#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
AAAS	8086	genome.wustl.edu	37	12	53708115	53708115	+	Missense_Mutation	SNP	A	A	G			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr12:53708115A>G	ENST00000209873.4	-	7	821	c.656T>C	c.(655-657)aTc>aCc	p.I219T	AAAS_ENST00000549983.1_5'UTR|AAAS_ENST00000394384.3_Missense_Mutation_p.I186T|AAAS_ENST00000550286.1_Missense_Mutation_p.I95T	NM_015665.5	NP_056480.1	Q9NRG9	AAAS_HUMAN	achalasia, adrenocortical insufficiency, alacrimia	219					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nucleocytoplasmic transport (GO:0006913)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of nucleocytoplasmic transport (GO:0046822)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	20						CAGGGTCCAGATAAGAATGCA	0.587																																						dbGAP											0													138.0	130.0	132.0					12																	53708115		2203	4300	6503	-	-	-	SO:0001583	missense	0			AJ289841	CCDS8856.1, CCDS53797.1	12q13	2013-06-27	2010-06-24		ENSG00000094914	ENSG00000094914		"""WD repeat domain containing"""	13666	protein-coding gene	gene with protein product	"""aladin"", ""Allgrove, triple-A"""	605378	"""achalasia, adrenocortical insufficiency, alacrimia (Allgrove, triple-A)"""			11062474	Standard	NM_015665		Approved		uc001scr.4	Q9NRG9	OTTHUMG00000169729	ENST00000209873.4:c.656T>C	12.37:g.53708115A>G	ENSP00000209873:p.Ile219Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5JB47|Q9NWI6|Q9UG19	Missense_Mutation	SNP	pfam_WD40_repeat,smart_WD40_repeat,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.I219T	ENST00000209873.4	37	c.656	CCDS8856.1	12	.	.	.	.	.	.	.	.	.	.	A	26.8	4.769533	0.90020	.	.	ENSG00000094914	ENST00000209873;ENST00000394384;ENST00000550286;ENST00000547757	D;D;D;T	0.96745	-4.11;-4.05;-4.11;-0.33	5.16	5.16	0.70880	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.119035	0.56097	D	0.000027	D	0.95541	0.8551	L	0.59436	1.845	0.48135	D	0.999598	P;D	0.53151	0.842;0.958	B;P	0.47528	0.185;0.549	D	0.95720	0.8765	10	0.87932	D	0	-30.7893	13.2841	0.60232	1.0:0.0:0.0:0.0	.	186;219	Q5JB47;Q9NRG9	.;AAAS_HUMAN	T	219;186;95;186	ENSP00000209873:I219T;ENSP00000377908:I186T;ENSP00000446885:I95T;ENSP00000448020:I186T	ENSP00000209873:I219T	I	-	2	0	AAAS	51994382	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.481000	0.90437	2.306000	0.77630	0.482000	0.46254	ATC	AAAS	-	smart_WD40_repeat,pfscan_WD40_repeat_dom	ENSG00000094914		0.587	AAAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AAAS	HGNC	protein_coding	OTTHUMT00000405632.1	86	0.00	0	A			53708115	53708115	-1	no_errors	ENST00000209873	ensembl	human	known	69_37n	missense	52	24.64	17	SNP	1.000	G
AADAT	51166	genome.wustl.edu	37	4	170988516	170988516	+	Silent	SNP	G	G	A			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr4:170988516G>A	ENST00000337664.4	-	9	1200	c.924C>T	c.(922-924)caC>caT	p.H308H	AADAT_ENST00000515480.1_Silent_p.H308H|AADAT_ENST00000509167.1_Silent_p.H312H|AADAT_ENST00000353187.2_Silent_p.H308H	NM_016228.3	NP_057312.1	Q8N5Z0	AADAT_HUMAN	aminoadipate aminotransferase	308					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|kynurenine metabolic process (GO:0070189)|L-kynurenine metabolic process (GO:0097052)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	mitochondrial matrix (GO:0005759)	2-aminoadipate transaminase activity (GO:0047536)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|pancreas(1)|stomach(1)	11		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0355)|LUSC - Lung squamous cell carcinoma(193;0.118)		CTCCCCATTCGTGTAGAAGCT	0.348																																						dbGAP											0													84.0	82.0	83.0					4																	170988516		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF097994	CCDS3814.1, CCDS75209.1	4q33	2010-12-09			ENSG00000109576	ENSG00000109576	2.6.1.39		17929	protein-coding gene	gene with protein product	"""kynurenine aminotransferase II"", ""L kynurenine/alpha aminoadipate aminotransferase"""	611754				12126930, 10441733	Standard	NM_182662		Approved	KATII, KAT2	uc003isr.3	Q8N5Z0	OTTHUMG00000160912	ENST00000337664.4:c.924C>T	4.37:g.170988516G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B3KP84|Q9UL02	Silent	SNP	pfam_Aminotransferase_I/II,superfamily_PyrdxlP-dep_Trfase_major_dom	p.H312	ENST00000337664.4	37	c.936	CCDS3814.1	4																																																																																			AADAT	-	pfam_Aminotransferase_I/II,superfamily_PyrdxlP-dep_Trfase_major_dom	ENSG00000109576		0.348	AADAT-004	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	AADAT	HGNC	protein_coding	OTTHUMT00000362952.1	85	0.00	0	G	NM_016228		170988516	170988516	-1	no_errors	ENST00000509167	ensembl	human	known	69_37n	silent	90	20.35	23	SNP	0.836	A
ABCB8	11194	genome.wustl.edu	37	7	150742383	150742384	+	Frame_Shift_Ins	INS	-	-	C	rs141053127		TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr7:150742383_150742384insC	ENST00000297504.6	+	17	2221_2222	c.2155_2156insC	c.(2155-2157)gccfs	p.A719fs	ABCB8_ENST00000498578.1_Frame_Shift_Ins_p.A677fs|ASIC3_ENST00000357922.4_5'Flank|ABCB8_ENST00000358849.4_Frame_Shift_Ins_p.A702fs|ABCB8_ENST00000542328.1_Frame_Shift_Ins_p.A614fs|ABCB8_ENST00000356058.4_3'UTR			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	719					transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Doxorubicin(DB00997)	GAGGACAGCGGCCCCACCGCCC	0.634																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AF047690	CCDS5913.1, CCDS64798.1, CCDS64799.1, CCDS64800.1	7q36.1	2012-05-16			ENSG00000197150	ENSG00000197150		"""ATP binding cassette transporters / subfamily B"""	49	protein-coding gene	gene with protein product	"""mitochondrial ABC protein"""	605464				8894702	Standard	NM_001282291		Approved	EST328128, M-ABC1, MABC1	uc003wik.4	Q9NUT2	OTTHUMG00000158686	ENST00000297504.6:c.2159dupC	7.37:g.150742387_150742387dupC	ENSP00000297504:p.Ala719fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Frame_Shift_Ins	INS	pfam_ABC_transptr_TM_dom,pfam_ABC_transporter-like,superfamily_ABC_transptrTM_dom_typ1,smart_AAA+_ATPase,pfscan_ABC_transporter-like,pfscan_ABC_transporter_type1	p.P721fs	ENST00000297504.6	37	c.2155_2156		7																																																																																			ABCB8	-	NULL	ENSG00000197150		0.634	ABCB8-003	KNOWN	basic	protein_coding	ABCB8	HGNC	protein_coding	OTTHUMT00000351733.2	29	0.00	0	-	NM_007188		150742383	150742384	+1	no_errors	ENST00000297504	ensembl	human	known	69_37n	frame_shift_ins	22	15.38	4	INS	0.000:0.001	C
