	1|2	0|0	CCDC136|CCDC136	128233988|128233988	0.997000|0.997000	0.39634|0.39634	0.994000|0.994000	0.49952|0.49952	0.971000|0.971000	0.66376|0.66376	2.027000|2.027000	0.41078|0.41078	1.325000|1.325000	0.45301|0.45301	0.655000|0.655000	0.94253|0.94253	GCC|TGC	CCDC136	-	NULL	ENSG00000128596		0.552	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CCDC136	HGNC	protein_coding	OTTHUMT00000350641.1	22	0.00	0	G	NM_022742		128446752	128446752	+1	no_errors	ENST00000297788	ensembl	human	known	69_37n	missense	36	24.49	12	SNP	0.798	A
CCL11	6356	genome.wustl.edu	37	17	32614626	32614626	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr17:32614626G>A	ENST00000305869.3	+	3	352	c.211G>A	c.(211-213)Gat>Aat	p.D71N		NM_002986.2	NP_002977.1	P51671	CCL11_HUMAN	chemokine (C-C motif) ligand 11	71					actin filament organization (GO:0007015)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|chronic inflammatory response (GO:0002544)|cytoskeleton organization (GO:0007010)|eosinophil chemotaxis (GO:0048245)|ERK1 and ERK2 cascade (GO:0070371)|immune response (GO:0006955)|inflammatory response (GO:0006954)|mammary duct terminal end bud growth (GO:0060763)|mast cell chemotaxis (GO:0002551)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of Rac GTPase activity (GO:0032855)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|response to interleukin-4 (GO:0070670)|response to radiation (GO:0009314)|response to virus (GO:0009615)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)	p.D71N(1)		breast(1)|lung(1)|prostate(1)	3	Breast(3;0.00224)	Breast(31;0.151)|Ovarian(249;0.17)		BRCA - Breast invasive adenocarcinoma(366;0.155)		ACTGGCCAAGGATATCTGTGC	0.418																																						dbGAP											1	Substitution - Missense(1)	breast(1)											77.0	72.0	73.0					17																	32614626		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB063614	CCDS11279.1	17q21.1-q21.2	2013-02-25	2002-08-22	2002-08-23	ENSG00000172156	ENSG00000172156		"""Chemokine ligands"", ""Endogenous ligands"""	10610	protein-coding gene	gene with protein product	"""eotaxin-1"""	601156	"""small inducible cytokine subfamily A (Cys-Cys), member 11 (eotaxin)"""	SCYA11		9169149	Standard	NM_002986		Approved	eotaxin, MGC22554	uc002hia.1	P51671	OTTHUMG00000132884	ENST00000305869.3:c.211G>A	17.37:g.32614626G>A	ENSP00000302234:p.Asp71Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	P50877|Q92490|Q92491	Missense_Mutation	SNP	pfam_Chemokine_IL8-like_dom,superfamily_Chemokine_IL8-like_dom,smart_Chemokine_IL8-like_dom	p.D71N	ENST00000305869.3	37	c.211	CCDS11279.1	17	.	.	.	.	.	.	.	.	.	.	G	13.66	2.303724	0.40795	.	.	ENSG00000172156	ENST00000305869	T	0.03889	3.77	5.1	-3.54	0.04653	CC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.982928	0.08306	N	0.966077	T	0.04227	0.0117	.	.	.	0.09310	N	1	P	0.41188	0.741	B	0.38755	0.281	T	0.38001	-0.9681	9	0.72032	D	0.01	.	6.781	0.23646	0.6285:0.1459:0.2256:0.0	.	71	P51671	CCL11_HUMAN	N	71	ENSP00000302234:D71N	ENSP00000302234:D71N	D	+	1	0	CCL11	29638739	0.004000	0.15560	0.002000	0.10522	0.877000	0.50540	0.131000	0.15870	-0.432000	0.07297	0.561000	0.74099	GAT	CCL11	-	pfam_Chemokine_IL8-like_dom,superfamily_Chemokine_IL8-like_dom,smart_Chemokine_IL8-like_dom	ENSG00000172156		0.418	CCL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CCL11	HGNC	protein_coding	OTTHUMT00000256377.2	156	0.64	1	G	NM_002986		32614626	32614626	+1	no_errors	ENST00000305869	ensembl	human	known	69_37n	missense	101	14.41	17	SNP	0.001	A
CD3G	917	genome.wustl.edu	37	11	118221279	118221279	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr11:118221279G>A	ENST00000532917.1	+	4	388	c.320G>A	c.(319-321)tGc>tAc	p.C107Y	CD3G_ENST00000392883.2_Intron|CD3G_ENST00000532903.1_3'UTR	NM_000073.2	NP_000064.1	P09693	CD3G_HUMAN	CD3g molecule, gamma (CD3-TCR complex)	107					cell surface receptor signaling pathway (GO:0007166)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|protein transport (GO:0015031)|regulation of immune response (GO:0050776)|regulation of lymphocyte apoptotic process (GO:0070228)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	alpha-beta T cell receptor complex (GO:0042105)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	protein heterodimerization activity (GO:0046982)|receptor signaling complex scaffold activity (GO:0030159)|T cell receptor binding (GO:0042608)|transmembrane signaling receptor activity (GO:0004888)	p.C107Y(1)		breast(2)|kidney(1)|large_intestine(2)|skin(1)	6	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)	Muromonab(DB00075)	TGTCAGAACTGCATTGAACTA	0.458																																						dbGAP											1	Substitution - Missense(1)	breast(1)											175.0	153.0	160.0					11																	118221279		2200	4296	6496	-	-	-	SO:0001583	missense	0			X60491	CCDS8395.1	11q23	2014-09-17	2006-03-28		ENSG00000160654	ENSG00000160654		"""CD molecules"""	1675	protein-coding gene	gene with protein product		186740	"""CD3g antigen, gamma polypeptide (TiT3 complex)"""				Standard	NM_000073		Approved		uc001psu.2	P09693	OTTHUMG00000166971	ENST00000532917.1:c.320G>A	11.37:g.118221279G>A	ENSP00000431445:p.Cys107Tyr	Somatic		WXS	Illumina GAIIx	Phase_IV	Q2HIZ6	Missense_Mutation	SNP	pfam_Phos_immunorcpt_sig_ITAM,smart_Ig_sub2,smart_Phos_immunorcpt_sig_ITAM,pfscan_Phos_immunorcpt_sig_ITAM	p.C107Y	ENST00000532917.1	37	c.320	CCDS8395.1	11	.	.	.	.	.	.	.	.	.	.	G	21.4	4.145476	0.77888	.	.	ENSG00000160654	ENST00000532917	T	0.56611	0.45	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.76307	0.3969	M	0.87971	2.92	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.80016	-0.1559	10	0.87932	D	0	.	15.4814	0.75530	0.0:0.0:1.0:0.0	.	107	P09693	CD3G_HUMAN	Y	107	ENSP00000431445:C107Y	ENSP00000431445:C107Y	C	+	2	0	CD3G	117726489	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.158000	0.64917	2.726000	0.93360	0.655000	0.94253	TGC	CD3G	-	NULL	ENSG00000160654		0.458	CD3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CD3G	HGNC	protein_coding	OTTHUMT00000392135.1	254	0.00	0	G	NM_000073		118221279	118221279	+1	no_errors	ENST00000532917	ensembl	human	known	69_37n	missense	155	11.43	20	SNP	1.000	A
CNTNAP4	85445	genome.wustl.edu	37	16	76350228	76350228	+	Missense_Mutation	SNP	T	T	C			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr16:76350228T>C	ENST00000476707.1	+	1	152	c.13T>C	c.(13-15)Tac>Cac	p.Y5H	CNTNAP4_ENST00000469589.1_Intron|CNTNAP4_ENST00000478060.1_Intron|CNTNAP4_ENST00000377504.4_Intron|CNTNAP4_ENST00000307431.8_Intron			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	0					cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)				breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						GTTGTTGTTTTACTTGTTGGT	0.383																																						dbGAP											0																																										-	-	-	SO:0001583	missense	0			AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.13T>C	16.37:g.76350228T>C	ENSP00000417628:p.Tyr5His	Somatic		WXS	Illumina GAIIx	Phase_IV	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	pfam_Laminin_G,pfam_Coagulation_fac_5/8-C_type_dom,superfamily_Galactose-bd-like,superfamily_ConA-like_lec_gl,superfamily_Fibrinogen_a/b/g_C,smart_Coagulation_fac_5/8-C_type_dom,smart_Laminin_G,smart_EGF-like,pfscan_EG-like_dom,pfscan_Coagulation_fac_5/8-C_type_dom,pfscan_Laminin_G	p.Y5H	ENST00000476707.1	37	c.13		16	.	.	.	.	.	.	.	.	.	.	T	5.642	0.303128	0.10678	.	.	ENSG00000152910	ENST00000476707	D	0.89415	-2.51	4.35	-2.61	0.06171	.	.	.	.	.	T	0.76212	0.3956	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.58364	-0.7649	8	0.22706	T	0.39	.	4.8746	0.13650	0.0:0.2813:0.3376:0.3811	.	5	E9PDN6	.	H	5	ENSP00000417628:Y5H	ENSP00000417628:Y5H	Y	+	1	0	CNTNAP4	74907729	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-0.891000	0.04135	-0.650000	0.05423	0.533000	0.62120	TAC	CNTNAP4	-	NULL	ENSG00000152910		0.383	CNTNAP4-005	PUTATIVE	basic	protein_coding	CNTNAP4	HGNC	protein_coding	OTTHUMT00000348216.1	69	0.00	0	T	NM_033401		76350228	76350228	+1	no_errors	ENST00000476707	ensembl	human	putative	69_37n	missense	18	51.35	19	SNP	0.000	C
COL14A1	7373	genome.wustl.edu	37	8	121209087	121209087	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr8:121209087G>A	ENST00000297848.3	+	6	764	c.494G>A	c.(493-495)gGt>gAt	p.G165D	COL14A1_ENST00000309791.4_Missense_Mutation_p.G165D|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000247781.3_Missense_Mutation_p.G165D|COL14A1_ENST00000537875.1_Missense_Mutation_p.G165D	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.G165D(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			CTGGTCGATGGTTCATGGAGT	0.438																																						dbGAP											1	Substitution - Missense(1)	breast(1)											199.0	187.0	191.0					8																	121209087		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"""Collagens"", ""Fibronectin type III domain containing"""	2191	protein-coding gene	gene with protein product		120324	"""undulin"""	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.494G>A	8.37:g.121209087G>A	ENSP00000297848:p.Gly165Asp	Somatic		WXS	Illumina GAIIx	Phase_IV		Nonsense_Mutation	SNP	pfam_Fibronectin_type3,pfam_VWF_A,superfamily_Fibronectin_type3,smart_VWF_A,smart_Fibronectin_type3,pfscan_Fibronectin_type3,pfscan_VWF_A	p.W16*	ENST00000297848.3	37	c.48	CCDS34938.1	8	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	30|30	5.055447|5.055447	0.93793|0.93793	.|.	.|.	ENSG00000187955|ENSG00000187955	ENST00000537875;ENST00000309791;ENST00000297848;ENST00000247781|ENST00000523142	D;D;D;D|.	0.85088|.	-1.94;-1.94;-1.94;-1.94|.	5.43|5.43	5.43|5.43	0.79202|0.79202	von Willebrand factor, type A (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.87928|.	0.6301|.	H|H	0.95224|0.95224	3.64|3.64	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|.	0.90828|.	0.4714|.	10|.	0.35671|.	T|.	0.21|.	.|.	19.4372|19.4372	0.94801|0.94801	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	165|.	Q05707|.	COEA1_HUMAN|.	D|X	165|16	ENSP00000443974:G165D;ENSP00000311809:G165D;ENSP00000297848:G165D;ENSP00000247781:G165D|.	ENSP00000247781:G165D|.	G|W	+|+	2|3	0|0	COL14A1|COL14A1	121278268|121278268	1.000000|1.000000	0.71417|0.71417	0.969000|0.969000	0.41365|0.41365	0.954000|0.954000	0.61252|0.61252	9.657000|9.657000	0.98554|0.98554	2.827000|2.827000	0.97445|0.97445	0.650000|0.650000	0.86243|0.86243	GGT|TGG	COL14A1	-	pfam_VWF_A,smart_VWF_A,pfscan_VWF_A	ENSG00000187955		0.438	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL14A1	HGNC	protein_coding	OTTHUMT00000313657.2	132	0.75	1	G	NM_021110		121209087	121209087	+1	no_start_codon:pseudogene:no_stop_codon	ENST00000523142	ensembl	human	putative	69_37n	nonsense	89	23.08	27	SNP	1.000	A
DNAH3	55567	genome.wustl.edu	37	16	21145740	21145740	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr16:21145740G>A	ENST00000261383.3	-	7	921	c.922C>T	c.(922-924)Cgg>Tgg	p.R308W	DNAH3_ENST00000415178.1_Missense_Mutation_p.R308W	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	308	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.R308W(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		ATAAAGAGCCGTTTTCTCTCC	0.507																																						dbGAP											2	Substitution - Missense(2)	breast(2)											79.0	76.0	77.0					16																	21145740		2201	4300	6501	-	-	-	SO:0001583	missense	0			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.922C>T	16.37:g.21145740G>A	ENSP00000261383:p.Arg308Trp	Somatic		WXS	Illumina GAIIx	Phase_IV	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	pfam_Dynein_heavy,pfam_Dynein_heavy_dom-2,pfam_ATPase_dyneun-rel_AAA,superfamily_Prefoldin,smart_AAA+_ATPase	p.R308W	ENST00000261383.3	37	c.922	CCDS10594.1	16	.	.	.	.	.	.	.	.	.	.	G	14.32	2.498968	0.44455	.	.	ENSG00000158486	ENST00000261383;ENST00000415178;ENST00000396036	T;T	0.27256	1.68;1.78	5.85	3.49	0.39957	.	0.062472	0.64402	D	0.000013	T	0.45955	0.1368	M	0.68317	2.08	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.34329	-0.9833	10	0.39692	T	0.17	.	11.7718	0.51962	0.0:0.0:0.2915:0.7085	.	308;279	Q8TD57;Q8TD57-2	DYH3_HUMAN;.	W	308;308;279	ENSP00000261383:R308W;ENSP00000394245:R308W	ENSP00000261383:R308W	R	-	1	2	DNAH3	21053241	0.999000	0.42202	0.589000	0.28718	0.058000	0.15608	1.345000	0.33953	1.052000	0.40392	-0.262000	0.10625	CGG	DNAH3	-	NULL	ENSG00000158486		0.507	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DNAH3	HGNC	protein_coding	OTTHUMT00000207361.1	135	0.74	1	G	NM_017539		21145740	21145740	-1	no_errors	ENST00000261383	ensembl	human	known	69_37n	missense	106	34.97	57	SNP	0.923	A
CTCF	10664	genome.wustl.edu	37	16	67645507	67645507	+	Missense_Mutation	SNP	A	A	G			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr16:67645507A>G	ENST00000264010.4	+	3	1216	c.772A>G	c.(772-774)Aaa>Gaa	p.K258E	AC009095.4_ENST00000388909.4_RNA|CTCF_ENST00000401394.1_Intron	NM_006565.3	NP_006556.1	P49711	CTCF_HUMAN	CCCTC-binding factor (zinc finger protein)	258					chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|DNA methylation (GO:0006306)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome positioning (GO:0016584)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone acetylation (GO:0035065)|regulation of histone methylation (GO:0031060)|regulation of molecular function, epigenetic (GO:0040030)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin insulator sequence binding (GO:0043035)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.K258E(1)		breast(6)|central_nervous_system(2)|cervix(1)|endometrium(34)|haematopoietic_and_lymphoid_tissue(7)|kidney(3)|large_intestine(9)|liver(1)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	79		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		AACAAAAATTAAAAAGAAAGG	0.368																																					Colon(175;1200 1966 6945 23069 27405)	dbGAP											1	Substitution - Missense(1)	breast(1)											50.0	55.0	53.0					16																	67645507		2188	4271	6459	-	-	-	SO:0001583	missense	0			U25435	CCDS10841.1, CCDS54029.1	16q21-q22.3	2013-01-08			ENSG00000102974	ENSG00000102974		"""Zinc fingers, C2H2-type"""	13723	protein-coding gene	gene with protein product	"""11 zinc finger transcriptional repressor"""	604167				8649389, 18550811	Standard	NM_006565		Approved		uc002etl.3	P49711	OTTHUMG00000137539	ENST00000264010.4:c.772A>G	16.37:g.67645507A>G	ENSP00000264010:p.Lys258Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	B5MC38|Q53XI7|Q59EL8	Missense_Mutation	SNP	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.K258E	ENST00000264010.4	37	c.772	CCDS10841.1	16	.	.	.	.	.	.	.	.	.	.	A	24.1	4.490305	0.84962	.	.	ENSG00000102974	ENST00000264010	T	0.09350	2.99	5.4	5.4	0.78164	.	0.000000	0.64402	D	0.000001	T	0.19765	0.0475	N	0.19112	0.55	0.80722	D	1	D	0.63880	0.993	D	0.70935	0.971	T	0.03112	-1.1071	10	0.62326	D	0.03	.	15.5974	0.76595	1.0:0.0:0.0:0.0	.	258	P49711	CTCF_HUMAN	E	258	ENSP00000264010:K258E	ENSP00000264010:K258E	K	+	1	0	CTCF	66203008	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.908000	0.92640	2.271000	0.75665	0.533000	0.62120	AAA	CTCF	-	NULL	ENSG00000102974		0.368	CTCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CTCF	HGNC	protein_coding	OTTHUMT00000268870.2	92	0.00	0	A	NM_006565		67645507	67645507	+1	no_errors	ENST00000264010	ensembl	human	known	69_37n	missense	26	43.48	20	SNP	1.000	G