ACTL6B	51412	genome.wustl.edu	37	7	100245130	100245131	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr7:100245130_100245131insG	ENST00000160382.5	-	8	801_802	c.695_696insC	c.(694-696)ccafs	p.P232fs		NM_016188.4	NP_057272.1	O94805	ACL6B_HUMAN	actin-like 6B	232					chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|nervous system development (GO:0007399)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	structural constituent of cytoskeleton (GO:0005200)|transcription coactivator activity (GO:0003713)			endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|skin(1)	13	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					TCTTCCAGTTTGGGGGGGCACC	0.609																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AB015906	CCDS5702.1	7q22	2008-02-01	2004-07-12	2004-07-14	ENSG00000077080	ENSG00000077080			160	protein-coding gene	gene with protein product		612458	"""actin-like 6"""	ACTL6		9799793	Standard	NM_016188		Approved	BAF53B	uc003uvy.3	O94805	OTTHUMG00000159661	ENST00000160382.5:c.696dupC	7.37:g.100245137_100245137dupG	ENSP00000160382:p.Pro232fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A4D2D0|O75421	Frame_Shift_Ins	INS	pfam_Actin-like,smart_Actin-like,prints_Actin-like	p.N233fs	ENST00000160382.5	37	c.696_695	CCDS5702.1	7																																																																																			ACTL6B	-	pfam_Actin-like,smart_Actin-like	ENSG00000077080		0.609	ACTL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ACTL6B	HGNC	protein_coding	OTTHUMT00000356745.1	13	0.00	0	-	NM_016188		100245130	100245131	-1	no_errors	ENST00000160382	ensembl	human	known	69_37n	frame_shift_ins	9	30.77	4	INS	1.000:1.000	G
ATP9B	374868	genome.wustl.edu	37	18	77137328	77137328	+	Missense_Mutation	SNP	T	T	G			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr18:77137328T>G	ENST00000426216.2	+	30	3406	c.3389T>G	c.(3388-3390)cTc>cGc	p.L1130R	ATP9B_ENST00000543761.1_Missense_Mutation_p.L440R|ATP9B_ENST00000307671.7_Missense_Mutation_p.L1119R	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	1130					establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		CTGTATGTCCTCAAGTACCTG	0.607																																						dbGAP											0													114.0	93.0	100.0					18																	77137328		2203	4300	6503	-	-	-	SO:0001583	missense	0			R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"""ATPases / P-type"""	13541	protein-coding gene	gene with protein product		614446	"""ATPase, Class II, type 9B"""			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.3389T>G	18.37:g.77137328T>G	ENSP00000398076:p.Leu1130Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	O60872|Q08AD8|Q08AD9	Missense_Mutation	SNP	pfam_ATPase_P-typ_ATPase-assoc-dom,pfam_Dehalogen-like_hydro,superfamily_HAD-like_dom,superfamily_ATPase_cation_domN,prints_ATPase_P-typ_ion-transptr,tigrfam_ATPase_P-typ_Plipid-transl,tigrfam_ATPase_P-typ_ion-transptr	p.L1130R	ENST00000426216.2	37	c.3389	CCDS12014.1	18	.	.	.	.	.	.	.	.	.	.	t	15.46	2.841454	0.51057	.	.	ENSG00000166377	ENST00000426216;ENST00000307671;ENST00000543761	T	0.43294	0.95	4.17	2.99	0.34606	.	0.136499	0.48767	D	0.000163	T	0.62539	0.2436	M	0.84082	2.675	0.44587	D	0.99755	D;D	0.69078	0.995;0.997	P;D	0.70716	0.895;0.97	T	0.63559	-0.6610	10	0.59425	D	0.04	.	9.7451	0.40442	0.0:0.0848:0.0:0.9152	.	1130;1119	O43861;O43861-2	ATP9B_HUMAN;.	R	1119;1130;440	ENSP00000442015:L440R	ENSP00000304500:L1130R	L	+	2	0	ATP9B	75238316	1.000000	0.71417	0.700000	0.30305	0.516000	0.34256	5.747000	0.68689	0.553000	0.29044	-0.332000	0.08345	CTC	ATP9B	-	tigrfam_ATPase_P-typ_Plipid-transl	ENSG00000166377		0.607	ATP9B-001	KNOWN	basic|CCDS	protein_coding	ATP9B	HGNC	protein_coding	OTTHUMT00000256402.3	43	0.00	0	T	NM_198531		77137328	77137328	+1	no_errors	ENST00000426216	ensembl	human	known	69_37n	missense	25	28.57	10	SNP	1.000	G
HSF1	3297	genome.wustl.edu	37	8	145512978	145512979	+	5'Flank	INS	-	-	G			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr8:145512978_145512979insG	ENST00000528838.1	+	0	0				BOP1_ENST00000307404.5_Frame_Shift_Ins_p.L36fs|BOP1_ENST00000529231.1_5'UTR	NM_005526.2	NP_005517.1	Q00613	HSF1_HUMAN	heat shock transcription factor 1						cellular response to heat (GO:0034605)|defense response (GO:0006952)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|female meiotic division (GO:0007143)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)|response to lipopolysaccharide (GO:0032496)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pronucleus (GO:0045120)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|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)|RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(1)|lung(3)|prostate(3)|skin(1)|urinary_tract(2)	11	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;1.12e-39)|all cancers(56;9.11e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0547)|Colorectal(110;0.055)			GGTGCAGAGGAGGGGGGGCTGC	0.639																																						dbGAP											0																																										-	-	-	SO:0001631	upstream_gene_variant	0			M64673	CCDS6419.1	8q24.3	2014-04-10			ENSG00000185122	ENSG00000185122			5224	protein-coding gene	gene with protein product		140580				1871105	Standard	NM_005526		Approved	HSTF1	uc003zbt.4	Q00613	OTTHUMG00000174604		8.37:g.145512985_145512985dupG	Exception_encountered	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K4L0|A8MW26|Q53XT4	Frame_Shift_Ins	INS	pfam_BOP1_N_dom,pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.L36fs	ENST00000528838.1	37	c.107_106	CCDS6419.1	8																																																																																			BOP1	-	NULL	ENSG00000170727		0.639	HSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BOP1	HGNC	protein_coding	OTTHUMT00000382053.1	19	0.00	0	-	NM_005526		145512978	145512979	-1	no_errors	ENST00000307404	ensembl	human	known	69_37n	frame_shift_ins	17	10.53	2	INS	0.008:0.001	G