DNMT1	1786	genome.wustl.edu	37	19	10290875	10290875	+	Intron	DEL	T	T	-			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr19:10290875delT	ENST00000340748.4	-	4	681				DNMT1_ENST00000540357.1_Intron|DNMT1_ENST00000359526.4_Frame_Shift_Del_p.T161fs			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1						cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	ctaatcccagttacttgggag	0.532																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.445+150A>-	19.37:g.10290875delT		Somatic		WXS	Illumina GAIIx	Phase_IV	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Frame_Shift_Del	DEL	pirsf_DNA_C5-MeTrfase_1_euk,pfam_C5_MeTfrase,pfam_BAH_dom,pfam_Cytosine_MeTrfase1_RFD,pfam_DMAP1-bd,pfam_Znf_CXXC,smart_BAH_dom,prints_C5_MeTfrase,pfscan_BAH_dom,pfscan_Znf_CXXC	p.T161fs	ENST00000340748.4	37	c.481	CCDS12228.1	19																																																																																			DNMT1	-	pirsf_DNA_C5-MeTrfase_1_euk	ENSG00000130816		0.532	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	DNMT1	HGNC	protein_coding	OTTHUMT00000451166.1	8	0.00	0	T	NM_001379		10290875	10290875	-1	no_errors	ENST00000359526	ensembl	human	known	69_37n	frame_shift_del	10	76.74	33	DEL	0.022	-
DNMT1	1786	genome.wustl.edu	37	19	10290878	10290879	+	Intron	INS	-	-	T			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr19:10290878_10290879insT	ENST00000340748.4	-	4	681				DNMT1_ENST00000540357.1_Intron|DNMT1_ENST00000359526.4_Frame_Shift_Ins_p.V160fs			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1						cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	atcccagttacttgggaggctg	0.53																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.445+146->A	19.37:g.10290880_10290880dupT		Somatic		WXS	Illumina GAIIx	Phase_IV	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Frame_Shift_Ins	INS	pirsf_DNA_C5-MeTrfase_1_euk,pfam_C5_MeTfrase,pfam_BAH_dom,pfam_Cytosine_MeTrfase1_RFD,pfam_DMAP1-bd,pfam_Znf_CXXC,smart_BAH_dom,prints_C5_MeTfrase,pfscan_BAH_dom,pfscan_Znf_CXXC	p.V159fs	ENST00000340748.4	37	c.478_477	CCDS12228.1	19																																																																																			DNMT1	-	pirsf_DNA_C5-MeTrfase_1_euk	ENSG00000130816		0.530	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	DNMT1	HGNC	protein_coding	OTTHUMT00000451166.1	10	0.00	0	-	NM_001379		10290878	10290879	-1	no_errors	ENST00000359526	ensembl	human	known	69_37n	frame_shift_ins	9	79.07	34	INS	0.010:0.007	T
DTX2	113878	genome.wustl.edu	37	7	76121509	76121509	+	Silent	SNP	C	C	T	rs148279131	byFrequency	TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr7:76121509C>T	ENST00000324432.5	+	6	1458	c.948C>T	c.(946-948)agC>agT	p.S316S	DTX2_ENST00000446820.2_Silent_p.S316S|DTX2_ENST00000307569.8_Silent_p.S316S|DTX2_ENST00000446600.1_Silent_p.S225S|DTX2_ENST00000430490.2_Silent_p.S316S|DTX2_ENST00000413936.2_Silent_p.S316S	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	316					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						GCCCAGGGAGCGTCCCTGCCA	0.632																																						dbGAP											0													6.0	10.0	9.0					7																	76121509		1723	3883	5606	-	-	-	SO:0001819	synonymous_variant	0				CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073		"""RING-type (C3HC4) zinc fingers"""	15973	protein-coding gene	gene with protein product		613141	"""deltex (Drosophila) homolog 2"", ""deltex homolog 2 (Drosophila)"""			12670957	Standard	NM_020892		Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.948C>T	7.37:g.76121509C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Missense_Mutation	SNP	NULL	p.R14C	ENST00000324432.5	37	c.40	CCDS5587.1	7																																																																																			DTX2	-	NULL	ENSG00000091073		0.632	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	DTX2	Clone_based_vega_gene	protein_coding	OTTHUMT00000253104.2	12	0.00	0	C			76121509	76121509	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000435251	ensembl	human	known	69_37n	missense	19	33.33	10	SNP	0.015	T
ENTPD6	955	genome.wustl.edu	37	20	25196322	25196322	+	Silent	SNP	G	G	A			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr20:25196322G>A	ENST00000376652.4	+	7	847	c.684G>A	c.(682-684)gcG>gcA	p.A228A	ENTPD6_ENST00000433259.2_Silent_p.A228A|ENTPD6_ENST00000360031.2_Silent_p.A227A|Y_RNA_ENST00000365544.1_RNA|ENTPD6_ENST00000354989.5_Silent_p.A211A			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)	228					response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)	p.A228A(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						GCGTTTCGGCGTGGATCACCA	0.507																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											128.0	116.0	120.0					20																	25196322		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"""interleukin 6 signal transducer-2"""	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.684G>A	20.37:g.25196322G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Missense_Mutation	SNP	pfam_GDA1_CD39_NTPase	p.R149H	ENST00000376652.4	37	c.446	CCDS13170.1	20	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.44|10.44	1.350934|1.350934	0.24512|0.24512	.|.	.|.	ENSG00000197586|ENSG00000197586	ENST00000433417;ENST00000427553;ENST00000447877|ENST00000376666	.|.	.|.	.|.	5.27|5.27	-10.5|-10.5	0.00291|0.00291	.|.	.|.	.|.	.|.	.|.	T|T	0.49457|0.49457	0.1558|0.1558	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.62248|0.62248	-0.6894|-0.6894	4|4	.|.	.|.	.|.	-2.1396|-2.1396	11.1269|11.1269	0.48324|0.48324	0.2364:0.6055:0.0907:0.0674|0.2364:0.6055:0.0907:0.0674	.|.	.|.	.|.	.|.	H|M	149;86;121|52	.|.	.|.	R|V	+|+	2|1	0|0	ENTPD6|ENTPD6	25144322|25144322	0.000000|0.000000	0.05858|0.05858	0.061000|0.061000	0.19648|0.19648	0.469000|0.469000	0.32828|0.32828	-4.137000|-4.137000	0.00287|0.00287	-2.225000|-2.225000	0.00724|0.00724	-0.176000|-0.176000	0.13171|0.13171	CGT|GTG	ENTPD6	-	pfam_GDA1_CD39_NTPase	ENSG00000197586		0.507	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ENTPD6	HGNC	protein_coding	OTTHUMT00000078414.2	82	0.00	0	G			25196322	25196322	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000433417	ensembl	human	known	69_37n	missense	27	35.71	15	SNP	0.027	A
EPHA3	2042	genome.wustl.edu	37	3	89391074	89391074	+	Silent	SNP	C	C	T			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr3:89391074C>T	ENST00000336596.2	+	5	1365	c.1140C>T	c.(1138-1140)gtC>gtT	p.V380V	EPHA3_ENST00000494014.1_Silent_p.V380V|EPHA3_ENST00000452448.2_Silent_p.V380V	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	380	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.V380V(2)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		GCCCAAATGTCCGCTTCCTCC	0.483										TSP Lung(6;0.00050)																												dbGAP											2	Substitution - coding silent(2)	breast(2)											114.0	103.0	107.0					3																	89391074		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1140C>T	3.37:g.89391074C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q9H2V3|Q9H2V4	Silent	SNP	pirsf_Tyr_kinase_ephrin_rcpt,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Ephrin_rcpt_lig-bd_dom,pfam_Prot_kinase_cat_dom,pfam_Fibronectin_type3,pfam_SAM_2,pfam_SAM_type1,pfam_Tyr-kin_ephrin_A/B_rcpt-like,superfamily_Galactose-bd-like,superfamily_Kinase-like_dom,superfamily_Fibronectin_type3,superfamily_SAM/pointed,superfamily_Growth_fac_rcpt,smart_Ephrin_rcpt_lig-bd_dom,smart_Fibronectin_type3,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_SAM,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Fibronectin_type3,pfscan_SAM,pfscan_Prot_kinase_cat_dom	p.V380	ENST00000336596.2	37	c.1140	CCDS2922.1	3																																																																																			EPHA3	-	pirsf_Tyr_kinase_ephrin_rcpt,pfam_Fibronectin_type3,superfamily_Fibronectin_type3,smart_Fibronectin_type3,pfscan_Fibronectin_type3	ENSG00000044524		0.483	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EPHA3	HGNC	protein_coding	OTTHUMT00000352995.1	139	0.00	0	C	NM_005233		89391074	89391074	+1	no_errors	ENST00000336596	ensembl	human	known	69_37n	silent	84	22.94	25	SNP	0.709	T
EPO	2056	genome.wustl.edu	37	7	100320315	100320316	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr7:100320315_100320316insG	ENST00000252723.2	+	4	456_457	c.275_276insG	c.(274-279)cagggcfs	p.QG92fs		NM_000799.2	NP_000790.2	P01588	EPO_HUMAN	erythropoietin	92					aging (GO:0007568)|apoptotic process (GO:0006915)|blood circulation (GO:0008015)|cellular hyperosmotic response (GO:0071474)|cellular response to hypoxia (GO:0071456)|embryo implantation (GO:0007566)|erythrocyte maturation (GO:0043249)|hemoglobin biosynthetic process (GO:0042541)|negative regulation of calcium ion transport into cytosol (GO:0010523)|negative regulation of cation channel activity (GO:2001258)|negative regulation of erythrocyte apoptotic process (GO:1902251)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to axon injury (GO:0048678)|response to electrical stimulus (GO:0051602)|response to estrogen (GO:0043627)|response to hyperoxia (GO:0055093)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to salt stress (GO:0009651)|response to testosterone (GO:0033574)|response to vitamin A (GO:0033189)|signal transduction (GO:0007165)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	protein kinase activator activity (GO:0030295)			central_nervous_system(2)|endometrium(2)|lung(7)|prostate(1)	12	Lung NSC(181;0.041)|all_lung(186;0.0581)					GAAGTCTGGCAGGGCCTGGCCC	0.658																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			X02157	CCDS5705.1	7q21	2014-01-30			ENSG00000130427	ENSG00000130427		"""Endogenous ligands"""	3415	protein-coding gene	gene with protein product		133170				9799793, 3838366	Standard	NM_000799		Approved	EP	uc003uwi.3	P01588	OTTHUMG00000152121	ENST00000252723.2:c.278dupG	7.37:g.100320318_100320318dupG	ENSP00000252723:p.Gln92fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q2M2L6|Q549U2|Q9UDZ0|Q9UEZ5|Q9UHA0	Frame_Shift_Ins	INS	pfam_EPO_TPO,superfamily_4_helix_cytokine-like_core,pirsf_Erythroptn,prints_Erythroptn	p.L94fs	ENST00000252723.2	37	c.275_276	CCDS5705.1	7																																																																																			EPO	-	pfam_EPO_TPO,superfamily_4_helix_cytokine-like_core,pirsf_Erythroptn,prints_Erythroptn	ENSG00000130427		0.658	EPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EPO	HGNC	protein_coding	OTTHUMT00000325323.1	42	0.00	0	-	NM_000799		100320315	100320316	+1	no_errors	ENST00000252723	ensembl	human	known	69_37n	frame_shift_ins	29	14.71	5	INS	1.000:1.000	G
FAM71E2	284418	genome.wustl.edu	37	19	55870662	55870662	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr19:55870662delG	ENST00000424985.3	-	9	1767	c.1574delC	c.(1573-1575)ccafs	p.P525fs	CTD-2105E13.6_ENST00000591954.3_Frame_Shift_Del_p.Q75fs	NM_001145402.1	NP_001138874.1	Q8N5Q1	F71E2_HUMAN	family with sequence similarity 71, member E2	525	Pro-rich.									NS(1)|breast(3)|endometrium(2)|kidney(1)|skin(1)	8						TTTCTTCTTTGGAGCAGTGGG	0.622																																						dbGAP											0													10.0	10.0	10.0					19																	55870662		692	1590	2282	-	-	-	SO:0001589	frameshift_variant	0			AL834316		19q13.42	2014-04-02	2007-11-20	2007-11-20	ENSG00000180043	ENSG00000180043			25278	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 16"""	C19orf16			Standard	NM_001145402		Approved	DKFZp434G1729	uc002qkr.2	Q8N5Q1	OTTHUMG00000170357	ENST00000424985.3:c.1574delC	19.37:g.55870662delG	ENSP00000398617:p.Pro525fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8ND99	Frame_Shift_Del	DEL	pfam_DUF3699	p.P525fs	ENST00000424985.3	37	c.1574		19																																																																																			FAM71E2	-	NULL	ENSG00000180043		0.622	FAM71E2-010	NOVEL	basic|appris_principal	protein_coding	FAM71E2	HGNC	protein_coding	OTTHUMT00000409063.4	33	0.00	0	G	NM_001145402		55870662	55870662	-1	no_errors	ENST00000424985	ensembl	human	novel	69_37n	frame_shift_del	6	25.00	2	DEL	0.001	-
FGFR4	2264	genome.wustl.edu	37	5	176524359	176524359	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr5:176524359delG	ENST00000292408.4	+	17	2465	c.2220delG	c.(2218-2220)gtgfs	p.V740fs	FGFR4_ENST00000393637.1_Frame_Shift_Del_p.V700fs|FGFR4_ENST00000393648.2_Frame_Shift_Del_p.V672fs|FGFR4_ENST00000502906.1_Frame_Shift_Del_p.V740fs|FGFR4_ENST00000292410.3_Frame_Shift_Del_p.V700fs	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	740	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	AGCAGCTGGTGGAGGCGCTGG	0.682										TSP Lung(9;0.080)																												dbGAP											0													33.0	33.0	33.0					5																	176524359		2203	4299	6502	-	-	-	SO:0001589	frameshift_variant	0			AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.2220delG	5.37:g.176524359delG	ENSP00000292408:p.Val740fs	Somatic		WXS	Illumina GAIIx	Phase_IV	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Frame_Shift_Del	DEL	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,pfam_Ig_I-set,pfam_Immunoglobulin,superfamily_Kinase-like_dom,smart_Ig_sub,smart_Ig_sub2,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pirsf_Tyr_kinase_fibroblast_GF_rcpt,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom,pfscan_Ig-like	p.E741fs	ENST00000292408.4	37	c.2220	CCDS4410.1	5																																																																																			FGFR4	-	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pirsf_Tyr_kinase_fibroblast_GF_rcpt,pfscan_Prot_kinase_cat_dom	ENSG00000160867		0.682	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FGFR4	HGNC	protein_coding	OTTHUMT00000253410.1	71	0.00	0	G			176524359	176524359	+1	no_errors	ENST00000292408	ensembl	human	known	69_37n	frame_shift_del	15	11.76	2	DEL	0.999	-