SMCO1	255798	genome.wustl.edu	37	3	196234930	196234930	+	Missense_Mutation	SNP	C	C	T			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr3:196234930C>T	ENST00000397537.2	-	3	629	c.473G>A	c.(472-474)aGg>aAg	p.R158K		NM_001077657.1	NP_001071125.1	Q147U7	SMCO1_HUMAN	single-pass membrane protein with coiled-coil domains 1	158						integral component of membrane (GO:0016021)											GTACATCTGCCTCACTTTAGC	0.463																																						dbGAP											0													175.0	166.0	169.0					3																	196234930		2067	4186	6253	-	-	-	SO:0001583	missense	0			AK123917	CCDS43192.1	3q29	2013-03-08	2013-03-08	2013-03-08	ENSG00000214097	ENSG00000214097			27407	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 43"""	C3orf43			Standard	NM_001077657		Approved	FLJ41923, DKFZp313B0440		Q147U7	OTTHUMG00000155581	ENST00000397537.2:c.473G>A	3.37:g.196234930C>T	ENSP00000380671:p.Arg158Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KW20	Missense_Mutation	SNP	NULL	p.R158K	ENST00000397537.2	37	c.473	CCDS43192.1	3	.	.	.	.	.	.	.	.	.	.	C	13.05	2.122053	0.37436	.	.	ENSG00000214097	ENST00000397537	T	0.39056	1.1	5.29	4.41	0.53225	.	.	.	.	.	T	0.41419	0.1158	L	0.34521	1.04	0.09310	N	0.999999	P;P	0.49961	0.93;0.93	P;P	0.47915	0.561;0.561	T	0.27054	-1.0085	9	0.87932	D	0	-14.0665	13.1644	0.59562	0.0:0.8393:0.1607:0.0	.	158;150	Q147U7;E9PGG7	CC043_HUMAN;.	K	158	ENSP00000380671:R158K	ENSP00000380671:R158K	R	-	2	0	C3orf43	197719327	0.465000	0.25815	0.025000	0.17156	0.002000	0.02628	4.336000	0.59304	1.219000	0.43474	-0.175000	0.13238	AGG	C3orf43	-	NULL	ENSG00000214097		0.463	SMCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C3orf43	HGNC	protein_coding	OTTHUMT00000340776.1	183	0.00	0	C	NM_001006109		196234930	196234930	-1	no_errors	ENST00000397537	ensembl	human	known	69_37n	missense	111	16.54	22	SNP	0.146	T
CBX2	84733	genome.wustl.edu	37	17	77758219	77758220	+	Frame_Shift_Ins	INS	-	-	C			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr17:77758219_77758220insC	ENST00000310942.4	+	5	1081_1082	c.977_978insC	c.(976-981)ggccccfs	p.GP326fs		NM_005189.2	NP_005180.1	Q14781	CBX2_HUMAN	chromobox homolog 2	326					cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|development of primary sexual characteristics (GO:0045137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			AACACAGGGGGCCCCCCGCACA	0.668																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			BC004252, BG354579	CCDS11764.1, CCDS32757.1	17q25.3	2010-07-06	2010-06-24		ENSG00000173894	ENSG00000173894			1552	protein-coding gene	gene with protein product	"""Pc class homolog (Drosophila)"""	602770	"""chromobox homolog 2 (Drosophila Pc class)"", ""cell division cycle associated 6"""	CDCA6		7782071, 2477932	Standard	NM_005189		Approved	MGC10561	uc002jxc.3	Q14781		ENST00000310942.4:c.983dupC	17.37:g.77758225_77758225dupC	ENSP00000308750:p.Gly326fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q0VDA5|Q9BTB1	Frame_Shift_Ins	INS	pfam_Chromo_domain,superfamily_Chromodomain-like,smart_Chromo_domain/shadow,pfscan_Chromo_domain/shadow	p.H329fs	ENST00000310942.4	37	c.977_978	CCDS32757.1	17																																																																																			CBX2	-	NULL	ENSG00000173894		0.668	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CBX2	HGNC	protein_coding	OTTHUMT00000437040.1	12	0.00	0	-	NM_032647		77758219	77758220	+1	no_errors	ENST00000310942	ensembl	human	known	69_37n	frame_shift_ins	4	33.33	2	INS	0.033:0.000	C
EFCC1	79825	genome.wustl.edu	37	3	128753127	128753128	+	Frame_Shift_Ins	INS	-	-	A			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr3:128753127_128753128insA	ENST00000480450.1	+	5	1404_1405	c.1404_1405insA	c.(1405-1407)actfs	p.T469fs	EFCC1_ENST00000436022.2_Frame_Shift_Ins_p.T32fs			Q9HA90	EFCC1_HUMAN	EF-hand and coiled-coil domain containing 1	469							calcium ion binding (GO:0005509)										AGCAGCTGAGGACTCAGGGCTG	0.594																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AK022119	CCDS3054.1, CCDS3054.2	3q21.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000114654	ENSG00000114654		"""EF-hand domain containing"""	25692	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 73"", ""coiled-coil domain containing 48"""	C3orf73, CCDC48			Standard	NM_024768		Approved	FLJ12057	uc011bkt.2	Q9HA90	OTTHUMG00000158996	ENST00000480450.1:c.1405dupA	3.37:g.128753128_128753128dupA	ENSP00000420075:p.Thr469fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A8MYE2	Frame_Shift_Ins	INS	NULL	p.T31fs	ENST00000480450.1	37	c.93_94	CCDS3054.2	3																																																																																			CCDC48	-	NULL	ENSG00000114654		0.594	EFCC1-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	CCDC48	HGNC	protein_coding	OTTHUMT00000352832.1	30	0.00	0	-	NM_024768		128753127	128753128	+1	no_errors	ENST00000436022	ensembl	human	known	69_37n	frame_shift_ins	14	41.67	10	INS	0.023:0.020	A
CDH24	64403	genome.wustl.edu	37	14	23523727	23523728	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr14:23523727_23523728insG	ENST00000267383.5	-	4	863_864	c.771_772insC	c.(769-774)cccaagfs	p.K258fs	CDH24_ENST00000397359.3_Frame_Shift_Ins_p.K258fs|CDH24_ENST00000554034.1_Frame_Shift_Ins_p.K258fs|CDH24_ENST00000487137.2_Frame_Shift_Ins_p.K258fs			Q86UP0	CAD24_HUMAN	cadherin 24, type 2	258	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)		TGTGGGAACTTGGGGGGGTTGT	0.614											OREG0022594	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											0									,	9,4255		0,9,2123					,	5.0	1.0			54	10,8244		0,10,4117	no	frameshift,frameshift	CDH24	NM_144985.3,NM_022478.3	,	0,19,6240	A1A1,A1R,RR		0.1212,0.2111,0.1518	,	,		19,12499				-	-	-	SO:0001589	frameshift_variant	0			AL137477	CCDS9585.1, CCDS9586.1	14q11.2	2010-08-20	2009-11-20		ENSG00000139880	ENSG00000139880		"""Cadherins / Major cadherins"""	14265	protein-coding gene	gene with protein product			"""cadherin-like 24"""			12734196	Standard	NM_022478		Approved	CDH11L	uc001wil.3	Q86UP0	OTTHUMG00000028715	ENST00000267383.5:c.772dupC	14.37:g.23523734_23523734dupG	ENSP00000267383:p.Lys258fs	Somatic	764	WXS	Illumina GAIIx	Phase_IV	D3DS44|Q86UP1|Q9NT84	Frame_Shift_Ins	INS	pfam_Cadherin,pfam_Cadherin_cytoplasmic-dom,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.K257fs	ENST00000267383.5	37	c.772_771	CCDS9585.1	14																																																																																			CDH24	-	superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	ENSG00000139880		0.614	CDH24-006	KNOWN	basic|CCDS	protein_coding	CDH24	HGNC	protein_coding	OTTHUMT00000257241.2	29	0.00	0	-	NM_022478		23523727	23523728	-1	no_errors	ENST00000267383	ensembl	human	known	69_37n	frame_shift_ins	17	22.73	5	INS	1.000:1.000	G