GAS7	8522	genome.wustl.edu	37	17	9837520	9837520	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr17:9837520G>A	ENST00000432992.2	-	9	1008	c.848C>T	c.(847-849)gCg>gTg	p.A283V	GAS7_ENST00000437099.2_Missense_Mutation_p.A219V|GAS7_ENST00000579158.1_Missense_Mutation_p.A219V|GAS7_ENST00000585266.1_Missense_Mutation_p.A223V|GAS7_ENST00000580865.1_Missense_Mutation_p.A143V|GAS7_ENST00000323816.4_Missense_Mutation_p.A223V|GAS7_ENST00000396115.2_Intron|GAS7_ENST00000583882.1_Intron|GAS7_ENST00000540214.1_Intron|GAS7_ENST00000542249.1_Missense_Mutation_p.A219V	NM_201433.1	NP_958839.1	O60861	GAS7_HUMAN	growth arrest-specific 7	283	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				actin filament bundle assembly (GO:0051017)|actin filament polymerization (GO:0030041)|cell cycle arrest (GO:0007050)|neuron projection morphogenesis (GO:0048812)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|ruffle (GO:0001726)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A283V(2)|p.A143V(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(7)|lung(18)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	39						TGCTTCGTCCGCCAGGCTCTT	0.537			T	MLL	AML*																																	dbGAP		Dom	yes		17	17p	8522	growth arrest-specific 7		L	3	Substitution - Missense(3)	breast(2)|large_intestine(1)											107.0	78.0	88.0					17																	9837520		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB007854	CCDS11152.1, CCDS42263.1, CCDS45611.1, CCDS58518.1	17p13.1	2004-02-18							4169	protein-coding gene	gene with protein product		603127				9736752	Standard	NM_001130831		Approved	KIAA0394, MGC1348	uc002gmg.1	O60861		ENST00000432992.2:c.848C>T	17.37:g.9837520G>A	ENSP00000407552:p.Ala283Val	Somatic		WXS	Illumina GAIIx	Phase_IV	A8KAC2|B2RCK9|O43144|Q53Y77|Q7Z571	Missense_Mutation	SNP	pfam_FCH,pfam_WW_Rsp5_WWP,pfam_SH3_domain,pfam_SH3_2,superfamily_SH3_domain,superfamily_WW_Rsp5_WWP,smart_SH3_domain,smart_WW_Rsp5_WWP,smart_FCH,pfscan_FCH,pfscan_SH3_domain,pfscan_WW_Rsp5_WWP	p.A283V	ENST00000432992.2	37	c.848	CCDS11152.1	17	.	.	.	.	.	.	.	.	.	.	G	16.06	3.015064	0.54468	.	.	ENSG00000007237	ENST00000323816;ENST00000396115;ENST00000437099;ENST00000432992;ENST00000537970;ENST00000541114	T;T	0.55234	2.23;0.53	4.93	4.93	0.64822	Fps/Fes/Fer/CIP4 homology (3);	0.134081	0.48286	D	0.000185	T	0.55689	0.1936	M	0.66939	2.045	0.53688	D	0.999973	D;D;P;D	0.59357	0.985;0.958;0.695;0.985	P;B;B;P	0.45660	0.489;0.353;0.124;0.489	T	0.59220	-0.7495	9	.	.	.	7.9507	15.1847	0.72989	0.0:0.0:1.0:0.0	.	235;223;143;283	B7Z2L1;A8KAC2;O60861-2;O60861	.;.;.;GAS7_HUMAN	V	283;223;222;143;223;97	ENSP00000379421:A223V;ENSP00000410108:A222V	.	A	-	2	0	GAS7	9778245	0.997000	0.39634	0.486000	0.27416	0.731000	0.41821	5.134000	0.64770	2.587000	0.87381	0.655000	0.94253	GCG	GAS7	-	pfam_FCH,smart_FCH,pfscan_FCH	ENSG00000007237		0.537	GAS7-017	KNOWN	basic|appris_principal|CCDS	protein_coding	GAS7	HGNC	protein_coding	OTTHUMT00000439883.1	210	0.00	0	G	NM_003644, NM_201432, NM_201433		9837520	9837520	-1	no_errors	ENST00000432992	ensembl	human	known	69_37n	missense	78	31.90	37	SNP	0.798	A
GPR155	151556	genome.wustl.edu	37	2	175335282	175335282	+	Splice_Site	SNP	G	G	C			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr2:175335282G>C	ENST00000392552.2	-	4	1100	c.862C>G	c.(862-864)Ctg>Gtg	p.L288V	GPR155_ENST00000295500.4_Splice_Site_p.L288V|GPR155_ENST00000392551.2_Splice_Site_p.L288V	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155	288					cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.L288V(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						GGCAGCACCAGACTGAAGAAA	0.448																																						dbGAP											1	Substitution - Missense(1)	breast(1)											70.0	61.0	64.0					2																	175335282		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0			AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328			22951	protein-coding gene	gene with protein product						12679517	Standard	NM_001033045		Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.861-1C>G	2.37:g.175335282G>C		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	Missense_Mutation	SNP	pfam_Auxin_eff,pfam_DEP_dom,smart_DEP_dom,pfscan_DEP_dom	p.L288V	ENST00000392552.2	37	c.862	CCDS2259.1	2	.	.	.	.	.	.	.	.	.	.	G	16.96	3.266843	0.59540	.	.	ENSG00000163328	ENST00000392552;ENST00000392551;ENST00000295500	T;T;T	0.55052	0.54;0.54;0.54	6.07	2.33	0.28932	.	0.000000	0.85682	D	0.000000	T	0.65026	0.2652	M	0.63428	1.95	0.58432	D	0.999996	D	0.76494	0.999	D	0.74348	0.983	T	0.62627	-0.6814	10	0.46703	T	0.11	-6.3696	10.3438	0.43895	0.2609:0.0:0.7391:0.0	.	288	Q7Z3F1	GP155_HUMAN	V	288	ENSP00000376335:L288V;ENSP00000376334:L288V;ENSP00000295500:L288V	ENSP00000295500:L288V	L	-	1	2	GPR155	175043528	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	1.482000	0.35486	0.459000	0.27016	-0.150000	0.13652	CTG	GPR155	-	pfam_Auxin_eff	ENSG00000163328		0.448	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPR155	HGNC	protein_coding	OTTHUMT00000255455.1	78	0.00	0	G	NM_152529	Missense_Mutation	175335282	175335282	-1	no_errors	ENST00000295500	ensembl	human	known	69_37n	missense	41	14.58	7	SNP	1.000	C
HDAC4	9759	genome.wustl.edu	37	2	240011772	240011772	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr2:240011772C>T	ENST00000345617.3	-	18	3097	c.2306G>A	c.(2305-2307)gGg>gAg	p.G769E	HDAC4_ENST00000543185.1_Missense_Mutation_p.G353E	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	769	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.G769V(1)|p.G769E(1)		NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		GCGGGCTGCCCCCGCCGAGTG	0.647																																						dbGAP											2	Substitution - Missense(2)	lung(1)|breast(1)											59.0	59.0	59.0					2																	240011772		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"""brachydactyly-mental retardation syndrome"""	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.2306G>A	2.37:g.240011772C>T	ENSP00000264606:p.Gly769Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q9UND6	Missense_Mutation	SNP	pfam_His_deacetylse_dom,pfam_Hist_deacetylase_Gln_rich_N,pfam_Arb2_domain,pirsf_Histone_deAcase_II_euk,prints_His_deacetylse	p.G769E	ENST00000345617.3	37	c.2306	CCDS2529.1	2	.	.	.	.	.	.	.	.	.	.	C	12.38	1.921244	0.33908	.	.	ENSG00000068024	ENST00000345617;ENST00000456922;ENST00000543185	T;T	0.67171	-0.25;-0.25	3.98	3.98	0.46160	Histone deacetylase domain (2);	0.099758	0.64402	D	0.000002	T	0.41026	0.1141	N	0.01473	-0.845	0.52501	D	0.999952	B;B	0.31893	0.023;0.345	B;B	0.38296	0.035;0.27	T	0.46911	-0.9157	10	0.06625	T	0.88	.	16.9494	0.86240	0.0:1.0:0.0:0.0	.	737;769	Q53SM2;P56524	.;HDAC4_HUMAN	E	769;657;353	ENSP00000264606:G769E;ENSP00000440481:G353E	ENSP00000264606:G769E	G	-	2	0	HDAC4	239676709	0.943000	0.32029	0.266000	0.24541	0.229000	0.25112	4.600000	0.61083	2.168000	0.68352	0.557000	0.71058	GGG	HDAC4	-	pfam_His_deacetylse_dom,pirsf_Histone_deAcase_II_euk	ENSG00000068024		0.647	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HDAC4	HGNC	protein_coding	OTTHUMT00000257174.2	35	0.00	0	C	NM_006037		240011772	240011772	-1	no_errors	ENST00000345617	ensembl	human	known	69_37n	missense	50	39.02	32	SNP	0.998	T
HMHA1	23526	genome.wustl.edu	37	19	1081038	1081039	+	Frame_Shift_Ins	INS	-	-	CGGC	rs550923844	byFrequency	TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr19:1081038_1081039insCGGC	ENST00000313093.2	+	17	2396_2397	c.2165_2166insCGGC	c.(2164-2169)tacttcfs	p.F723fs	HMHA1_ENST00000590214.1_Frame_Shift_Ins_p.F750fs|HMHA1_ENST00000586866.1_Frame_Shift_Ins_p.F727fs|HMHA1_ENST00000590577.1_Frame_Shift_Ins_p.F358fs|HMHA1_ENST00000543365.1_Frame_Shift_Ins_p.F606fs|HMHA1_ENST00000536472.1_Frame_Shift_Ins_p.F591fs|HMHA1_ENST00000539243.2_Frame_Shift_Ins_p.F739fs	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	723					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(7)|ovary(1)|prostate(2)	16		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGCTACGTCTACTTCCAGGGTG	0.688																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			D86976	CCDS32863.1, CCDS58637.1, CCDS74242.1, CCDS74243.1	19p13.3	2011-09-07				ENSG00000180448		"""Rho GTPase activating proteins"""	17102	protein-coding gene	gene with protein product		601155				9820596, 9039502	Standard	NM_012292		Approved	KIAA0223, HA-1, ARHGAP45	uc010xgd.2	Q92619		Exception_encountered	19.37:g.1081038_1081039insCGGC	ENSP00000316772:p.Phe723fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Frame_Shift_Ins	INS	pfam_RhoGAP_dom,superfamily_Rho_GTPase_activation_prot,smart_FCH,smart_Prot_Kinase_C-like_PE/DAG-bd,smart_RhoGAP_dom,pfscan_Prot_Kinase_C-like_PE/DAG-bd,pfscan_RhoGAP_dom	p.F723fs	ENST00000313093.2	37	c.2165_2166	CCDS32863.1	19																																																																																			HMHA1	-	smart_Prot_Kinase_C-like_PE/DAG-bd,pfscan_Prot_Kinase_C-like_PE/DAG-bd	ENSG00000180448		0.688	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	HMHA1	HGNC	protein_coding	OTTHUMT00000458026.1	12	0.00	0	-			1081038	1081039	+1	no_errors	ENST00000313093	ensembl	human	known	69_37n	frame_shift_ins	3	62.50	5	INS	1.000:1.000	CGGC
IGHV1-18	28468	genome.wustl.edu	37	14	106641745	106641745	+	RNA	SNP	G	G	T	rs375042034		TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr14:106641745G>T	ENST00000390605.2	-	0	227									immunoglobulin heavy variable 1-18																		GGGGCCTGTCGCACCCAGCTG	0.552																																						dbGAP											0													182.0	171.0	175.0					14																	106641745		2001	4171	6172	-	-	-			0			M99641		14q32.33	2012-02-08			ENSG00000211945	ENSG00000211945		"""Immunoglobulins / IGH locus"""	5549	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152276		14.37:g.106641745G>T		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	pfam_Ig_V-set,smart_Ig_V-set_subgr,pfscan_Ig-like	p.R57	ENST00000390605.2	37	c.169		14																																																																																			IGHV1-18	-	pfam_Ig_V-set,smart_Ig_V-set_subgr,pfscan_Ig-like	ENSG00000211945		0.552	IGHV1-18-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IGHV1-18	HGNC	IG_V_gene	OTTHUMT00000325664.1	192	0.52	1	G	NG_001019		106641745	106641745	-1	no_stop_codon	ENST00000390605	ensembl	human	known	69_37n	silent	134	35.10	73	SNP	0.897	T
IRS1	3667	genome.wustl.edu	37	2	227661200	227661200	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr2:227661200delC	ENST00000305123.5	-	1	3275	c.2255delG	c.(2254-2256)ggcfs	p.G752fs	IRS1_ENST00000498335.1_5'Flank	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	752					cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid catabolic process (GO:0016042)|mammary gland development (GO:0030879)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein kinase B signaling (GO:0043491)|protein localization to nucleus (GO:0034504)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	caveola (GO:0005901)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|insulin receptor complex (GO:0005899)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		GTCCTCAGGGCCGTAGTAGCA	0.612																																						dbGAP											0													129.0	144.0	139.0					2																	227661200		2203	4299	6502	-	-	-	SO:0001589	frameshift_variant	0				CCDS2463.1	2q36	2013-01-10			ENSG00000169047	ENSG00000169047		"""Pleckstrin homology (PH) domain containing"""	6125	protein-coding gene	gene with protein product		147545				1648180	Standard	NM_005544		Approved	HIRS-1	uc002voh.4	P35568	OTTHUMG00000133179	ENST00000305123.5:c.2255delG	2.37:g.227661200delC	ENSP00000304895:p.Gly752fs	Somatic		WXS	Illumina GAIIx	Phase_IV		Frame_Shift_Del	DEL	pfam_Insln_rcpt_S1,pfam_Pleckstrin_homology,smart_Pleckstrin_homology,smart_Insln_rcpt_S1,prints_Insln_rcpt_S1,pfscan_Pleckstrin_homology,pfscan_Insln_rcpt_S1	p.G752fs	ENST00000305123.5	37	c.2255	CCDS2463.1	2																																																																																			IRS1	-	NULL	ENSG00000169047		0.612	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IRS1	HGNC	protein_coding	OTTHUMT00000256886.3	34	0.00	0	C	NM_005544		227661200	227661200	-1	no_errors	ENST00000305123	ensembl	human	known	69_37n	frame_shift_del	8	20.00	2	DEL	0.406	-
KCNA3	3738	genome.wustl.edu	37	1	111216103	111216104	+	Frame_Shift_Ins	INS	-	-	AA			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr1:111216103_111216104insAA	ENST00000369769.2	-	1	1551_1552	c.1328_1329insTT	c.(1327-1329)acafs	p.T443fs		NM_002232.3	NP_002223.3	P22001	KCNA3_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 3	443					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	membrane raft (GO:0045121)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|voltage-gated ion channel activity (GO:0005244)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(7)|ovary(4)|pancreas(1)|prostate(3)|skin(1)	38		all_cancers(81;3.92e-06)|all_epithelial(167;1.28e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0235)|Colorectal(144;0.0306)|all cancers(265;0.0752)|Epithelial(280;0.0821)|COAD - Colon adenocarcinoma(174;0.132)|LUSC - Lung squamous cell carcinoma(189;0.133)	Dalfampridine(DB06637)	AACCCACTGTTGTCATGGTTAC	0.564																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			L23499	CCDS828.2	1p13.3	2012-07-05			ENSG00000177272	ENSG00000177272		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6221	protein-coding gene	gene with protein product		176263				2251283, 16382104	Standard	NM_002232		Approved	Kv1.3, MK3, HLK3, HPCN3	uc001dzv.1	P22001	OTTHUMG00000034493	ENST00000369769.2:c.1328_1329insTT	1.37:g.111216103_111216104insAA	ENSP00000358784:p.Thr443fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5VWN2	Frame_Shift_Ins	INS	pfam_Ion_trans_dom,pfam_T1-type_BTB,pfam_Ion_trans_2,superfamily_BTB/POZ_fold,smart_BTB/POZ-like,prints_K_chnl,prints_K_chnl_volt-dep_Kv1.3,prints_K_chnl_volt-dep_Kv1,prints_K_chnl_volt-dep_Kv	p.T444fs	ENST00000369769.2	37	c.1329_1328	CCDS828.2	1																																																																																			KCNA3	-	pfam_Ion_trans_dom,pfam_Ion_trans_2,prints_K_chnl	ENSG00000177272		0.564	KCNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KCNA3	HGNC	protein_coding	OTTHUMT00000083391.1	81	0.00	0	-	NM_002232		111216103	111216104	-1	no_errors	ENST00000369769	ensembl	human	known	69_37n	frame_shift_ins	24	36.84	14	INS	0.746:1.000	AA