CSAD	51380	genome.wustl.edu	37	12	53552403	53552403	+	Silent	SNP	G	G	A	rs573982825		TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr12:53552403G>A	ENST00000444623.1	-	17	1641	c.1374C>T	c.(1372-1374)caC>caT	p.H458H	CSAD_ENST00000453446.2_Silent_p.H458H|CSAD_ENST00000379846.1_Silent_p.H311H|CSAD_ENST00000267085.4_Silent_p.H485H|CSAD_ENST00000379843.3_Silent_p.H311H|RP11-1136G11.8_ENST00000550908.1_lincRNA	NM_001244705.1	NP_001231634.1	Q9Y600	CSAD_HUMAN	cysteine sulfinic acid decarboxylase	458					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|taurine biosynthetic process (GO:0042412)		pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(4)	14					L-Cysteine(DB00151)	CCCGGGTCCCGTGGGGCTGGT	0.617													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19166	0.0		0.0	False		,,,				2504	0.0				Ovarian(109;252 1546 16882 28524 44645)	dbGAP											0													70.0	54.0	60.0					12																	53552403		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB044561	CCDS8848.2, CCDS58235.1	12q13.11-q14.3	2008-08-04			ENSG00000139631	ENSG00000139631			18966	protein-coding gene	gene with protein product	"""P-selectin cytoplasmic tail-associated protein"""					15489334	Standard	NM_015989		Approved	PCAP, CSD	uc001sbz.3	Q9Y600	OTTHUMG00000048076	ENST00000444623.1:c.1374C>T	12.37:g.53552403G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K0U4|Q4QQH9|Q9UNJ5|Q9Y601	Missense_Mutation	SNP	pfam_PyrdxlP-dep_de-COase,pfam_Aminotrans_V/Cys_dSase,pfam_ArAA_b-elim_lyase/Thr_aldolase,superfamily_PyrdxlP-dep_Trfase_major_dom	p.R484W	ENST00000444623.1	37	c.1450	CCDS58235.1	12	.	.	.	.	.	.	.	.	.	.	G	1.918	-0.448976	0.04572	.	.	ENSG00000139631	ENST00000379850	.	.	.	4.49	-6.64	0.01801	.	.	.	.	.	T	0.59702	0.2213	.	.	.	0.45979	D	0.998792	.	.	.	.	.	.	T	0.62709	-0.6797	4	.	.	.	-14.9852	13.4142	0.60959	0.2583:0.1056:0.6361:0.0	.	.	.	.	W	484	.	.	R	-	1	2	CSAD	51838670	0.000000	0.05858	0.470000	0.27216	0.394000	0.30568	-2.150000	0.01290	-1.279000	0.02405	-0.417000	0.06048	CGG	CSAD	-	superfamily_PyrdxlP-dep_Trfase_major_dom	ENSG00000139631		0.617	CSAD-017	KNOWN	basic|appris_principal|CCDS	protein_coding	CSAD	HGNC	protein_coding	OTTHUMT00000343697.1	35	0.00	0	G	NM_015989		53552403	53552403	-1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000379850	ensembl	human	novel	69_37n	missense	18	35.71	10	SNP	0.061	A
CTNNA2	1496	genome.wustl.edu	37	2	80773103	80773103	+	Frame_Shift_Del	DEL	C	C	-			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr2:80773103delC	ENST00000402739.4	+	10	1460	c.1455delC	c.(1453-1455)ttcfs	p.F485fs	CTNNA2_ENST00000343114.3_Frame_Shift_Del_p.F164fs|CTNNA2_ENST00000496558.1_Frame_Shift_Del_p.F485fs|CTNNA2_ENST00000466387.1_Frame_Shift_Del_p.F485fs|CTNNA2_ENST00000541047.1_Frame_Shift_Del_p.F485fs|CTNNA2_ENST00000361291.4_Frame_Shift_Del_p.F519fs|CTNNA2_ENST00000540488.1_Frame_Shift_Del_p.F485fs	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	485					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						TGGACGTCTTCAAAGACCAGT	0.512																																						dbGAP											0													66.0	75.0	72.0					2																	80773103		2065	4213	6278	-	-	-	SO:0001589	frameshift_variant	0				CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"""cadherin-associated protein, related"", ""cancer/testis antigen 114"""	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.1455delC	2.37:g.80773103delC	ENSP00000384638:p.Phe485fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Frame_Shift_Del	DEL	pfam_Vinculin/catenin,superfamily_Vinculin/catenin,prints_Alpha_catenin,prints_Vinculin	p.F519fs	ENST00000402739.4	37	c.1557		2																																																																																			CTNNA2	-	pfam_Vinculin/catenin,superfamily_Vinculin/catenin	ENSG00000066032		0.512	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	CTNNA2	HGNC	protein_coding	OTTHUMT00000328511.4	62	0.00	0	C	NM_004389		80773103	80773103	+1	no_errors	ENST00000361291	ensembl	human	known	69_37n	frame_shift_del	39	55.32	52	DEL	1.000	-
EDDM3A	10876	genome.wustl.edu	37	14	21216114	21216114	+	Missense_Mutation	SNP	C	C	A			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr14:21216114C>A	ENST00000326842.2	+	2	502	c.375C>A	c.(373-375)ttC>ttA	p.F125L		NM_006683.4	NP_006674.2	Q14507	EP3A_HUMAN	epididymal protein 3A	125					sperm displacement (GO:0007321)	extracellular space (GO:0005615)				breast(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6						ACATTGAATTCCATTGTGGCG	0.433																																						dbGAP											0													93.0	78.0	83.0					14																	21216114		2203	4300	6503	-	-	-	SO:0001583	missense	0			X76383	CCDS9556.1	14q11.1	2010-03-19	2010-01-27	2010-01-27	ENSG00000181562	ENSG00000181562			16978	protein-coding gene	gene with protein product		611580	"""family with sequence similarity 12, member A"""	FAM12A		7514008	Standard	NM_006683		Approved	HE3-ALPHA	uc001vyc.3	Q14507	OTTHUMG00000029581	ENST00000326842.2:c.375C>A	14.37:g.21216114C>A	ENSP00000315098:p.Phe125Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q4KN33	Missense_Mutation	SNP	superfamily_RNaseA_domain	p.F125L	ENST00000326842.2	37	c.375	CCDS9556.1	14	.	.	.	.	.	.	.	.	.	.	C	14.02	2.409961	0.42715	.	.	ENSG00000181562	ENST00000326842	T	0.71341	-0.56	2.46	1.54	0.23209	Ribonuclease A, domain (2);	0.141481	0.32987	N	0.005414	T	0.61825	0.2378	L	0.46157	1.445	0.18873	N	0.999988	P	0.36577	0.558	B	0.41202	0.35	T	0.56577	-0.7956	10	0.87932	D	0	.	5.0639	0.14572	0.0:0.8171:0.0:0.1829	.	125	Q14507	EP3A_HUMAN	L	125	ENSP00000315098:F125L	ENSP00000315098:F125L	F	+	3	2	EDDM3A	20285954	1.000000	0.71417	0.250000	0.24296	0.220000	0.24768	0.486000	0.22340	0.345000	0.23873	0.313000	0.20887	TTC	EDDM3A	-	superfamily_RNaseA_domain	ENSG00000181562		0.433	EDDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EDDM3A	HGNC	protein_coding	OTTHUMT00000073742.3	160	0.00	0	C			21216114	21216114	+1	no_errors	ENST00000326842	ensembl	human	known	69_37n	missense	108	12.90	16	SNP	0.315	A