KLHL22	84861	genome.wustl.edu	37	22	20800742	20800742	+	Silent	SNP	C	C	T			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr22:20800742C>T	ENST00000328879.4	-	6	1683	c.1527G>A	c.(1525-1527)agG>agA	p.R509R	KLHL22_ENST00000440659.2_Silent_p.R366R	NM_032775.3	NP_116164.2	Q53GT1	KLH22_HUMAN	kelch-like family member 22	509					cell division (GO:0051301)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein monoubiquitination (GO:0006513)	centrosome (GO:0005813)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|polar microtubule (GO:0005827)		p.R509R(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|skin(2)|upper_aerodigestive_tract(1)	20	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			GGTGCACGTCCCTCCTGTATC	0.582																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											64.0	54.0	58.0					22																	20800742		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS13780.1	22q11.21	2013-01-30	2013-01-30		ENSG00000099910	ENSG00000099910		"""Kelch-like"", ""BTB/POZ domain containing"""	25888	protein-coding gene	gene with protein product			"""kelch-like 22 (Drosophila)"""			12477932	Standard	NM_032775		Approved	FLJ14360, KELCHL	uc002zsl.2	Q53GT1	OTTHUMG00000150778	ENST00000328879.4:c.1527G>A	22.37:g.20800742C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K3Q4|A8MTV3|B7Z2G1|D3DX30|Q96B68|Q96KC6	Missense_Mutation	SNP	pfam_Kelch_1	p.G56R	ENST00000328879.4	37	c.166	CCDS13780.1	22																																																																																			KLHL22	-	NULL	ENSG00000099910		0.582	KLHL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KLHL22	HGNC	protein_coding	OTTHUMT00000320045.2	189	0.53	1	C	NM_032775		20800742	20800742	-1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000429594	ensembl	human	known	69_37n	missense	89	64.98	167	SNP	0.875	T
KRI1	65095	genome.wustl.edu	37	19	10670359	10670359	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr19:10670359G>A	ENST00000312962.6	-	11	990	c.971C>T	c.(970-972)gCg>gTg	p.A324V	KRI1_ENST00000361821.5_Missense_Mutation_p.A320V|KRI1_ENST00000537964.1_5'Flank	NM_023008.3	NP_075384.3	Q8N9T8	KRI1_HUMAN	KRI1 homolog (S. cerevisiae)	318	Glu-rich.					nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.A324V(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			CACGGAGGACGCGATGCTGCG	0.622																																						dbGAP											1	Substitution - Missense(1)	breast(1)											85.0	82.0	83.0					19																	10670359		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS12242.1	19p13.2	2008-02-05			ENSG00000129347	ENSG00000129347			25769	protein-coding gene	gene with protein product						12878157	Standard	NM_023008		Approved	FLJ12949	uc002moy.1	Q8N9T8	OTTHUMG00000150343	ENST00000312962.6:c.971C>T	19.37:g.10670359G>A	ENSP00000320917:p.Ala324Val	Somatic		WXS	Illumina GAIIx	Phase_IV	Q2M1R5|Q2M1R7|Q7L5J7|Q96G92|Q9BU50|Q9H6I1|Q9H978	Missense_Mutation	SNP	pfam_KRR1-interact_protein_1	p.A324V	ENST00000312962.6	37	c.971	CCDS12242.1	19	.	.	.	.	.	.	.	.	.	.	G	9.831	1.188448	0.21954	.	.	ENSG00000129347	ENST00000312962;ENST00000361821;ENST00000541101	T;T	0.10573	3.03;2.86	5.25	3.11	0.35812	.	0.240637	0.40064	N	0.001184	T	0.10981	0.0268	M	0.66297	2.02	0.09310	N	1	P;B	0.37731	0.607;0.302	B;B	0.29176	0.099;0.04	T	0.13656	-1.0501	10	0.35671	T	0.21	-9.9359	11.0822	0.48066	0.1564:0.0:0.8436:0.0	.	324;320	Q8N9T8;D3YTE0	KRI1_HUMAN;.	V	324;320;324	ENSP00000320917:A324V;ENSP00000355366:A320V	ENSP00000320917:A324V	A	-	2	0	KRI1	10531359	0.332000	0.24722	0.009000	0.14445	0.073000	0.16967	3.154000	0.50693	0.601000	0.29879	0.591000	0.81541	GCG	KRI1	-	NULL	ENSG00000129347		0.622	KRI1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	KRI1	HGNC	protein_coding	OTTHUMT00000317705.1	156	0.64	1	G	NM_023008		10670359	10670359	-1	no_errors	ENST00000312962	ensembl	human	known	69_37n	missense	52	74.29	156	SNP	0.039	A
KRTAP4-3	85290	genome.wustl.edu	37	17	39324182	39324182	+	Silent	SNP	C	C	T			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr17:39324182C>T	ENST00000391356.2	-	1	242	c.243G>A	c.(241-243)agG>agA	p.R81R		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	81	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R81R(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			agcaggaaggcctgcagcaac	0.617																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											3.0	4.0	4.0					17																	39324182		1460	3277	4737	-	-	-	SO:0001819	synonymous_variant	0			AJ406935	CCDS42331.1	17q21.2	2013-06-25			ENSG00000196156	ENSG00000196156		"""Keratin associated proteins"""	18908	protein-coding gene	gene with protein product							Standard	NM_033187		Approved	KAP4.3	uc010cxl.3	Q9BYR4	OTTHUMG00000133639	ENST00000391356.2:c.243G>A	17.37:g.39324182C>T		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	pfam_Keratin-assoc	p.R81	ENST00000391356.2	37	c.243	CCDS42331.1	17																																																																																			KRTAP4-3	-	pfam_Keratin-assoc	ENSG00000196156		0.617	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KRTAP4-3	HGNC	protein_coding	OTTHUMT00000257784.1	123	0.00	0	C			39324182	39324182	-1	no_errors	ENST00000391356	ensembl	human	known	69_37n	silent	48	17.24	10	SNP	0.000	T
KRTAP4-3	85290	genome.wustl.edu	37	17	39324272	39324272	+	Silent	SNP	C	C	T			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr17:39324272C>T	ENST00000391356.2	-	1	152	c.153G>A	c.(151-153)agG>agA	p.R51R		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	51	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R51R(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			agcaggaaggcctgcagcaac	0.652																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											7.0	9.0	8.0					17																	39324272		1802	3691	5493	-	-	-	SO:0001819	synonymous_variant	0			AJ406935	CCDS42331.1	17q21.2	2013-06-25			ENSG00000196156	ENSG00000196156		"""Keratin associated proteins"""	18908	protein-coding gene	gene with protein product							Standard	NM_033187		Approved	KAP4.3	uc010cxl.3	Q9BYR4	OTTHUMG00000133639	ENST00000391356.2:c.153G>A	17.37:g.39324272C>T		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	pfam_Keratin-assoc	p.R51	ENST00000391356.2	37	c.153	CCDS42331.1	17																																																																																			KRTAP4-3	-	pfam_Keratin-assoc	ENSG00000196156		0.652	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KRTAP4-3	HGNC	protein_coding	OTTHUMT00000257784.1	134	0.00	0	C			39324272	39324272	-1	no_errors	ENST00000391356	ensembl	human	known	69_37n	silent	75	12.50	11	SNP	0.000	T
LPGAT1	9926	genome.wustl.edu	37	1	211956599	211956600	+	Frame_Shift_Ins	INS	-	-	CT			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr1:211956599_211956600insCT	ENST00000366997.4	-	5	924_925	c.698_699insAG	c.(697-699)agtfs	p.S233fs	LPGAT1_ENST00000366996.1_Frame_Shift_Ins_p.S233fs	NM_014873.2	NP_055688.1	Q92604	LGAT1_HUMAN	lysophosphatidylglycerol acyltransferase 1	233					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring acyl groups (GO:0016746)	p.S233fs*11(1)		breast(1)|endometrium(2)|large_intestine(1)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				OV - Ovarian serous cystadenocarcinoma(81;0.00773)|all cancers(67;0.0765)|Epithelial(68;0.114)		CTCCTGCTGGACTTCCATTTTT	0.351																																						dbGAP											1	Insertion - Frameshift(1)	breast(1)																																								-	-	-	SO:0001589	frameshift_variant	0			D86960	CCDS31018.1	1q32.3	2008-05-14	2004-11-25	2004-11-26	ENSG00000123684	ENSG00000123684			28985	protein-coding gene	gene with protein product		610473	"""family with sequence similarity 34, member A"""	FAM34A		9039502, 15485873	Standard	NM_014873		Approved	KIAA0205, FAM34A1, NET8	uc001hiv.3	Q92604	OTTHUMG00000037120	ENST00000366997.4:c.697_698dupAG	1.37:g.211956600_211956601dupCT	ENSP00000355964:p.Ser233fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q53YL2	Frame_Shift_Ins	INS	pfam_Acyltransferase,smart_Acyltransferase	p.S233fs	ENST00000366997.4	37	c.699_698	CCDS31018.1	1																																																																																			LPGAT1	-	NULL	ENSG00000123684		0.351	LPGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LPGAT1	HGNC	protein_coding	OTTHUMT00000090150.1	90	0.00	0	-	NM_014873		211956599	211956600	-1	no_errors	ENST00000366996	ensembl	human	known	69_37n	frame_shift_ins	52	53.15	59	INS	1.000:1.000	CT
MAN1A2	10905	genome.wustl.edu	37	1	117910860	117910860	+	Silent	SNP	C	C	T			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr1:117910860C>T	ENST00000356554.3	+	1	790	c.55C>T	c.(55-57)Ctg>Ttg	p.L19L	RP11-188D8.1_ENST00000604156.1_lincRNA|MAN1A2_ENST00000482811.1_3'UTR	NM_006699.3	NP_006690.1	O60476	MA1A2_HUMAN	mannosidase, alpha, class 1A, member 2	19					cellular protein metabolic process (GO:0044267)|lung alveolus development (GO:0048286)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.L19L(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	27	Lung SC(450;0.225)	all_cancers(81;7.9e-06)|all_epithelial(167;7.39e-07)|all_lung(203;2.84e-06)|Lung NSC(69;1.99e-05)		Lung(183;0.0688)|Kidney(133;0.114)|LUSC - Lung squamous cell carcinoma(189;0.223)|KIRC - Kidney renal clear cell carcinoma(1967;0.237)|Colorectal(144;0.243)		ACCTCTGAACCTGGGGCCGCC	0.483																																					Ovarian(33;199 881 8228 13687 31538)	dbGAP											1	Substitution - coding silent(1)	breast(1)											89.0	93.0	92.0					1																	117910860		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF027156	CCDS895.1	1p13	2008-02-05			ENSG00000198162	ENSG00000198162			6822	protein-coding gene	gene with protein product		604345				9592125	Standard	NM_006699		Approved	MAN1B	uc001ehd.1	O60476	OTTHUMG00000012149	ENST00000356554.3:c.55C>T	1.37:g.117910860C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q9H510	Silent	SNP	pfam_Glyco_hydro_47,superfamily_Glyco_hydro_47,prints_Glyco_hydro_47	p.L19	ENST00000356554.3	37	c.55	CCDS895.1	1																																																																																			MAN1A2	-	NULL	ENSG00000198162		0.483	MAN1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MAN1A2	HGNC	protein_coding	OTTHUMT00000033593.1	68	0.00	0	C	NM_006699		117910860	117910860	+1	no_errors	ENST00000356554	ensembl	human	known	69_37n	silent	57	36.67	33	SNP	1.000	T
MAP1A	4130	genome.wustl.edu	37	15	43820168	43820168	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr15:43820168C>A	ENST00000300231.5	+	4	6947	c.6497C>A	c.(6496-6498)tCa>tAa	p.S2166*	MAP1A_ENST00000399453.1_Nonsense_Mutation_p.S2166*|MAP1A_ENST00000382031.1_Nonsense_Mutation_p.S2404*			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	2166					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)	p.S2166*(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	TTCCCTGCTTCAGCCTTTGGC	0.622																																						dbGAP											1	Substitution - Nonsense(1)	breast(1)											89.0	99.0	95.0					15																	43820168		2017	4163	6180	-	-	-	SO:0001587	stop_gained	0			U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.6497C>A	15.37:g.43820168C>A	ENSP00000300231:p.Ser2166*	Somatic		WXS	Illumina GAIIx	Phase_IV	O95643|Q12973|Q15882|Q9UJT4	Nonsense_Mutation	SNP	NULL	p.S2166*	ENST00000300231.5	37	c.6497	CCDS42031.1	15	.	.	.	.	.	.	.	.	.	.	C	49	15.131706	0.99823	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	.	.	.	4.75	4.75	0.60458	.	0.000000	0.28589	N	0.014802	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.7596	14.7616	0.69610	0.0:1.0:0.0:0.0	.	.	.	.	X	2404;2166;2166	.	ENSP00000300231:S2166X	S	+	2	0	MAP1A	41607460	1.000000	0.71417	0.999000	0.59377	0.978000	0.69477	4.868000	0.63021	2.458000	0.83093	0.655000	0.94253	TCA	MAP1A	-	NULL	ENSG00000166963		0.622	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	MAP1A	HGNC	protein_coding	OTTHUMT00000132894.5	67	0.00	0	C	NM_002373		43820168	43820168	+1	no_errors	ENST00000399453	ensembl	human	known	69_37n	nonsense	16	27.27	6	SNP	1.000	A
MPHOSPH10	10199	genome.wustl.edu	37	2	71360269	71360269	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr2:71360269G>A	ENST00000244230.2	+	2	683	c.331G>A	c.(331-333)Gaa>Aaa	p.E111K	MPHOSPH10_ENST00000498451.2_Missense_Mutation_p.E111K|MPHOSPH10_ENST00000468427.1_3'UTR|MCEE_ENST00000244217.5_5'Flank	NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	111					negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)	p.E111K(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						CCCAGAGAGTGAAGAACAGGA	0.408																																						dbGAP											1	Substitution - Missense(1)	breast(1)											67.0	66.0	66.0					2																	71360269		2203	4300	6503	-	-	-	SO:0001583	missense	0			X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 106"""	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.331G>A	2.37:g.71360269G>A	ENSP00000244230:p.Glu111Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	A0AVJ8	Missense_Mutation	SNP	pfam_Mpp10,pirsf_snoRNP_Mpp10	p.E111K	ENST00000244230.2	37	c.331	CCDS1916.1	2	.	.	.	.	.	.	.	.	.	.	G	18.52	3.641661	0.67244	.	.	ENSG00000124383	ENST00000244230	T	0.09911	2.93	4.59	3.71	0.42584	.	0.275863	0.39407	N	0.001377	T	0.19525	0.0469	L	0.48642	1.525	0.41765	D	0.989733	D;D	0.76494	0.999;0.992	D;P	0.83275	0.996;0.883	T	0.11891	-1.0569	10	0.16896	T	0.51	.	7.083	0.25241	0.0971:0.1746:0.7283:0.0	.	111;111	B3KPV5;O00566	.;MPP10_HUMAN	K	111	ENSP00000244230:E111K	ENSP00000244230:E111K	E	+	1	0	MPHOSPH10	71213777	0.995000	0.38212	0.006000	0.13384	0.956000	0.61745	3.701000	0.54793	1.244000	0.43870	0.555000	0.69702	GAA	MPHOSPH10	-	pfam_Mpp10,pirsf_snoRNP_Mpp10	ENSG00000124383		0.408	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MPHOSPH10	HGNC	protein_coding	OTTHUMT00000251924.2	113	0.00	0	G	NM_005791		71360269	71360269	+1	no_errors	ENST00000244230	ensembl	human	known	69_37n	missense	66	10.81	8	SNP	0.206	A
MTMR7	9108	genome.wustl.edu	37	8	17188758	17188758	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr8:17188758C>T	ENST00000180173.5	-	7	800	c.766G>A	c.(766-768)Ggc>Agc	p.G256S	MTMR7_ENST00000521857.1_Missense_Mutation_p.G256S	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	256	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				inositol phosphate dephosphorylation (GO:0046855)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	protein tyrosine phosphatase activity (GO:0004725)	p.G256S(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(8)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	32				Colorectal(111;0.112)		TTCTCATAGCCTTTCCCTGCA	0.393																																						dbGAP											1	Substitution - Missense(1)	breast(1)											175.0	149.0	158.0					8																	17188758		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF073482	CCDS34851.1	8p22	2011-06-09			ENSG00000003987	ENSG00000003987		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7454	protein-coding gene	gene with protein product		603562				9736772, 12890864	Standard	NM_004686		Approved		uc003wxm.3	Q9Y216	OTTHUMG00000163771	ENST00000180173.5:c.766G>A	8.37:g.17188758C>T	ENSP00000180173:p.Gly256Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	A1L4K9|B4DG87|Q68DX4	Missense_Mutation	SNP	pfam_Myotub-related,smart_Tyr_Pase_cat,pfscan_Tyr/Dual-specificity_Pase	p.G256S	ENST00000180173.5	37	c.766	CCDS34851.1	8	.	.	.	.	.	.	.	.	.	.	C	35	5.470603	0.96274	.	.	ENSG00000003987	ENST00000180173;ENST00000521857	D;D	0.94793	-3.52;-3.52	4.84	4.84	0.62591	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.000000	0.85682	D	0.000000	D	0.98463	0.9488	H	0.97829	4.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99517	1.0957	10	0.87932	D	0	.	18.5404	0.91025	0.0:1.0:0.0:0.0	.	256;256	Q9Y216-2;Q9Y216	.;MTMR7_HUMAN	S	256	ENSP00000180173:G256S;ENSP00000429733:G256S	ENSP00000180173:G256S	G	-	1	0	MTMR7	17233129	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.630000	0.83225	2.683000	0.91414	0.655000	0.94253	GGC	MTMR7	-	pfam_Myotub-related	ENSG00000003987		0.393	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MTMR7	HGNC	protein_coding	OTTHUMT00000375311.1	170	0.00	0	C	NM_004686		17188758	17188758	-1	no_errors	ENST00000180173	ensembl	human	known	69_37n	missense	68	43.33	52	SNP	1.000	T
MYH13	8735	genome.wustl.edu	37	17	10233721	10233721	+	Silent	SNP	C	C	T			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr17:10233721C>T	ENST00000418404.3	-	20	2581	c.2418G>A	c.(2416-2418)aaG>aaA	p.K806K	RP11-401O9.3_ENST00000577743.1_RNA|MYH13_ENST00000252172.4_Silent_p.K806K			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	806	IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.				cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.K806K(2)		breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						CCATCATCTTCTTGAACTCCA	0.537																																						dbGAP											2	Substitution - coding silent(2)	breast(2)											97.0	100.0	99.0					17																	10233721		2201	4299	6500	-	-	-	SO:0001819	synonymous_variant	0			AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"""Myosins / Myosin superfamily : Class II"""	7571	protein-coding gene	gene with protein product	"""extraocular muscle myosin heavy chain"", ""extraocular myosin heavy chain"""	603487	"""myosin, heavy polypeptide 13, skeletal muscle"""			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.2418G>A	17.37:g.10233721C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	O95252|Q9P0U8	Silent	SNP	pfam_Myosin_tail,pfam_Myosin_head_motor_dom,pfam_Myosin_N,superfamily_Prefoldin,smart_Myosin_head_motor_dom,prints_Myosin_head_motor_dom,pfscan_IQ_motif_EF-hand-BS	p.K806	ENST00000418404.3	37	c.2418	CCDS45613.1	17																																																																																			MYH13	-	pfscan_IQ_motif_EF-hand-BS	ENSG00000006788		0.537	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	MYH13	HGNC	protein_coding	OTTHUMT00000442255.1	136	0.00	0	C	NM_003802		10233721	10233721	-1	no_errors	ENST00000252172	ensembl	human	known	69_37n	silent	121	14.79	21	SNP	1.000	T
NACC1	112939	genome.wustl.edu	37	19	13246395	13246395	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr19:13246395delC	ENST00000292431.4	+	2	500	c.374delC	c.(373-375)tccfs	p.S125fs		NM_052876.3	NP_443108.1	Q96RE7	NACC1_HUMAN	nucleus accumbens associated 1, BEN and BTB (POZ) domain containing	125					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|protein homooligomerization (GO:0051260)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear body (GO:0016604)|nucleus (GO:0005634)				endometrium(3)|large_intestine(2)|lung(3)|skin(1)	9						AAGGTGAGCTCCCCGAGCTGC	0.647																																						dbGAP											0													23.0	21.0	22.0					19																	13246395		2202	4298	6500	-	-	-	SO:0001589	frameshift_variant	0			AF395817	CCDS12294.1	19p13.13	2013-01-09	2008-10-03	2008-10-03		ENSG00000160877		"""BEN domain containing"", ""BTB/POZ domain containing"""	20967	protein-coding gene	gene with protein product	"""nucleus accumbens associated 1"", ""BEN domain containing 8"""	610672	"""BTB (POZ) domain containing 14B"""	BTBD14B		12477932	Standard	NM_052876		Approved	NAC1, NAC-1, BEND8, BTBD30	uc002mwm.4	Q96RE7		ENST00000292431.4:c.374delC	19.37:g.13246395delC	ENSP00000292431:p.Ser125fs	Somatic		WXS	Illumina GAIIx	Phase_IV		Frame_Shift_Del	DEL	pfam_BTB_POZ,pfam_BEN_domain,superfamily_BTB/POZ_fold,smart_BTB/POZ-like,pfscan_BTB/POZ-like	p.P126fs	ENST00000292431.4	37	c.374	CCDS12294.1	19																																																																																			NACC1	-	NULL	ENSG00000160877		0.647	NACC1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NACC1	HGNC	protein_coding	OTTHUMT00000452879.1	27	0.00	0	C	NM_052876		13246395	13246395	+1	no_errors	ENST00000292431	ensembl	human	known	69_37n	frame_shift_del	4	33.33	2	DEL	1.000	-
NHS	4810	genome.wustl.edu	37	X	17744061	17744061	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chrX:17744061C>T	ENST00000380060.3	+	6	2110	c.1772C>T	c.(1771-1773)aCg>aTg	p.T591M	NHS_ENST00000398097.3_Missense_Mutation_p.T435M	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	612					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.T435M(1)|p.T591M(1)		breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					TGCATCTCCACGGCTGGCGTC	0.602																																						dbGAP											2	Substitution - Missense(2)	breast(2)											79.0	66.0	70.0					X																	17744061		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.1772C>T	X.37:g.17744061C>T	ENSP00000369400:p.Thr591Met	Somatic		WXS	Illumina GAIIx	Phase_IV	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Missense_Mutation	SNP	NULL	p.T591M	ENST00000380060.3	37	c.1772	CCDS14181.1	X	.	.	.	.	.	.	.	.	.	.	C	14.38	2.516821	0.44763	.	.	ENSG00000188158	ENST00000380060;ENST00000398097;ENST00000380057	T;T	0.52057	0.68;0.69	5.86	5.0	0.66597	.	0.193913	0.56097	D	0.000036	T	0.64057	0.2564	L	0.56769	1.78	0.44380	D	0.997284	P;P;P;D	0.89917	0.934;0.934;0.934;1.0	B;B;B;D	0.69824	0.255;0.255;0.255;0.966	T	0.66818	-0.5827	10	0.72032	D	0.01	-6.8184	14.0633	0.64812	0.0:0.9262:0.0:0.0738	.	612;433;435;591	B7ZVX8;C9IYM8;Q6T4R5-2;Q6T4R5	.;.;.;NHS_HUMAN	M	591;435;433	ENSP00000369400:T591M;ENSP00000381170:T435M	ENSP00000369397:T433M	T	+	2	0	NHS	17653982	1.000000	0.71417	0.837000	0.33122	0.730000	0.41778	5.644000	0.67902	1.235000	0.43724	0.600000	0.82982	ACG	NHS	-	NULL	ENSG00000188158		0.602	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NHS	HGNC	protein_coding	OTTHUMT00000059120.1	125	0.00	0	C	NM_198270		17744061	17744061	+1	no_errors	ENST00000380060	ensembl	human	known	69_37n	missense	54	25.00	18	SNP	0.998	T
NINL	22981	genome.wustl.edu	37	20	25477324	25477324	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr20:25477324C>T	ENST00000278886.6	-	10	1358	c.1285G>A	c.(1285-1287)Gag>Aag	p.E429K	NINL_ENST00000422516.1_Missense_Mutation_p.E429K	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	429					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)	p.E429K(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						GTGAGCTGCTCCAGGGTGGAG	0.597																																						dbGAP											1	Substitution - Missense(1)	breast(1)											89.0	78.0	81.0					20																	25477324		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"""EF-hand domain containing"""	29163	protein-coding gene	gene with protein product	"""ninein-like protein"""	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.1285G>A	20.37:g.25477324C>T	ENSP00000278886:p.Glu429Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	pfam_EF-hand,smart_EF_hand_Ca-bd,pfscan_EF_HAND_2	p.E429K	ENST00000278886.6	37	c.1285	CCDS33452.1	20	.	.	.	.	.	.	.	.	.	.	C	21.4	4.146217	0.77888	.	.	ENSG00000101004	ENST00000278886;ENST00000422516	T;T	0.61158	0.4;0.13	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.77096	0.4080	M	0.78637	2.42	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.996	T	0.80079	-0.1532	10	0.87932	D	0	-38.52	17.3181	0.87229	0.0:1.0:0.0:0.0	.	429;429	Q9Y2I6-2;Q9Y2I6	.;NINL_HUMAN	K	429	ENSP00000278886:E429K;ENSP00000410431:E429K	ENSP00000278886:E429K	E	-	1	0	NINL	25425324	1.000000	0.71417	1.000000	0.80357	0.337000	0.28794	4.227000	0.58612	2.615000	0.88500	0.557000	0.71058	GAG	NINL	-	NULL	ENSG00000101004		0.597	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NINL	HGNC	protein_coding	OTTHUMT00000078445.3	93	0.00	0	C	NM_025176		25477324	25477324	-1	no_errors	ENST00000278886	ensembl	human	known	69_37n	missense	25	30.56	11	SNP	1.000	T
TENM2	57451	genome.wustl.edu	37	5	167631625	167631625	+	Splice_Site	SNP	C	C	T			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr5:167631625C>T	ENST00000518659.1	+	19	3862	c.3823C>T	c.(3823-3825)Cga>Tga	p.R1275*	TENM2_ENST00000519204.1_Splice_Site_p.R1154*|TENM2_ENST00000545108.1_Splice_Site_p.R1275*|TENM2_ENST00000403607.2_Splice_Site_p.R1099*|TENM2_ENST00000520394.1_Splice_Site_p.R1043C	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1275					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R1275*(1)|p.R1108*(1)|p.R1154*(1)									CTTGGAGTTACGGTAAATGGC	0.507																																						dbGAP											3	Substitution - Nonsense(3)	breast(3)											83.0	79.0	80.0					5																	167631625		1950	4145	6095	-	-	-	SO:0001630	splice_region_variant	0			AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.3824+1C>T	5.37:g.167631625C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q9ULU2	Nonsense_Mutation	SNP	pfam_Ten_N,pfam_EGF_extracell,superfamily_CarboxyPept-like_regulatory,superfamily_Quino_amine_DH_bsu,superfamily_ConA-like_lec_gl,superfamily_Cytokine_IL1-like,smart_EGF-like,smart_EGF-like_Ca-bd,pfscan_EG-like_dom,tigrfam_YD,tigrfam_Rhs_assc_core	p.R1275*	ENST00000518659.1	37	c.3823		5	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	42|42	9.468816|9.468816	0.99180|0.99180	.|.	.|.	ENSG00000145934|ENSG00000145934	ENST00000520394|ENST00000518659;ENST00000545108;ENST00000519204;ENST00000403607	D|.	0.90261|.	-2.64|.	4.9|4.9	2.02|2.02	0.26589|0.26589	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|.	0.21062|.	0.0507|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;P|.	0.91635|.	0.999;0.901|.	T|.	0.38757|.	-0.9646|.	8|.	0.72032|0.02654	D|T	0.01|1	.|.	8.5235|8.5235	0.33291|0.33291	0.4997:0.4231:0.0:0.0771|0.4997:0.4231:0.0:0.0771	.|.	1275;1043|.	F5H2D1;F8VNQ3|.	.;.|.	C|X	1043|1275;1275;1154;1099	ENSP00000427874:R1043C|.	ENSP00000427874:R1043C|ENSP00000384905:R1099X	R|R	+|+	1|1	0|2	ODZ2|ODZ2	167564203|167564203	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	2.979000|2.979000	0.49313|0.49313	0.088000|0.088000	0.17205|0.17205	0.550000|0.550000	0.68814|0.68814	CGC|CGA	ODZ2	-	superfamily_ConA-like_lec_gl	ENSG00000145934		0.507	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	ODZ2	HGNC	protein_coding	OTTHUMT00000376096.1	117	0.00	0	C	NM_001122679	Nonsense_Mutation	167631625	167631625	+1	no_errors	ENST00000518659	ensembl	human	known	69_37n	nonsense	72	30.10	31	SNP	1.000	T
PCOLCE	5118	genome.wustl.edu	37	7	100202789	100202790	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr7:100202789_100202790insC	ENST00000223061.5	+	4	819_820	c.539_540insC	c.(538-543)taccccfs	p.YP180fs	PCOLCE-AS1_ENST00000446022.1_RNA|PCOLCE-AS1_ENST00000442166.2_RNA|PCOLCE-AS1_ENST00000544873.1_RNA	NM_002593.3	NP_002584.2	Q15113	PCOC1_HUMAN	procollagen C-endopeptidase enhancer	180	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				multicellular organismal development (GO:0007275)|positive regulation of peptidase activity (GO:0010952)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|peptidase activator activity (GO:0016504)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					GAGTCCGATTACCCCCCGGGCA	0.708																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			L33799	CCDS5700.1	7q22	2008-07-18			ENSG00000106333	ENSG00000106333			8738	protein-coding gene	gene with protein product	"""procollagen, type 1, COOH-terminal proteinase enhancer"", ""procollagen C-proteinase enhancer 1"""	600270				8824813, 9799793	Standard	NM_002593		Approved	PCPE, PCPE1	uc003uvo.3	Q15113	OTTHUMG00000156675	ENST00000223061.5:c.545dupC	7.37:g.100202795_100202795dupC	ENSP00000223061:p.Tyr180fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B2R9E1|O14550	Frame_Shift_Ins	INS	pfam_CUB,pfam_Netrin_module_non-TIMP,superfamily_CUB,superfamily_TIMP-like_OB-fold,smart_CUB,smart_Netrin_module_non-TIMP,pfscan_CUB,pfscan_Netrin_domain	p.G184fs	ENST00000223061.5	37	c.539_540	CCDS5700.1	7																																																																																			PCOLCE	-	pfam_CUB,superfamily_CUB,smart_CUB,pfscan_CUB	ENSG00000106333		0.708	PCOLCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCOLCE	HGNC	protein_coding	OTTHUMT00000345285.1	80	0.00	0	-	NM_002593		100202789	100202790	+1	no_errors	ENST00000223061	ensembl	human	known	69_37n	frame_shift_ins	13	13.33	2	INS	1.000:1.000	C
PIGO	84720	genome.wustl.edu	37	9	35091522	35091523	+	Frame_Shift_Ins	INS	-	-	G	rs144233446		TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr9:35091522_35091523insG	ENST00000378617.3	-	7	2755_2756	c.2361_2362insC	c.(2359-2364)cccactfs	p.T788fs	PIGO_ENST00000298004.5_Intron|PIGO_ENST00000361778.2_Intron|PIGO_ENST00000341666.3_Frame_Shift_Ins_p.T788fs	NM_032634.3	NP_116023.2	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class O	788					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)	p.T788fs*5(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)	38			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			GCTTGAGAAGTGGGGGGGCCTG	0.604																																						dbGAP											1	Insertion - Frameshift(1)	ovary(1)																																								-	-	-	SO:0001589	frameshift_variant	0			AB083625	CCDS6575.1, CCDS6576.1	9p13.2	2013-02-26	2006-06-28		ENSG00000165282	ENSG00000165282		"""Phosphatidylinositol glycan anchor biosynthesis"""	23215	protein-coding gene	gene with protein product		614730	"""phosphatidylinositol glycan, class O"""			10781593	Standard	NM_032634		Approved	DKFZp434M222, FLJ00135	uc003zwd.3	Q8TEQ8	OTTHUMG00000019854	ENST00000378617.3:c.2362dupC	9.37:g.35091529_35091529dupG	ENSP00000367880:p.Thr788fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B1AML3|Q6P154|Q6UX80|Q8TDS8|Q96CS9|Q9BVN9|Q9Y4B0	Frame_Shift_Ins	INS	pfam_Phosphodiest/P_Trfase,pfam_Metalloenzyme,pfam_Sulfatase,superfamily_Alkaline_phosphatase_core	p.T787fs	ENST00000378617.3	37	c.2362_2361	CCDS6575.1	9																																																																																			PIGO	-	NULL	ENSG00000165282		0.604	PIGO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PIGO	HGNC	protein_coding	OTTHUMT00000052284.1	72	0.00	0	-	NM_032634		35091522	35091523	-1	no_errors	ENST00000341666	ensembl	human	known	69_37n	frame_shift_ins	40	11.11	5	INS	0.637:0.393	G