ENPP7	339221	genome.wustl.edu	37	17	77709202	77709203	+	Frame_Shift_Ins	INS	-	-	CC			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr17:77709202_77709203insCC	ENST00000328313.5	+	3	981_982	c.760_761insCC	c.(760-762)aaafs	p.K254fs		NM_178543.3	NP_848638.3			ectonucleotide pyrophosphatase/phosphodiesterase 7											breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(6)|skin(3)	34			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GACCGTGGACAAACGGGCTGGC	0.604																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AY230663	CCDS11763.1	17q25.3	2014-04-09			ENSG00000182156	ENSG00000182156			23764	protein-coding gene	gene with protein product	"""alkaline sphingomyelinase"""					12885774	Standard	NM_178543		Approved	alk-SMase, NPP7	uc002jxa.3	Q6UWV6	OTTHUMG00000177462	Exception_encountered	17.37:g.77709202_77709203insCC	ENSP00000332656:p.Lys254fs	Somatic		WXS	Illumina GAIIx	Phase_IV		Frame_Shift_Ins	INS	pfam_Phosphodiest/P_Trfase,pfam_Metalloenzyme,superfamily_Alkaline_phosphatase_core	p.K254fs	ENST00000328313.5	37	c.760_761	CCDS11763.1	17																																																																																			ENPP7	-	pfam_Phosphodiest/P_Trfase,superfamily_Alkaline_phosphatase_core	ENSG00000182156		0.604	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	ENPP7	HGNC	protein_coding	OTTHUMT00000437038.1	38	0.00	0	-	NM_178543		77709202	77709203	+1	no_errors	ENST00000328313	ensembl	human	known	69_37n	frame_shift_ins	37	33.93	19	INS	0.544:0.531	CC
GDAP1	54332	genome.wustl.edu	37	8	75276444	75276444	+	Missense_Mutation	SNP	A	A	G			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr8:75276444A>G	ENST00000220822.7	+	6	999	c.919A>G	c.(919-921)Aca>Gca	p.T307A	GDAP1_ENST00000434412.2_Missense_Mutation_p.T239A|GDAP1_ENST00000521096.1_3'UTR	NM_001040875.2|NM_018972.2	NP_001035808.1|NP_061845.2	Q8TB36	GDAP1_HUMAN	ganglioside induced differentiation associated protein 1	307	GST C-terminal.				cell death (GO:0008219)|mitochondrial fission (GO:0000266)|protein targeting to mitochondrion (GO:0006626)|response to retinoic acid (GO:0032526)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)			AGTGCTGCCAACAGCATTCCG	0.428																																						dbGAP											0													70.0	74.0	73.0					8																	75276444		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS34911.1, CCDS47877.1	8q13.3	2014-09-17	2012-02-09						15968	protein-coding gene	gene with protein product		606598	"""Charcot-Marie-Tooth neuropathy 4A"""	CMT4A		8268915, 11743579	Standard	NM_018972		Approved	CMT4	uc003yah.3	Q8TB36		ENST00000220822.7:c.919A>G	8.37:g.75276444A>G	ENSP00000220822:p.Thr307Ala	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K957|E7FJF3|E7FJF4	Missense_Mutation	SNP	pfam_Glutathione_S-Trfase_N,pfam_GST_C,superfamily_Thioredoxin-like_fold,superfamily_Glutathione-S-Trfase_C-like	p.T307A	ENST00000220822.7	37	c.919	CCDS34911.1	8	.	.	.	.	.	.	.	.	.	.	A	14.61	2.587105	0.46110	.	.	ENSG00000104381	ENST00000220822;ENST00000434412	D;D	0.97378	-4.36;-4.36	4.99	4.99	0.66335	Glutathione S-transferase/chloride channel, C-terminal (1);	0.126851	0.53938	D	0.000044	D	0.93926	0.8056	N	0.25647	0.755	0.41343	D	0.987314	B	0.29552	0.248	B	0.32465	0.146	D	0.92847	0.6294	10	0.40728	T	0.16	-14.4058	15.1492	0.72684	1.0:0.0:0.0:0.0	.	307	Q8TB36	GDAP1_HUMAN	A	307;239	ENSP00000220822:T307A;ENSP00000417006:T239A	ENSP00000220822:T307A	T	+	1	0	GDAP1	75438999	0.992000	0.36948	1.000000	0.80357	0.999000	0.98932	3.844000	0.55873	2.234000	0.73211	0.533000	0.62120	ACA	GDAP1	-	NULL	ENSG00000104381		0.428	GDAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GDAP1	HGNC	protein_coding	OTTHUMT00000379061.1	140	0.71	1	A	NM_018972		75276444	75276444	+1	no_errors	ENST00000220822	ensembl	human	known	69_37n	missense	241	12.36	34	SNP	1.000	G
GPR101	83550	genome.wustl.edu	37	X	136112380	136112380	+	Missense_Mutation	SNP	G	G	C			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chrX:136112380G>C	ENST00000298110.1	-	1	1453	c.1454C>G	c.(1453-1455)cCa>cGa	p.P485R		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	485						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42	Acute lymphoblastic leukemia(192;0.000127)					GGGCAGGTCTGGGTGGCTATC	0.468																																						dbGAP											0													98.0	94.0	95.0					X																	136112380		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF411115	CCDS14662.1	Xq26.3	2014-01-30			ENSG00000165370	ENSG00000165370		"""GPCR / Class A : Orphans"""	14963	protein-coding gene	gene with protein product		300393				11574155	Standard	NM_054021		Approved		uc011mwh.2	Q96P66	OTTHUMG00000022521	ENST00000298110.1:c.1454C>G	X.37:g.136112380G>C	ENSP00000298110:p.Pro485Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5JSM8|Q8NG93	Missense_Mutation	SNP	pfam_7TM_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,pfam_7TM_GPCR_serpentine_rcpt_Srv,pfscan_GPCR_Rhodpsn_supfam,prints_7TM_GPCR_Rhodpsn	p.P485R	ENST00000298110.1	37	c.1454	CCDS14662.1	X	.	.	.	.	.	.	.	.	.	.	G	11.28	1.592770	0.28357	.	.	ENSG00000165370	ENST00000298110	T	0.35789	1.29	4.65	3.7	0.42460	.	.	.	.	.	T	0.18676	0.0448	L	0.27053	0.805	0.28221	N	0.926526	B	0.30281	0.275	B	0.26310	0.068	T	0.18209	-1.0344	9	0.08381	T	0.77	-3.7738	4.3184	0.11003	0.1174:0.0:0.6561:0.2264	.	485	Q96P66	GP101_HUMAN	R	485	ENSP00000298110:P485R	ENSP00000298110:P485R	P	-	2	0	GPR101	135940046	0.986000	0.35501	0.976000	0.42696	0.487000	0.33371	1.835000	0.39181	2.248000	0.74166	0.429000	0.28392	CCA	GPR101	-	NULL	ENSG00000165370		0.468	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPR101	HGNC	protein_coding	OTTHUMT00000058519.1	173	0.00	0	G			136112380	136112380	-1	no_errors	ENST00000298110	ensembl	human	known	69_37n	missense	114	35.59	63	SNP	0.873	C
GYLTL1B	120071	genome.wustl.edu	37	11	45948372	45948373	+	Frame_Shift_Ins	INS	-	-	C	rs376236828		TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr11:45948372_45948373insC	ENST00000531526.1	+	10	1386_1387	c.1275_1276insC	c.(1276-1278)cccfs	p.P426fs	GYLTL1B_ENST00000325468.5_Frame_Shift_Ins_p.P426fs|GYLTL1B_ENST00000401752.1_Frame_Shift_Ins_p.P426fs|GYLTL1B_ENST00000389968.3_Frame_Shift_Ins_p.P153fs|GYLTL1B_ENST00000536139.1_Frame_Shift_Ins_p.P395fs|GYLTL1B_ENST00000529052.1_Frame_Shift_Ins_p.P395fs	NM_152312.3	NP_689525.3	Q8N3Y3	LARG2_HUMAN	glycosyltransferase-like 1B	426					muscle cell cellular homeostasis (GO:0046716)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)	p.R428fs*68(1)		breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(35;0.226)		ATGAACCGCCACCCCCCCGGCC	0.649																																						dbGAP											1	Insertion - Frameshift(1)	lung(1)								6,4258		0,6,2126						-8.6	0.0			47	11,8243		0,11,4116	no	frameshift	GYLTL1B	NM_152312.3		0,17,6242	A1A1,A1R,RR		0.1333,0.1407,0.1358				17,12501				-	-	-	SO:0001589	frameshift_variant	0				CCDS31473.1	11p11.12	2013-02-22			ENSG00000165905	ENSG00000165905		"""Glycosyltransferase family 8 domain containing"""	16522	protein-coding gene	gene with protein product		609709				15661757, 15958417	Standard	XM_005252785		Approved	PP5656, FLJ35207, LARGE2	uc001nbv.1	Q8N3Y3	OTTHUMG00000167037	ENST00000531526.1:c.1282dupC	11.37:g.45948379_45948379dupC	ENSP00000432869:p.Pro426fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NN75|Q8N8Y6|Q8NAK3|Q8WY62	Frame_Shift_Ins	INS	pfam_Glyco_trans_8	p.R427fs	ENST00000531526.1	37	c.1275_1276	CCDS31473.1	11																																																																																			GYLTL1B	-	NULL	ENSG00000165905		0.649	GYLTL1B-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	GYLTL1B	HGNC	protein_coding	OTTHUMT00000392572.1	18	0.00	0	-	NM_152312		45948372	45948373	+1	no_errors	ENST00000325468	ensembl	human	known	69_37n	frame_shift_ins	10	16.67	2	INS	0.002:0.023	C
HHEX	3087	genome.wustl.edu	37	10	94454508	94454509	+	Frame_Shift_Ins	INS	-	-	CC			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr10:94454508_94454509insCC	ENST00000282728.5	+	4	2595_2596	c.796_797insCC	c.(796-798)tatfs	p.Y266fs	HHEX_ENST00000472590.2_Frame_Shift_Ins_p.Y94fs|HHEX_ENST00000492654.2_Frame_Shift_Ins_p.Y94fs	NM_002729.4	NP_002720.1	Q03014	HHEX_HUMAN	hematopoietically expressed homeobox	266					anterior/posterior pattern specification (GO:0009952)|B cell differentiation (GO:0030183)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|DNA conformation change (GO:0071103)|embryonic heart tube development (GO:0035050)|endoderm development (GO:0007492)|forebrain morphogenesis (GO:0048853)|gall bladder development (GO:0061010)|hepatic duct development (GO:0061011)|hepatoblast differentiation (GO:0061017)|hepatocyte differentiation (GO:0070365)|in utero embryonic development (GO:0001701)|interkinetic nuclear migration (GO:0022027)|mRNA export from nucleus (GO:0006406)|multicellular organism growth (GO:0035264)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription by transcription factor localization (GO:0010621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|pancreas development (GO:0031016)|poly(A)+ mRNA export from nucleus (GO:0016973)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|primary lung bud formation (GO:0060431)|primitive streak formation (GO:0090009)|protein localization to nucleus (GO:0034504)|regulation of cell proliferation (GO:0042127)|response to peptide hormone (GO:0043434)|response to wounding (GO:0009611)|thyroid gland development (GO:0030878)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|eukaryotic initiation factor 4E binding (GO:0008190)|protein homodimerization activity (GO:0042803)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			kidney(2)|large_intestine(2)|lung(5)|ovary(1)	10						CGATAAAAGCTATTTTAATGCT	0.431																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			Z21533	CCDS7423.1	10q23.33	2011-06-20	2007-02-15		ENSG00000152804	ENSG00000152804		"""Homeoboxes / ANTP class : NKL subclass"""	4901	protein-coding gene	gene with protein product		604420		PRHX		8096636, 8103988	Standard	NM_002729		Approved	HEX, HOX11L-PEN	uc001kid.3	Q03014	OTTHUMG00000018762	Exception_encountered	10.37:g.94454508_94454509insCC	ENSP00000282728:p.Tyr266fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B1AQ17|Q96CE9	Frame_Shift_Ins	INS	pfam_Homeodomain,superfamily_Homeodomain-like,smart_Homeodomain,pfscan_Homeodomain,prints_Homeobox_metazoa	p.Y266fs	ENST00000282728.5	37	c.796_797	CCDS7423.1	10																																																																																			HHEX	-	NULL	ENSG00000152804		0.431	HHEX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HHEX	HGNC	protein_coding	OTTHUMT00000049402.2	84	0.00	0	-			94454508	94454509	+1	no_errors	ENST00000282728	ensembl	human	known	69_37n	frame_shift_ins	60	47.83	55	INS	1.000:1.000	CC
HIPK2	28996	genome.wustl.edu	37	7	139281654	139281654	+	Frame_Shift_Del	DEL	A	A	-			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr7:139281654delA	ENST00000406875.3	-	12	2620	c.2526delT	c.(2524-2526)tgtfs	p.C842fs	HIPK2_ENST00000428878.2_Frame_Shift_Del_p.C815fs|HIPK2_ENST00000342645.6_Intron	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	842	Interaction with CTBP1. {ECO:0000250}.|Interaction with HMGA1. {ECO:0000250}.|Interaction with POU4F1. {ECO:0000250}.|Interaction with SKI and SMAD1.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|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)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					GCACCATGGCACAGCGGGGAG	0.627																																						dbGAP											0													49.0	55.0	53.0					7																	139281654		2151	4252	6403	-	-	-	SO:0001589	frameshift_variant	0			AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"""homeodomain-interacting protein kinase 2"""			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.2526delT	7.37:g.139281654delA	ENSP00000385571:p.Cys842fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q75MR7|Q8WWI4|Q9H2Y1	Frame_Shift_Del	DEL	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_LipoPS_kinase,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	p.C842fs	ENST00000406875.3	37	c.2526		7																																																																																			HIPK2	-	NULL	ENSG00000064393		0.627	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	HIPK2	HGNC	protein_coding	OTTHUMT00000349430.3	60	0.00	0	A	NM_022740		139281654	139281654	-1	no_errors	ENST00000406875	ensembl	human	known	69_37n	frame_shift_del	32	30.43	14	DEL	0.991	-
KIAA0195	9772	genome.wustl.edu	37	17	73487171	73487172	+	Frame_Shift_Ins	INS	-	-	G	rs536497827		TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr17:73487171_73487172insG	ENST00000314256.7	+	12	1564_1565	c.1170_1171insG	c.(1171-1173)gggfs	p.G391fs	KIAA0195_ENST00000579208.1_Frame_Shift_Ins_p.G42fs|KIAA0195_ENST00000375248.5_Frame_Shift_Ins_p.G401fs	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	391						integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.G391R(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(7)|lung(17)|ovary(5)|skin(2)|stomach(1)|urinary_tract(1)	42	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			TGAGGGTGCTCGGGGGGACATC	0.619																																						dbGAP											1	Substitution - Missense(1)	ovary(1)																																								-	-	-	SO:0001589	frameshift_variant	0				CCDS32732.1	17q25.1	2012-03-01			ENSG00000177728	ENSG00000177728			28983	protein-coding gene	gene with protein product						8724849	Standard	NM_014738		Approved	TMEM94	uc002jnz.4	Q12767		ENST00000314256.7:c.1176dupG	17.37:g.73487177_73487177dupG	ENSP00000313885:p.Gly391fs	Somatic		WXS	Illumina GAIIx	Phase_IV	O75536|Q86XF1	Frame_Shift_Ins	INS	pfam_ATPase_P-typ_cation-transptr_C	p.T392fs	ENST00000314256.7	37	c.1170_1171	CCDS32732.1	17																																																																																			KIAA0195	-	NULL	ENSG00000177728		0.619	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KIAA0195	HGNC	protein_coding	OTTHUMT00000447303.1	19	0.00	0	-	NM_014738		73487171	73487172	+1	no_errors	ENST00000314256	ensembl	human	known	69_37n	frame_shift_ins	17	10.53	2	INS	0.998:0.997	G