PCSK5	5125	genome.wustl.edu	37	9	78790207	78790207	+	Intron	SNP	C	C	A	rs55947300|rs10124596|rs71372053	byFrequency	TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	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		16	0.00	0	C			78790207	78790207	+1	no_errors	ENST00000376767	ensembl	human	known	69_37n	silent	8	46.67	7	SNP	0.000	A
PIK3CA	5290	genome.wustl.edu	37	3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	rs104886003		TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr3:178936091G>A	ENST00000263967.3	+	10	1790	c.1633G>A	c.(1633-1635)Gag>Aag	p.E545K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	545	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> A (in CWS5 and HCC; also found in a glioblastoma multiforme sample). {ECO:0000269|PubMed:15608678, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:23246288}.|E -> G (in KERSEB; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:17673550}.|E -> K (in MCAP, KERSEB, CRC and BC; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N-terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E545K(881)|p.E545Q(18)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TGAAATCACTGAGCAGGAGAA	0.353	E545K(BC3C_URINARY_TRACT)|E545K(BFTC909_KIDNEY)|E545K(DLD1_LARGE_INTESTINE)|E545K(ESS1_ENDOMETRIUM)|E545K(HCC202_BREAST)|E545K(HCT15_LARGE_INTESTINE)|E545K(HSC4_UPPER_AERODIGESTIVE_TRACT)|E545K(HT1197_URINARY_TRACT)|E545K(HUH28_BILIARY_TRACT)|E545K(KYSE510_OESOPHAGUS)|E545K(L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|E545K(MCF7_BREAST)|E545K(MDAMB361_BREAST)|E545K(MKN1_STOMACH)|E545K(NCIH460_LUNG)|E545K(NCIH508_LARGE_INTESTINE)|E545K(NCIH596_LUNG)|E545K(RERFLCSQ1_LUNG)|E545K(TCCSUP_URINARY_TRACT)|E545K(TE5_OESOPHAGUS)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	dbGAP		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	899	Substitution - Missense(899)	breast(308)|large_intestine(286)|urinary_tract(97)|lung(44)|endometrium(37)|ovary(25)|stomach(17)|upper_aerodigestive_tract(16)|skin(14)|central_nervous_system(13)|cervix(13)|thyroid(7)|oesophagus(7)|penis(4)|kidney(3)|soft_tissue(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|biliary_tract(1)|NS(1)|pituitary(1)											61.0	60.0	60.0					3																	178936091		1813	4072	5885	-	-	-	SO:0001583	missense	0				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1633G>A	3.37:g.178936091G>A	ENSP00000263967:p.Glu545Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q14CW1|Q99762	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,pfam_PI3K_adapt-bd_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.E545K	ENST00000263967.3	37	c.1633	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	G	36	5.703347	0.96812	.	.	ENSG00000121879	ENST00000263967	T	0.63255	-0.03	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.73822	0.3636	L	0.51914	1.62	0.80722	D	1	D	0.62365	0.991	D	0.62955	0.909	T	0.68872	-0.5294	10	0.32370	T	0.25	-25.7963	20.0024	0.97423	0.0:0.0:1.0:0.0	.	545	P42336	PK3CA_HUMAN	K	545	ENSP00000263967:E545K	ENSP00000263967:E545K	E	+	1	0	PIK3CA	180418785	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAG	PIK3CA	-	pfam_PInositide-3_kin_accessory_dom,superfamily_ARM-type_fold,smart_PInositide-3_kin_accessory_dom	ENSG00000121879		0.353	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	124	0.00	0	G			178936091	178936091	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	92	17.86	20	SNP	1.000	A
PIWIL1	9271	genome.wustl.edu	37	12	130856048	130856048	+	Missense_Mutation	SNP	C	C	G			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr12:130856048C>G	ENST00000245255.3	+	21	2763	c.2491C>G	c.(2491-2493)Cct>Gct	p.P831A		NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	831	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)|P granule (GO:0043186)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)|single-stranded RNA binding (GO:0003727)	p.P831A(1)		breast(6)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(26)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	57	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		TGTTCCTGCTCCTTGCCAGTA	0.438																																						dbGAP											1	Substitution - Missense(1)	breast(1)											208.0	201.0	203.0					12																	130856048		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF104260	CCDS9268.1	12q24.33	2014-01-21	2013-02-15		ENSG00000125207	ENSG00000125207		"""Argonaute/PIWI family"""	9007	protein-coding gene	gene with protein product		605571	"""piwi (Drosophila)-like 1"", ""piwi-like 1 (Drosophila)"""			9851978, 12906857	Standard	NM_004764		Approved	PIWI, HIWI, CT80.1	uc001uik.3	Q96J94	OTTHUMG00000168382	ENST00000245255.3:c.2491C>G	12.37:g.130856048C>G	ENSP00000245255:p.Pro831Ala	Somatic		WXS	Illumina GAIIx	Phase_IV	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	Missense_Mutation	SNP	pfam_Piwi,pfam_PAZ,pfam_GAGE,superfamily_RNaseH-like_dom,superfamily_PAZ,smart_PAZ,smart_Piwi,pfscan_PAZ,pfscan_Piwi	p.P831A	ENST00000245255.3	37	c.2491	CCDS9268.1	12	.	.	.	.	.	.	.	.	.	.	C	26.4	4.734826	0.89482	.	.	ENSG00000125207	ENST00000245255	T	0.42131	0.98	5.31	5.31	0.75309	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.72771	0.3502	M	0.91038	3.17	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79482	-0.1785	10	0.66056	D	0.02	-2.506	17.9752	0.89124	0.0:1.0:0.0:0.0	.	831	Q96J94	PIWL1_HUMAN	A	831	ENSP00000245255:P831A	ENSP00000245255:P831A	P	+	1	0	PIWIL1	129422001	1.000000	0.71417	0.842000	0.33263	0.974000	0.67602	6.065000	0.71176	2.461000	0.83175	0.655000	0.94253	CCT	PIWIL1	-	pfam_Piwi,superfamily_RNaseH-like_dom,smart_Piwi,pfscan_Piwi	ENSG00000125207		0.438	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PIWIL1	HGNC	protein_coding	OTTHUMT00000399510.1	615	0.00	0	C			130856048	130856048	+1	no_errors	ENST00000245255	ensembl	human	known	69_37n	missense	208	10.30	24	SNP	1.000	G
PKN1	5585	genome.wustl.edu	37	19	14574911	14574911	+	Silent	SNP	G	G	A			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr19:14574911G>A	ENST00000242783.6	+	12	1842	c.1677G>A	c.(1675-1677)tcG>tcA	p.S559S	PKN1_ENST00000342216.4_Silent_p.S565S	NM_002741.3	NP_002732.3	Q16512	PKN1_HUMAN	protein kinase N1	559		Cleavage; by caspase-3.			activation of JUN kinase activity (GO:0007257)|epithelial cell migration (GO:0010631)|histone H3-T11 phosphorylation (GO:0035407)|hyperosmotic response (GO:0006972)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|GTP-Rho binding (GO:0017049)|histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)|histone kinase activity (H3-T11 specific) (GO:0035402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)	p.S559S(1)		breast(3)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)	31						GCACTGACTCGGACAGCTCAC	0.637																																					NSCLC(185;2539 2965 10733 52867)	dbGAP											1	Substitution - coding silent(1)	breast(1)											75.0	79.0	77.0					19																	14574911		2062	4199	6261	-	-	-	SO:0001819	synonymous_variant	0			S75546	CCDS42513.1, CCDS42514.1	19p13.12	2008-05-14	2004-07-01	2004-07-01	ENSG00000123143	ENSG00000123143			9405	protein-coding gene	gene with protein product		601032	"""protein kinase C-like 1"""	PRKCL1		9570957	Standard	NM_002741		Approved	DBK, PRK1, PKN, MGC46204, PAK1	uc002myq.3	Q16512	OTTHUMG00000039611	ENST00000242783.6:c.1677G>A	19.37:g.14574911G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K7W5|B2R9R4|B3KVN3|Q15143|Q504U4|Q8IUV5|Q9UD44	Silent	SNP	pfam_Prot_kinase_cat_dom,pfam_HR1_rho-bd,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Pkinase_C,superfamily_Kinase-like_dom,superfamily_HR1_rho-bd,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_HR1_rho-bd,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_AGC-kinase_C,pfscan_Prot_kinase_cat_dom	p.S565	ENST00000242783.6	37	c.1695	CCDS42513.1	19																																																																																			PKN1	-	NULL	ENSG00000123143		0.637	PKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PKN1	HGNC	protein_coding	OTTHUMT00000095510.1	46	0.00	0	G	NM_002741, NM_213560		14574911	14574911	+1	no_errors	ENST00000342216	ensembl	human	known	69_37n	silent	25	34.21	13	SNP	0.000	A
PPL	5493	genome.wustl.edu	37	16	4935600	4935600	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr16:4935600delG	ENST00000345988.2	-	22	3145	c.3056delC	c.(3055-3057)gcafs	p.A1019fs	PPL_ENST00000590782.2_Frame_Shift_Del_p.A1017fs	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1019					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						CCGCCTCAGTGCCTCCAGCTC	0.687																																						dbGAP											0													52.0	57.0	55.0					16																	4935600		2197	4298	6495	-	-	-	SO:0001589	frameshift_variant	0			AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.3056delC	16.37:g.4935600delG	ENSP00000340510:p.Ala1019fs	Somatic		WXS	Illumina GAIIx	Phase_IV	O60314|O60454|Q14C98	Frame_Shift_Del	DEL	pfam_Plectin_repeat,smart_Spectrin/alpha-actinin,smart_Plectin_repeat	p.A1019fs	ENST00000345988.2	37	c.3056	CCDS10526.1	16																																																																																			PPL	-	NULL	ENSG00000118898		0.687	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PPL	HGNC	protein_coding	OTTHUMT00000251715.1	31	0.00	0	G	NM_002705		4935600	4935600	-1	no_errors	ENST00000345988	ensembl	human	known	69_37n	frame_shift_del	8	33.33	4	DEL	0.703	-
PPL	5493	genome.wustl.edu	37	16	4935601	4935602	+	Frame_Shift_Ins	INS	-	-	TT			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr16:4935601_4935602insTT	ENST00000345988.2	-	22	3143_3144	c.3054_3055insAA	c.(3052-3057)gaggcafs	p.A1019fs	PPL_ENST00000590782.2_Frame_Shift_Ins_p.A1017fs	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1019					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						CGCCTCAGTGCCTCCAGCTCCT	0.688																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.3054_3055insAA	16.37:g.4935601_4935602insTT	ENSP00000340510:p.Ala1019fs	Somatic		WXS	Illumina GAIIx	Phase_IV	O60314|O60454|Q14C98	Frame_Shift_Ins	INS	pfam_Plectin_repeat,smart_Spectrin/alpha-actinin,smart_Plectin_repeat	p.A1018fs	ENST00000345988.2	37	c.3055_3054	CCDS10526.1	16																																																																																			PPL	-	NULL	ENSG00000118898		0.688	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PPL	HGNC	protein_coding	OTTHUMT00000251715.1	31	0.00	0	-	NM_002705		4935601	4935602	-1	no_errors	ENST00000345988	ensembl	human	known	69_37n	frame_shift_ins	8	33.33	4	INS	0.989:0.989	TT
PROX2	283571	genome.wustl.edu	37	14	75321979	75321979	+	Silent	SNP	G	G	A			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr14:75321979G>A	ENST00000445876.1	-	5	1634	c.1635C>T	c.(1633-1635)gcC>gcT	p.A545A	PROX2_ENST00000556084.2_Silent_p.A318A|RP11-316E14.6_ENST00000553381.1_RNA|PROX2_ENST00000556489.2_Silent_p.A545A			Q3B8N5	PROX2_HUMAN	prospero homeobox 2	545	Prospero-like.				multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A545A(1)		kidney(1)|large_intestine(2)|lung(3)	6			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00652)		ACGTCAAGCTGGCAATTTCCA	0.473																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											39.0	36.0	37.0					14																	75321979		1886	4120	6006	-	-	-	SO:0001819	synonymous_variant	0				CCDS45136.1, CCDS45136.2, CCDS73663.1	14q24.3	2012-10-02			ENSG00000119608	ENSG00000119608		"""Homeoboxes / PROS class"""	26715	protein-coding gene	gene with protein product		615094					Standard	NM_001080408		Approved	FLJ36749	uc031qpi.1	Q3B8N5	OTTHUMG00000171481	ENST00000445876.1:c.1635C>T	14.37:g.75321979G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	C9J5W1|Q8N9Q3	Silent	SNP	pfam_Prox1,superfamily_Homeodomain-like	p.A545	ENST00000445876.1	37	c.1635	CCDS45136.2	14	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.16|15.16	2.749847|2.749847	0.49257|0.49257	.|.	.|.	ENSG00000119596|ENSG00000119608	ENST00000554107|ENST00000556084	.|.	.|.	.|.	5.22|5.22	4.29|4.29	0.51040|0.51040	.|.	.|.	.|.	.|.	.|.	T|T	0.60025|0.60025	0.2237|0.2237	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.57069|0.57069	-0.7874|-0.7874	4|4	.|.	.|.	.|.	.|.	9.3633|9.3633	0.38208|0.38208	0.076:0.145:0.779:0.0|0.076:0.145:0.779:0.0	.|.	.|.	.|.	.|.	S|L	89|318	.|.	.|.	G|P	+|-	1|2	0|0	YLPM1|PROX2	74391732|74391732	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	1.369000|1.369000	0.34227|0.34227	2.446000|2.446000	0.82766|0.82766	0.462000|0.462000	0.41574|0.41574	GGC|CCA	PROX2	-	pfam_Prox1,superfamily_Homeodomain-like	ENSG00000119608		0.473	PROX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PROX2	HGNC	protein_coding		72	0.00	0	G			75321979	75321979	-1	no_errors	ENST00000445876	ensembl	human	known	69_37n	silent	61	27.38	23	SNP	1.000	A
SAT1	6303	genome.wustl.edu	37	X	23801965	23801965	+	Missense_Mutation	SNP	T	T	C			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chrX:23801965T>C	ENST00000379270.4	+	3	346	c.167T>C	c.(166-168)gTt>gCt	p.V56A	RP13-314C10.5_ENST00000366134.2_RNA|Y_RNA_ENST00000365402.1_RNA|SAT1_ENST00000379254.1_Intron|SAT1_ENST00000379253.3_Missense_Mutation_p.V56A|SAT1_ENST00000379251.3_Missense_Mutation_p.V86A|SAT1_ENST00000489394.1_3'UTR	NM_002970.2	NP_002961.1	Q9H2B4	S26A1_HUMAN	spermidine/spermine N1-acetyltransferase 1	0					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)	p.V56A(1)|p.V86A(1)		breast(1)|endometrium(3)|kidney(3)|lung(3)	10						CACTGCCTGGTTGCAGAAGTG	0.547																																						dbGAP											2	Substitution - Missense(2)	breast(2)											104.0	90.0	95.0					X																	23801965		2203	4300	6503	-	-	-	SO:0001583	missense	0			M55580	CCDS14207.1	Xp22.1	2011-11-16	2006-08-24	2006-08-24	ENSG00000130066	ENSG00000130066	2.3.1.57		10540	protein-coding gene	gene with protein product	"""diamine N-acetyltransferase 1"""	313020	"""spermidine/spermine N1-acetyltransferase"""	SAT		1985966, 1417826	Standard	NM_002970		Approved	SSAT	uc004dau.3	P21673	OTTHUMG00000021256	ENST00000379270.4:c.167T>C	X.37:g.23801965T>C	ENSP00000368572:p.Val56Ala	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K9N2|Q7Z5R3|Q96BK0	Missense_Mutation	SNP	pfam_GNAT_dom,superfamily_Acyl_CoA_acyltransferase,pfscan_GNAT_dom	p.V56A	ENST00000379270.4	37	c.167	CCDS14207.1	X	.	.	.	.	.	.	.	.	.	.	T	34	5.355893	0.95854	.	.	ENSG00000130066	ENST00000379270;ENST00000379253;ENST00000379251;ENST00000342463	T;T;T	0.55052	0.54;0.54;0.54	5.51	5.51	0.81932	GCN5-related N-acetyltransferase (GNAT) domain (1);Acyl-CoA N-acyltransferase (2);	0.171877	0.51477	D	0.000081	T	0.75324	0.3834	M	0.92833	3.35	0.80722	D	1	D;P	0.61080	0.989;0.935	P;P	0.58077	0.832;0.723	T	0.82577	-0.0388	10	0.87932	D	0	-2.4643	14.813	0.70010	0.0:0.0:0.0:1.0	.	56;56	A6NM56;P21673	.;SAT1_HUMAN	A	56;56;86;80	ENSP00000368572:V56A;ENSP00000368555:V56A;ENSP00000368553:V86A	ENSP00000343343:V80A	V	+	2	0	SAT1	23711886	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.630000	0.83225	1.947000	0.56498	0.486000	0.48141	GTT	SAT1	-	superfamily_Acyl_CoA_acyltransferase,pfscan_GNAT_dom	ENSG00000130066		0.547	SAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SAT1	HGNC	protein_coding	OTTHUMT00000056056.1	139	0.71	1	T	NM_002970		23801965	23801965	+1	no_errors	ENST00000379270	ensembl	human	known	69_37n	missense	61	49.59	60	SNP	1.000	C
SDR9C7	121214	genome.wustl.edu	37	12	57323336	57323336	+	Splice_Site	SNP	G	G	A	rs150520393		TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr12:57323336G>A	ENST00000293502.1	-	3	705	c.562C>T	c.(562-564)Cgt>Tgt	p.R188C		NM_148897.2	NP_683695.1	Q8NEX9	DR9C7_HUMAN	short chain dehydrogenase/reductase family 9C, member 7	188					oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	retinol dehydrogenase activity (GO:0004745)	p.R188C(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|pancreas(1)	7						TAGAGCTCACGCCTGGGAAAG	0.527													G|||	1	0.000199681	0.0	0.0	5008	,	,		18257	0.001		0.0	False		,,,				2504	0.0					dbGAP											1	Substitution - Missense(1)	breast(1)											81.0	76.0	77.0					12																	57323336		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0			AY044434	CCDS8926.1	12q13.3	2014-09-04			ENSG00000170426	ENSG00000170426	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	29958	protein-coding gene	gene with protein product		609769				12234675, 19027726	Standard	NM_148897		Approved	SDR-O, RDHS	uc010sqw.2	Q8NEX9	OTTHUMG00000171004	ENST00000293502.1:c.561-1C>T	12.37:g.57323336G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B3KVB4	Missense_Mutation	SNP	pfam_DH_sc/Rdtase_SDR,prints_Glc/ribitol_DH,prints_DH_sc/Rdtase_SDR	p.R188C	ENST00000293502.1	37	c.562	CCDS8926.1	12	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	17.64	3.438549	0.62955	.	.	ENSG00000170426	ENST00000293502	D	0.88201	-2.35	5.17	5.17	0.71159	NAD(P)-binding domain (1);	0.088664	0.45361	D	0.000380	D	0.92067	0.7486	M	0.91717	3.235	0.49483	D	0.999797	P	0.36599	0.56	B	0.42163	0.378	D	0.91823	0.5469	10	0.41790	T	0.15	.	13.4493	0.61161	0.0:0.0:0.8426:0.1574	.	188	Q8NEX9	DR9C7_HUMAN	C	188	ENSP00000293502:R188C	ENSP00000293502:R188C	R	-	1	0	SDR9C7	55609603	0.999000	0.42202	1.000000	0.80357	0.817000	0.46193	1.586000	0.36611	2.582000	0.87167	0.655000	0.94253	CGT	SDR9C7	-	pfam_DH_sc/Rdtase_SDR,prints_Glc/ribitol_DH,prints_DH_sc/Rdtase_SDR	ENSG00000170426		0.527	SDR9C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SDR9C7	HGNC	protein_coding	OTTHUMT00000411211.1	140	0.71	1	G	NM_148897	Missense_Mutation	57323336	57323336	-1	no_errors	ENST00000293502	ensembl	human	known	69_37n	missense	81	30.77	36	SNP	1.000	A
SLC22A11	55867	genome.wustl.edu	37	11	64323714	64323715	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr11:64323714_64323715insC	ENST00000301891.4	+	1	617_618	c.243_244insC	c.(244-246)cccfs	p.P82fs	SLC22A11_ENST00000377581.3_Frame_Shift_Ins_p.P82fs|SLC22A11_ENST00000377585.3_Frame_Shift_Ins_p.P82fs|SLC22A11_ENST00000490834.1_3'UTR	NM_018484.2	NP_060954.1	Q9NSA0	S22AB_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 11	82					organic anion transport (GO:0015711)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23					Aminohippurate(DB00345)|Aspartame(DB00168)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Estradiol(DB00783)|Furosemide(DB00695)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Novobiocin(DB01051)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Salicylic acid(DB00936)|Tetracycline(DB00759)|Zidovudine(DB00495)	CCAACCAGGGGCCCCACCAGTG	0.644											OREG0004031	type=REGULATORY REGION|Gene=SLC22A11|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																										dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AB026116	CCDS8074.1	11q13.3	2013-05-22	2008-01-11		ENSG00000168065	ENSG00000168065		"""Solute carriers"""	18120	protein-coding gene	gene with protein product		607097				10660625, 15576633, 17229912	Standard	NM_018484		Approved	OAT4	uc001oai.3	Q9NSA0	OTTHUMG00000045142	ENST00000301891.4:c.247dupC	11.37:g.64323718_64323718dupC	ENSP00000301891:p.Pro82fs	Somatic	1075	WXS	Illumina GAIIx	Phase_IV	A8K426|Q53GR2|Q6ZP72|Q8NBU4	Frame_Shift_Ins	INS	pfam_Sub_transporter,pfam_MFS,superfamily_MFS_dom_general_subst_transpt,pfscan_MFS_dom	p.H82fs	ENST00000301891.4	37	c.243_244	CCDS8074.1	11																																																																																			SLC22A11	-	NULL	ENSG00000168065		0.644	SLC22A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC22A11	HGNC	protein_coding	OTTHUMT00000104886.4	52	0.00	0	-	NM_018484		64323714	64323715	+1	no_errors	ENST00000301891	ensembl	human	known	69_37n	frame_shift_ins	5	44.44	4	INS	0.011:0.110	C
SLC25A31	83447	genome.wustl.edu	37	4	128665852	128665852	+	Silent	SNP	T	T	C			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr4:128665852T>C	ENST00000281154.4	+	2	426	c.258T>C	c.(256-258)aaT>aaC	p.N86N		NM_031291.2	NP_112581.1	Q9H0C2	ADT4_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 31	86					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|nucleus (GO:0005634)	transporter activity (GO:0005215)	p.N86N(1)		NS(1)|breast(1)|large_intestine(10)|lung(8)|skin(2)	22						GGCGTGGCAATTTGGCAAATG	0.318																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											134.0	136.0	136.0					4																	128665852		2202	4299	6501	-	-	-	SO:0001819	synonymous_variant	0			AL136857	CCDS3733.1	4q28	2013-05-22			ENSG00000151475	ENSG00000151475		"""Solute carriers"""	25319	protein-coding gene	gene with protein product		610796				15670820	Standard	NM_031291		Approved	DKFZP434N1235, ANT4	uc003ifl.3	Q9H0C2	OTTHUMG00000133300	ENST00000281154.4:c.258T>C	4.37:g.128665852T>C		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	pfam_Mitochondrial_sb/sol_carrier,superfamily_Mt_carrier_dom,prints_Mit_carrier,prints_Aden_trnslctor,pfscan_Mitochondrial_sb/sol_carrier	p.N86	ENST00000281154.4	37	c.258	CCDS3733.1	4																																																																																			SLC25A31	-	pfam_Mitochondrial_sb/sol_carrier,superfamily_Mt_carrier_dom,prints_Mit_carrier,pfscan_Mitochondrial_sb/sol_carrier	ENSG00000151475		0.318	SLC25A31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC25A31	HGNC	protein_coding	OTTHUMT00000257094.2	237	0.00	0	T	NM_031291		128665852	128665852	+1	no_errors	ENST00000281154	ensembl	human	known	69_37n	silent	202	12.17	28	SNP	1.000	C
SLC27A3	11000	genome.wustl.edu	37	1	153747748	153747748	+	5'Flank	DEL	C	C	-			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr1:153747748delC	ENST00000368661.3	+	0	0				SLC27A3_ENST00000271857.2_Frame_Shift_Del_p.G53fs	NM_024330.1	NP_077306.1	Q5K4L6	S27A3_HUMAN	solute carrier family 27 (fatty acid transporter), member 3						fatty acid metabolic process (GO:0006631)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	fatty-acyl-CoA synthase activity (GO:0004321)|ligase activity (GO:0016874)|nucleotide binding (GO:0000166)			NS(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	14	all_lung(78;6.47e-32)|Lung NSC(65;2.52e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GGGGGGAGGGCTGGGAGTCCG	0.741																																						dbGAP											0																																										-	-	-	SO:0001631	upstream_gene_variant	0			BC009916	CCDS1053.1	1q21.1	2013-05-22			ENSG00000143554	ENSG00000143554		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10997	protein-coding gene	gene with protein product		604193				9671728	Standard	NM_024330		Approved	FATP3, MGC4365, ACSVL3	uc001fcz.3	Q5K4L6	OTTHUMG00000037155		1.37:g.153747748delC	Exception_encountered	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5VUQ7|Q5VUQ8|Q5VUR3|Q6ZV16|Q8N2X7|Q8TEJ0|Q96SW5|Q9BTJ5|Q9BTY5	Frame_Shift_Del	DEL	pfam_AMP-dep_Synth/Lig	p.W54fs	ENST00000368661.3	37	c.159	CCDS1053.1	1																																																																																			SLC27A3	-	NULL	ENSG00000143554		0.741	SLC27A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC27A3	HGNC	protein_coding		8	0.00	0	C	NM_024330		153747748	153747748	+1	no_errors	ENST00000271857	ensembl	human	novel	69_37n	frame_shift_del	7	36.36	4	DEL	0.808	-
SNX8	29886	genome.wustl.edu	37	7	2297060	2297062	+	In_Frame_Del	DEL	GCT	GCT	-	rs200222167		TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	GCT	GCT					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr7:2297060_2297062delGCT	ENST00000222990.3	-	9	1114_1116	c.1072_1074delAGC	c.(1072-1074)agcdel	p.S358del		NM_013321.2	NP_037453.1	Q9Y5X2	SNX8_HUMAN	sorting nexin 8	358					early endosome to Golgi transport (GO:0034498)|intracellular protein transport (GO:0006886)	early endosome membrane (GO:0031901)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			breast(2)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(2)|skin(3)	26		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0853)|OV - Ovarian serous cystadenocarcinoma(56;3.79e-14)		GCGCGGTGGCGCTCATCATCTGC	0.685																																						dbGAP											0																																										-	-	-	SO:0001651	inframe_deletion	0			AF121858	CCDS5331.1	7p22.3	2010-08-05			ENSG00000106266	ENSG00000106266		"""Sorting nexins"""	14972	protein-coding gene	gene with protein product		614905					Standard	NM_013321		Approved	Mvp1	uc003slw.3	Q9Y5X2	OTTHUMG00000151512	ENST00000222990.3:c.1072_1074delAGC	7.37:g.2297060_2297062delGCT	ENSP00000222990:p.Ser358del	Somatic		WXS	Illumina GAIIx	Phase_IV	A4D207|Q96I67	In_Frame_Del	DEL	pfam_Phox,superfamily_Phox,smart_Phox,pfscan_Phox	p.S358in_frame_del	ENST00000222990.3	37	c.1074_1072	CCDS5331.1	7																																																																																			SNX8	-	NULL	ENSG00000106266		0.685	SNX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SNX8	HGNC	protein_coding	OTTHUMT00000322949.2	25	0.00	0	GCT			2297060	2297062	-1	no_errors	ENST00000222990	ensembl	human	known	69_37n	in_frame_del	3	57.14	4	DEL	0.983:1.000:1.000	-
SVEP1	79987	genome.wustl.edu	37	9	113169977	113169977	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr9:113169977C>A	ENST00000401783.2	-	38	8239	c.7903G>T	c.(7903-7905)Gag>Tag	p.E2635*	SVEP1_ENST00000297826.5_Nonsense_Mutation_p.E561*|SVEP1_ENST00000374469.1_Nonsense_Mutation_p.E2612*	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2635					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)	p.E2638*(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TCTTCTTGCTCAAAATATCCC	0.443																																						dbGAP											1	Substitution - Nonsense(1)	breast(1)											216.0	212.0	213.0					9																	113169977		1895	4124	6019	-	-	-	SO:0001587	stop_gained	0			AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.7903G>T	9.37:g.113169977C>A	ENSP00000384917:p.Glu2635*	Somatic		WXS	Illumina GAIIx	Phase_IV	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Nonsense_Mutation	SNP	pfam_Sushi_SCR_CCP,pfam_EGF-like_dom,pfam_Tyr-kin_ephrin_A/B_rcpt-like,pfam_Hyalin,pfam_VWF_A,pfam_Pentaxin,pfam_EGF_extracell,pfam_EGF-like_Ca-bd,superfamily_ConA-like_lec_gl,superfamily_Complement_control_module,superfamily_Growth_fac_rcpt,smart_VWF_A,smart_Sushi_SCR_CCP,smart_EGF-like_Ca-bd,smart_EGF-like,smart_Pentaxin,pfscan_EG-like_dom,pfscan_Hyalin,pfscan_Sushi_SCR_CCP,pfscan_VWF_A,prints_Pentaxin	p.E2635*	ENST00000401783.2	37	c.7903	CCDS48004.1	9	.	.	.	.	.	.	.	.	.	.	C	48	14.207253	0.99784	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826;ENST00000374463	.	.	.	5.4	4.49	0.54785	.	0.617854	0.16770	N	0.200249	.	.	.	.	.	.	0.19945	N	0.999948	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	.	11.5415	0.50669	0.0:0.8466:0.0:0.1534	.	.	.	.	X	2635;2612;561;307	.	ENSP00000297826:E561X	E	-	1	0	SVEP1	112209798	0.008000	0.16893	0.994000	0.49952	0.120000	0.20174	0.836000	0.27545	1.237000	0.43756	0.585000	0.79938	GAG	SVEP1	-	NULL	ENSG00000165124		0.443	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	SVEP1	HGNC	protein_coding		40	0.00	0	C			113169977	113169977	-1	no_errors	ENST00000401783	ensembl	human	known	69_37n	nonsense	42	12.50	6	SNP	0.075	A
TBC1D10C	374403	genome.wustl.edu	37	11	67174406	67174406	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr11:67174406delC	ENST00000542590.1	+	7	771	c.757delC	c.(757-759)cccfs	p.P253fs	TBC1D10C_ENST00000312390.5_Frame_Shift_Del_p.P253fs|TBC1D10C_ENST00000526387.1_Intron			Q8IV04	TB10C_HUMAN	TBC1 domain family, member 10C	253	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				retrograde transport, endosome to Golgi (GO:0042147)	filopodium membrane (GO:0031527)|membrane (GO:0016020)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			GCTGTACCTGCCCGAGTGGTT	0.682																																						dbGAP											0													131.0	140.0	137.0					11																	67174406		2200	4295	6495	-	-	-	SO:0001589	frameshift_variant	0			BC035630	CCDS8162.1, CCDS58150.1	11q13.1	2013-07-09			ENSG00000175463	ENSG00000175463			24702	protein-coding gene	gene with protein product		610831				17230191, 20404108	Standard	NM_001256508		Approved	FLJ00332, Carabin, EPI64C	uc001ola.4	Q8IV04	OTTHUMG00000167139	ENST00000542590.1:c.757delC	11.37:g.67174406delC	ENSP00000443654:p.Pro253fs	Somatic		WXS	Illumina GAIIx	Phase_IV	G3V1D6	Frame_Shift_Del	DEL	pfam_Rab-GTPase-TBC_dom,superfamily_Rab-GTPase-TBC_dom,smart_Rab-GTPase-TBC_dom,pfscan_Rab-GTPase-TBC_dom	p.E254fs	ENST00000542590.1	37	c.757	CCDS8162.1	11																																																																																			TBC1D10C	-	pfam_Rab-GTPase-TBC_dom,superfamily_Rab-GTPase-TBC_dom,smart_Rab-GTPase-TBC_dom,pfscan_Rab-GTPase-TBC_dom	ENSG00000175463		0.682	TBC1D10C-007	KNOWN	basic|appris_principal|CCDS	protein_coding	TBC1D10C	HGNC	protein_coding	OTTHUMT00000395492.2	45	0.00	0	C	NM_198517		67174406	67174406	+1	no_errors	ENST00000312390	ensembl	human	known	69_37n	frame_shift_del	8	20.00	2	DEL	1.000	-