LAMB2	3913	genome.wustl.edu	37	3	49158663	49158663	+	Missense_Mutation	SNP	T	T	A			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr3:49158663T>A	ENST00000418109.1	-	33	5557	c.5393A>T	c.(5392-5394)cAg>cTg	p.Q1798L	USP19_ENST00000398898.2_5'Flank|USP19_ENST00000398888.2_5'Flank|USP19_ENST00000417901.1_5'Flank|USP19_ENST00000488993.1_5'Flank|USP19_ENST00000453664.1_5'Flank|USP19_ENST00000398892.3_5'Flank|LAMB2_ENST00000305544.4_Missense_Mutation_p.Q1798L|USP19_ENST00000434032.2_5'Flank	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	1798	Domain I.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CAGGGGTCACTGGCAGGTGTT	0.597																																						dbGAP											0													67.0	61.0	63.0					3																	49158663		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"""Laminins"""	6487	protein-coding gene	gene with protein product	"""laminin S"""	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.5393A>T	3.37:g.49158663T>A	ENSP00000388325:p.Gln1798Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q16321	Missense_Mutation	SNP	pfam_EGF_laminin,pfam_Laminin_N,smart_Laminin_N,smart_EGF_laminin,smart_EGF-like,pfscan_Laminin_IV,pfscan_EGF_laminin,pfscan_Laminin_N	p.Q1798L	ENST00000418109.1	37	c.5393	CCDS2789.1	3	.	.	.	.	.	.	.	.	.	.	T	25.4	4.639436	0.87760	.	.	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.36699	1.24;1.24	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.52533	0.1740	L	0.42245	1.32	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.55159	-0.8184	10	0.72032	D	0.01	.	15.1868	0.73009	0.0:0.0:0.0:1.0	.	1798	P55268	LAMB2_HUMAN	L	1798	ENSP00000388325:Q1798L;ENSP00000307156:Q1798L	ENSP00000307156:Q1798L	Q	-	2	0	LAMB2	49133667	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	4.845000	0.62853	1.982000	0.57802	0.459000	0.35465	CAG	LAMB2	-	NULL	ENSG00000172037		0.597	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LAMB2	HGNC	protein_coding	OTTHUMT00000345939.1	19	0.00	0	T	NM_002292		49158663	49158663	-1	no_errors	ENST00000305544	ensembl	human	known	69_37n	missense	13	26.32	5	SNP	1.000	A
LEKR1	389170	genome.wustl.edu	37	3	156763225	156763225	+	Frame_Shift_Del	DEL	A	A	-			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr3:156763225delA	ENST00000470811.1	+	14	2188	c.853delA	c.(853-855)agtfs	p.S285fs	LEKR1_ENST00000356539.4_Frame_Shift_Del_p.S589fs			Q6ZMV7	LEKR1_HUMAN	leucine, glutamate and lysine rich 1	285										breast(1)|large_intestine(5)|lung(3)|ovary(1)|skin(1)	11			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			CCTGGAGCTCAGTAAGCTTCG	0.498																																						dbGAP											0													91.0	92.0	92.0					3																	156763225		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			AK131473	CCDS54660.1	3q25.31	2014-02-12	2008-02-21		ENSG00000197980	ENSG00000197980			33765	protein-coding gene	gene with protein product		613536					Standard	NM_001004316		Approved	FLJ16641	uc021xgh.1	Q6ZMV7	OTTHUMG00000160130	ENST00000470811.1:c.853delA	3.37:g.156763225delA	ENSP00000418214:p.Ser285fs	Somatic		WXS	Illumina GAIIx	Phase_IV		Frame_Shift_Del	DEL	superfamily_Ribosomal_L29	p.S589fs	ENST00000470811.1	37	c.1765		3																																																																																			LEKR1	-	NULL	ENSG00000178110		0.498	LEKR1-010	KNOWN	upstream_ATG|basic	protein_coding	LEKR1	HGNC	protein_coding	OTTHUMT00000351625.3	196	0.00	0	A	NM_001004316		156763225	156763225	+1	no_errors	ENST00000356539	ensembl	human	known	69_37n	frame_shift_del	66	54.00	81	DEL	0.968	-
MAP3K1	4214	genome.wustl.edu	37	5	56178399	56178400	+	Frame_Shift_Ins	INS	-	-	T			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr5:56178399_56178400insT	ENST00000399503.3	+	14	3372_3373	c.3372_3373insT	c.(3373-3375)aatfs	p.N1125fs		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1125					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		GATTAGATGTCAATACAGAGCT	0.436																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	Exception_encountered	5.37:g.56178399_56178400insT	ENSP00000382423:p.Asn1125fs	Somatic		WXS	Illumina GAIIx	Phase_IV		Frame_Shift_Ins	INS	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Znf_RING,pfscan_Znf_SWIM,pfscan_Prot_kinase_cat_dom	p.N1124fs	ENST00000399503.3	37	c.3372_3373	CCDS43318.1	5																																																																																			MAP3K1	-	NULL	ENSG00000095015		0.436	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	MAP3K1	HGNC	protein_coding	OTTHUMT00000132309.2	224	0.00	0	-	XM_042066		56178399	56178400	+1	no_errors	ENST00000399503	ensembl	human	novel	69_37n	frame_shift_ins	90	25.62	31	INS	1.000:1.000	T
MAP3K1	4214	genome.wustl.edu	37	5	56178400	56178400	+	Missense_Mutation	SNP	A	A	G			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr5:56178400A>G	ENST00000399503.3	+	14	3373	c.3373A>G	c.(3373-3375)Aat>Gat	p.N1125D		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1125					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		ATTAGATGTCAATACAGAGCT	0.433																																						dbGAP											0													121.0	117.0	119.0					5																	56178400		1970	4162	6132	-	-	-	SO:0001583	missense	0			U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.3373A>G	5.37:g.56178400A>G	ENSP00000382423:p.Asn1125Asp	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Znf_RING,pfscan_Znf_SWIM,pfscan_Prot_kinase_cat_dom	p.N1125D	ENST00000399503.3	37	c.3373	CCDS43318.1	5	.	.	.	.	.	.	.	.	.	.	A	13.85	2.358696	0.41801	.	.	ENSG00000095015	ENST00000399503	T	0.68624	-0.34	5.86	5.86	0.93980	.	0.235254	0.43919	D	0.000515	T	0.62048	0.2396	L	0.47716	1.5	0.42012	D	0.990944	B	0.21821	0.061	B	0.20577	0.03	T	0.58370	-0.7648	10	0.39692	T	0.17	.	16.2453	0.82441	1.0:0.0:0.0:0.0	.	1125	Q13233	M3K1_HUMAN	D	1125	ENSP00000382423:N1125D	ENSP00000382423:N1125D	N	+	1	0	MAP3K1	56214157	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	4.173000	0.58249	2.241000	0.73720	0.533000	0.62120	AAT	MAP3K1	-	NULL	ENSG00000095015		0.433	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	MAP3K1	HGNC	protein_coding	OTTHUMT00000132309.2	226	0.00	0	A	XM_042066		56178400	56178400	+1	no_errors	ENST00000399503	ensembl	human	novel	69_37n	missense	89	28.23	35	SNP	1.000	G