TBC1D12	23232	genome.wustl.edu	37	10	96291202	96291203	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr10:96291202_96291203insA	ENST00000225235.4	+	12	2354_2355	c.2244_2245insA	c.(2245-2247)aaafs	p.K749fs	TBC1D12_ENST00000485048.1_3'UTR	NM_015188.1	NP_056003.1	O60347	TBC12_HUMAN	TBC1 domain family, member 12	749							Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(2)	20		Colorectal(252;0.0429)				AGAATAGCACCAAAAAATGGAC	0.322																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AB011180	CCDS41553.1	10q23.33	2013-09-20			ENSG00000108239	ENSG00000108239			29082	protein-coding gene	gene with protein product						9628581	Standard	NM_015188		Approved	KIAA0608	uc001kjr.2	O60347	OTTHUMG00000018794	ENST00000225235.4:c.2250dupA	10.37:g.96291208_96291208dupA	ENSP00000225235:p.Lys749fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5VYA6|Q8WX26|Q8WX59|Q9UG83	Frame_Shift_Ins	INS	pfam_Rab-GTPase-TBC_dom,superfamily_Rab-GTPase-TBC_dom,smart_Rab-GTPase-TBC_dom,pfscan_Rab-GTPase-TBC_dom	p.W750fs	ENST00000225235.4	37	c.2244_2245	CCDS41553.1	10																																																																																			TBC1D12	-	NULL	ENSG00000108239		0.322	TBC1D12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TBC1D12	HGNC	protein_coding	OTTHUMT00000049482.2	27	0.00	0	-			96291202	96291203	+1	no_errors	ENST00000225235	ensembl	human	known	69_37n	frame_shift_ins	18	10.00	2	INS	1.000:1.000	A
TBX3	6926	genome.wustl.edu	37	12	115115457	115115458	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr12:115115457_115115458insT	ENST00000257566.3	-	5	1257_1258	c.868_869insA	c.(868-870)accfs	p.T290fs	TBX3_ENST00000349155.2_Frame_Shift_Ins_p.T270fs	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	290					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T290fs*37(1)		breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		TTTTAACTGGGTTATCTATTGG	0.371																																						dbGAP											1	Insertion - Frameshift(1)	breast(1)																																								-	-	-	SO:0001589	frameshift_variant	0			BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"""T-boxes"""	11602	protein-coding gene	gene with protein product		601621	"""ulnar mammary syndrome"""	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.869dupA	12.37:g.115115459_115115459dupT	ENSP00000257566:p.Thr290fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8TB20|Q9UKF8	Frame_Shift_Ins	INS	pfam_TF_T-box,pfam_TBX,superfamily_p53-like_TF_DNA-bd,smart_TF_T-box,pfscan_TF_T-box,prints_TF_T-box	p.T290fs	ENST00000257566.3	37	c.869_868	CCDS9176.1	12																																																																																			TBX3	-	pfam_TF_T-box,superfamily_p53-like_TF_DNA-bd,smart_TF_T-box,pfscan_TF_T-box	ENSG00000135111		0.371	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TBX3	HGNC	protein_coding	OTTHUMT00000404947.2	229	0.43	1	-	NM_016569, NM_005996		115115457	115115458	-1	no_errors	ENST00000257566	ensembl	human	known	69_37n	frame_shift_ins	80	33.33	40	INS	1.000:1.000	T
TIRAP	114609	genome.wustl.edu	37	11	126162498	126162498	+	Missense_Mutation	SNP	C	C	T	rs370756926		TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr11:126162498C>T	ENST00000392680.2	+	5	599	c.194C>T	c.(193-195)aCg>aTg	p.T65M	RP11-712L6.7_ENST00000533378.1_RNA|RP11-712L6.5_ENST00000528876.1_5'Flank|TIRAP_ENST00000392678.3_Missense_Mutation_p.T65M|TIRAP_ENST00000392679.1_Missense_Mutation_p.T65M	NM_001039661.1	NP_001034750.1	P58753	TIRAP_HUMAN	toll-interleukin 1 receptor (TIR) domain containing adaptor protein	65					3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine (C-X-C motif) ligand 1 production (GO:2000340)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-15 production (GO:0032738)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of toll-like receptor 2 signaling pathway (GO:0034137)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of innate immune response (GO:0045088)|regulation of interferon-beta production (GO:0032648)|response to lipopolysaccharide (GO:0032496)|TIRAP-dependent toll-like receptor 4 signaling pathway (GO:0035665)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein binding, bridging (GO:0030674)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|Toll-like receptor 2 binding (GO:0035663)|Toll-like receptor 4 binding (GO:0035662)	p.T65M(2)		breast(1)|endometrium(1)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	6	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0739)		AGCTCAGTCACGTCTCCCAGC	0.592																																						dbGAP											2	Substitution - Missense(2)	breast(2)											103.0	87.0	92.0					11																	126162498		2201	4298	6499	-	-	-	SO:0001583	missense	0			AF378129	CCDS8472.1, CCDS41731.1	11q24.2	2008-02-05	2002-01-14		ENSG00000150455	ENSG00000150455			17192	protein-coding gene	gene with protein product	"""MyD88 adapter-like"""	606252	"""Toll-interleukin 1 receptor (TIR) domain-containing adaptor protein"""			11526399, 11544529	Standard	XM_005271399		Approved	Mal, wyatt	uc001qdl.1	P58753	OTTHUMG00000140373	ENST00000392680.2:c.194C>T	11.37:g.126162498C>T	ENSP00000376447:p.Thr65Met	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KW65|Q56UH9|Q56UI0|Q8N5E5	Missense_Mutation	SNP	pfam_TIR_dom,superfamily_TIR_dom,pirsf_Tol-interleuk_rcpt_adapt_Tirap,pfscan_TIR_dom	p.T65M	ENST00000392680.2	37	c.194	CCDS8472.1	11	.	.	.	.	.	.	.	.	.	.	C	7.310	0.614774	0.14129	.	.	ENSG00000150455	ENST00000392679;ENST00000279992;ENST00000392678;ENST00000392680	T;T;T	0.08984	3.05;3.03;3.05	4.58	-9.16	0.00694	.	4.095150	0.00424	N	0.000072	T	0.03390	0.0098	N	0.08118	0	0.09310	N	1	B;B	0.19935	0.022;0.04	B;B	0.08055	0.002;0.003	T	0.30090	-0.9990	10	0.40728	T	0.16	-9.2592	2.8446	0.05539	0.2322:0.257:0.3886:0.1221	.	65;65	P58753;Q56UH9	TIRAP_HUMAN;.	M	65	ENSP00000376446:T65M;ENSP00000376445:T65M;ENSP00000376447:T65M	ENSP00000279992:T65M	T	+	2	0	TIRAP	125667708	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.839000	0.00738	-2.790000	0.00356	-0.176000	0.13171	ACG	TIRAP	-	pirsf_Tol-interleuk_rcpt_adapt_Tirap	ENSG00000150455		0.592	TIRAP-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	TIRAP	HGNC	protein_coding	OTTHUMT00000277092.1	175	0.00	0	C	NM_148910		126162498	126162498	+1	no_errors	ENST00000392678	ensembl	human	known	69_37n	missense	60	54.55	72	SNP	0.000	T
TRPV6	55503	genome.wustl.edu	37	7	142575020	142575020	+	Missense_Mutation	SNP	A	A	C			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr7:142575020A>C	ENST00000359396.3	-	4	607	c.362T>G	c.(361-363)cTg>cGg	p.L121R	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	121					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)	p.L121R(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					AGCGATGTGCAGTGCAGTCTG	0.622																																						dbGAP											1	Substitution - Missense(1)	breast(1)											80.0	75.0	77.0					7																	142575020		2203	4300	6503	-	-	-	SO:0001583	missense	0			AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	14006	protein-coding gene	gene with protein product		606680	"""epithelial calcium channel 2"""	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.362T>G	7.37:g.142575020A>C	ENSP00000352358:p.Leu121Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Missense_Mutation	SNP	pfam_Ankyrin_rpt,pfam_Ion_trans_dom,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,prints_TRPV5/TRPV6_channel,prints_TRPV6_channel,prints_Ankyrin_rpt,tigrfam_TRP_channel	p.L121R	ENST00000359396.3	37	c.362	CCDS5874.1	7	.	.	.	.	.	.	.	.	.	.	A	20.6	4.023111	0.75275	.	.	ENSG00000165125	ENST00000359396;ENST00000431833	D;T	0.82167	-1.58;-1.36	3.86	3.86	0.44501	Ankyrin repeat-containing domain (4);	0.072136	0.64402	D	0.000019	D	0.93080	0.7797	H	0.96208	3.785	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	D	0.94475	0.7688	10	0.87932	D	0	-13.698	12.0125	0.53295	1.0:0.0:0.0:0.0	.	121	Q9H1D0	TRPV6_HUMAN	R	121;48	ENSP00000352358:L121R;ENSP00000415917:L48R	ENSP00000352358:L121R	L	-	2	0	TRPV6	142285142	1.000000	0.71417	0.994000	0.49952	0.999000	0.98932	8.602000	0.90868	1.624000	0.50355	0.533000	0.62120	CTG	TRPV6	-	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,tigrfam_TRP_channel	ENSG00000165125		0.622	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TRPV6	HGNC	protein_coding	OTTHUMT00000347662.1	162	0.00	0	A	NM_014274		142575020	142575020	-1	no_errors	ENST00000359396	ensembl	human	known	69_37n	missense	60	29.89	26	SNP	1.000	C
TUB	7275	genome.wustl.edu	37	11	8118904	8118905	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	AA	AA					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr11:8118904_8118905delAA	ENST00000299506.2	+	7	966_967	c.817_818delAA	c.(817-819)aagfs	p.K274fs	TUB_ENST00000305253.4_Frame_Shift_Del_p.K329fs|TUB_ENST00000534099.1_Frame_Shift_Del_p.K280fs	NM_177972.2	NP_813977.1	P50607	TUB_HUMAN	tubby bipartite transcription factor	274					multicellular organismal macromolecule metabolic process (GO:0044259)|phagocytosis (GO:0006909)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|response to hormone (GO:0009725)|retina development in camera-type eye (GO:0060041)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled photoreceptor activity (GO:0008020)|protein complex binding (GO:0032403)			breast(1)|cervix(1)|endometrium(9)|large_intestine(7)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	26		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)		CACTCGGGACAAGAAAGGGATG	0.564																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			U54644	CCDS7786.1, CCDS7787.1	11p15.5	2013-08-06	2013-08-06		ENSG00000166402	ENSG00000166402			12406	protein-coding gene	gene with protein product		601197	"""tubby (mouse) homolog"", ""tubby homolog (mouse)"""			8612280	Standard	NM_003320		Approved	rd5	uc001mfy.3	P50607	OTTHUMG00000165690	ENST00000299506.2:c.817_818delAA	11.37:g.8118904_8118905delAA	ENSP00000299506:p.Lys274fs	Somatic		WXS	Illumina GAIIx	Phase_IV	D3DQU4|O00293|Q6B007	Frame_Shift_Del	DEL	pfam_Tubby_C,superfamily_Tubby_C-like,prints_Tubby_N,prints_Tubby_C	p.K328fs	ENST00000299506.2	37	c.982_983	CCDS7787.1	11																																																																																			TUB	-	pfam_Tubby_C,superfamily_Tubby_C-like	ENSG00000166402		0.564	TUB-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	TUB	HGNC	protein_coding	OTTHUMT00000385823.1	98	0.00	0	AA	NM_003320		8118904	8118905	+1	no_errors	ENST00000305253	ensembl	human	known	69_37n	frame_shift_del	59	47.32	53	DEL	1.000:1.000	-
TXLNG	55787	genome.wustl.edu	37	X	16838307	16838307	+	Missense_Mutation	SNP	A	A	T			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chrX:16838307A>T	ENST00000380122.5	+	3	488	c.427A>T	c.(427-429)Atg>Ttg	p.M143L	TXLNG_ENST00000398155.4_Intron	NM_018360.2	NP_060830.2	Q9NUQ3	TXLNG_HUMAN	taxilin gamma	143					cell cycle (GO:0007049)|regulation of bone mineralization (GO:0030500)|regulation of cell cycle (GO:0051726)|regulation of cell cycle process (GO:0010564)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)	protein heterodimerization activity (GO:0046982)	p.M143L(1)		breast(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	15						TTTATTACTGATGCAAGCCCT	0.398																																						dbGAP											1	Substitution - Missense(1)	breast(1)											147.0	144.0	145.0					X																	16838307		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK002071	CCDS14178.1, CCDS55373.1	Xp22.2	2014-05-07	2010-04-20	2010-04-20	ENSG00000086712	ENSG00000086712			18578	protein-coding gene	gene with protein product	"""lipopolysaccharide specific response-5 protein"", ""factor inhibiting activating transcription factor 4 (ATF4)-mediated transcription"""	300677	"""chromosome X open reading frame 15"""	CXorf15		15911876, 15184072, 16831913	Standard	NM_018360		Approved	FLJ11209, LSR5, FIAT, MGC126621, MGC126625, TXLNGX	uc004cxq.2	Q9NUQ3	OTTHUMG00000021196	ENST00000380122.5:c.427A>T	X.37:g.16838307A>T	ENSP00000369465:p.Met143Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q2KQ75|Q5JNZ7|Q9P0X1	Missense_Mutation	SNP	pfam_Taxilin	p.M143L	ENST00000380122.5	37	c.427	CCDS14178.1	X	.	.	.	.	.	.	.	.	.	.	A	24.3	4.521681	0.85600	.	.	ENSG00000086712	ENST00000380122	T	0.27890	1.64	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.37544	0.1007	L	0.53561	1.675	0.80722	D	1	P	0.41597	0.756	P	0.45971	0.499	T	0.07597	-1.0764	10	0.30078	T	0.28	-19.2533	15.0473	0.71838	1.0:0.0:0.0:0.0	.	143	Q9NUQ3	TXLNG_HUMAN	L	143	ENSP00000369465:M143L	ENSP00000369465:M143L	M	+	1	0	TXLNG	16748228	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.255000	0.95524	2.004000	0.58718	0.417000	0.27973	ATG	TXLNG	-	pfam_Taxilin	ENSG00000086712		0.398	TXLNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TXLNG	HGNC	protein_coding	OTTHUMT00000055912.1	99	0.00	0	A	NM_018360		16838307	16838307	+1	no_errors	ENST00000380122	ensembl	human	known	69_37n	missense	81	30.77	36	SNP	1.000	T
VNN1	8876	genome.wustl.edu	37	6	133004427	133004427	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A0FS-01A-11W-A050-09	TCGA-AN-A0FS-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	9bb76d20-cefb-4f7a-80c2-aa2178e302a9	608d90c1-f205-43fa-a9cd-dcdf54bb927d	g.chr6:133004427G>A	ENST00000367928.4	-	7	1407	c.1394C>T	c.(1393-1395)cCa>cTa	p.P465L		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	465					acute inflammatory response (GO:0002526)|cellular component movement (GO:0006928)|chronic inflammatory response (GO:0002544)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|pantothenate metabolic process (GO:0015939)|positive regulation of T cell differentiation in thymus (GO:0033089)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|pantetheine hydrolase activity (GO:0017159)			NS(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	31	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		TCCGGATGTTGGCTTCAGACT	0.418																																						dbGAP											0													112.0	101.0	105.0					6																	133004427		2203	4300	6503	-	-	-	SO:0001583	missense	0			AJ132099	CCDS5159.1	6q23-q24	2013-02-13			ENSG00000112299	ENSG00000112299	3.5.1.92	"""Vanins"""	12705	protein-coding gene	gene with protein product		603570				9790769	Standard	NM_004666		Approved	Tiff66	uc003qdo.3	O95497	OTTHUMG00000015587	ENST00000367928.4:c.1394C>T	6.37:g.133004427G>A	ENSP00000356905:p.Pro465Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	pfam_C-N_Hydrolase,superfamily_C-N_Hydrolase,pirsf_Biotinidase_euk,pfscan_C-N_Hydrolase	p.P465L	ENST00000367928.4	37	c.1394	CCDS5159.1	6	.	.	.	.	.	.	.	.	.	.	G	15.12	2.739923	0.49045	.	.	ENSG00000112299	ENST00000367928	D	0.92965	-3.14	5.86	4.97	0.65823	.	0.413845	0.24735	N	0.036040	D	0.85856	0.5794	M	0.68317	2.08	0.36056	D	0.841121	B	0.33512	0.415	B	0.32533	0.147	D	0.84352	0.0533	10	0.33940	T	0.23	-7.9611	11.0499	0.47880	0.0:0.2096:0.6835:0.1069	.	465	O95497	VNN1_HUMAN	L	465	ENSP00000356905:P465L	ENSP00000356905:P465L	P	-	2	0	VNN1	133046120	0.183000	0.23186	0.966000	0.40874	0.951000	0.60555	1.750000	0.38329	2.771000	0.95319	0.650000	0.86243	CCA	VNN1	-	pirsf_Biotinidase_euk	ENSG00000112299		0.418	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VNN1	HGNC	protein_coding	OTTHUMT00000042263.1	244	0.81	2	G			133004427	133004427	-1	no_errors	ENST00000367928	ensembl	human	known	69_37n	missense	173	27.62	66	SNP	0.713	A