MAP3K1	4214	genome.wustl.edu	37	5	56189387	56189387	+	Frame_Shift_Del	DEL	C	C	-			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr5:56189387delC	ENST00000399503.3	+	20	4419	c.4419delC	c.(4417-4419)atcfs	p.I1473fs		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1473	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		CTCCATCGATCCCTTCACATT	0.448																																						dbGAP											0													135.0	130.0	132.0					5																	56189387		1995	4158	6153	-	-	-	SO:0001589	frameshift_variant	0			U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.4419delC	5.37:g.56189387delC	ENSP00000382423:p.Ile1473fs	Somatic		WXS	Illumina GAIIx	Phase_IV		Frame_Shift_Del	DEL	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Znf_RING,pfscan_Znf_SWIM,pfscan_Prot_kinase_cat_dom	p.P1474fs	ENST00000399503.3	37	c.4419	CCDS43318.1	5																																																																																			MAP3K1	-	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	ENSG00000095015		0.448	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	MAP3K1	HGNC	protein_coding	OTTHUMT00000132309.2	102	0.00	0	C	XM_042066		56189387	56189387	+1	no_errors	ENST00000399503	ensembl	human	novel	69_37n	frame_shift_del	76	26.21	27	DEL	1.000	-
KMT2C	58508	genome.wustl.edu	37	7	151904386	151904386	+	Splice_Site	SNP	T	T	C			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr7:151904386T>C	ENST00000262189.6	-	24	4058	c.3840A>G	c.(3838-3840)ccA>ccG	p.P1280P	KMT2C_ENST00000355193.2_Splice_Site_p.P1280P	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1280					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										GCACTATACCTGGTCTGTATG	0.363																																						dbGAP											0													58.0	55.0	56.0					7																	151904386		2203	4297	6500	-	-	-	SO:0001630	splice_region_variant	0			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.3841+1A>G	7.37:g.151904386T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	pfam_Znf_PHD-finger,pfam_SET_dom,pfam_FYrich_C,pfam_FYrich_N,superfamily_Znf_FYVE_PHD,superfamily_HMG_superfamily,smart_Znf_PHD,smart_Znf_RING,smart_HMG_superfamily,smart_FYrich_N,smart_FYrich_C,smart_SET_dom,smart_Post-SET_dom,pfscan_SET_dom,pfscan_Post-SET_dom,pfscan_Znf_DHHC_palmitoyltrfase,pfscan_Znf_PHD-finger,pfscan_Znf_RING	p.P1280	ENST00000262189.6	37	c.3840	CCDS5931.1	7																																																																																			MLL3	-	NULL	ENSG00000055609		0.363	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	MLL3	HGNC	protein_coding	OTTHUMT00000318887.3	488	0.00	0	T		Silent	151904386	151904386	-1	no_errors	ENST00000355193	ensembl	human	known	69_37n	silent	176	43.23	134	SNP	1.000	C
MUC6	4588	genome.wustl.edu	37	11	1016078	1016079	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr11:1016078_1016079insG	ENST00000421673.2	-	31	6772_6773	c.6722_6723insC	c.(6721-6723)ctafs	p.L2241fs		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	2241	Ser-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGCTGGAGGCTAGGTGGCTGGA	0.609																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.6722_6723insC	11.37:g.1016078_1016079insG	ENSP00000406861:p.Leu2241fs	Somatic		WXS	Illumina GAIIx	Phase_IV	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Frame_Shift_Ins	INS	pfam_VWF_type-D,pfam_Unchr_dom_Cys-rich,pfam_TIL_dom,superfamily_TIL_dom,smart_VWF_type-D,smart_Unchr_dom_Cys-rich,smart_VWC_out,smart_Cys_knot_C,pfscan_Cys_knot_C	p.A2242fs	ENST00000421673.2	37	c.6723_6722	CCDS44513.1	11																																																																																			MUC6	-	NULL	ENSG00000184956		0.609	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MUC6	HGNC	protein_coding	OTTHUMT00000382120.2	21	0.00	0	-	XM_290540		1016078	1016079	-1	no_errors	ENST00000421673	ensembl	human	known	69_37n	frame_shift_ins	21	34.38	11	INS	0.000:0.000	G
MYCBP2	23077	genome.wustl.edu	37	13	77671946	77671946	+	Missense_Mutation	SNP	T	T	C	rs150834693		TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr13:77671946T>C	ENST00000544440.2	-	56	9246	c.9229A>G	c.(9229-9231)Atc>Gtc	p.I3077V	MYCBP2_ENST00000357337.6_Missense_Mutation_p.I3077V|MYCBP2_ENST00000407578.2_Missense_Mutation_p.I3115V|MYCBP2_ENST00000482517.1_5'Flank|MYCBP2-AS1_ENST00000593933.1_RNA					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TTTTTGTTGATGCTACCCATC	0.358													T|||	1	0.000199681	0.0	0.0014	5008	,	,		20146	0.0		0.0	False		,,,				2504	0.0					dbGAP											0													105.0	100.0	102.0					13																	77671946		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"""MYC binding protein 2"""			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.9229A>G	13.37:g.77671946T>C	ENSP00000444596:p.Ile3077Val	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_PHR,pfam_Reg_chr_condens,pfam_Filamin/ABP280_repeat-like,superfamily_Reg_csome_cond/b-lactamase_inh,superfamily_Galactose-bd-like,superfamily_Ig_E-set,superfamily_ARM-type_fold,smart_Znf_RING,prints_Reg_chr_condens,pfscan_Filamin/ABP280_repeat-like,pfscan_Znf_RING,pfscan_Reg_chr_condens	p.I3115V	ENST00000544440.2	37	c.9343		13	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	7.242	0.601554	0.13939	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.27720	1.65;1.65;1.65	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.39733	0.1089	L	0.36672	1.1	0.54753	D	0.999981	P;P;P	0.52577	0.954;0.876;0.518	P;D;P	0.64595	0.763;0.927;0.558	T	0.11743	-1.0575	10	0.05620	T	0.96	.	15.7365	0.77849	0.0:0.0:0.0:1.0	.	463;3077;3077	Q9UG08;O75592-2;O75592	.;.;MYCB2_HUMAN	V	3077;3115;3077	ENSP00000349892:I3077V;ENSP00000384288:I3115V;ENSP00000444596:I3077V	ENSP00000349892:I3077V	I	-	1	0	MYCBP2	76569947	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.698000	0.84413	2.120000	0.65058	0.482000	0.46254	ATC	MYCBP2	-	superfamily_ARM-type_fold	ENSG00000005810		0.358	MYCBP2-001	KNOWN	basic	protein_coding	MYCBP2	HGNC	protein_coding	OTTHUMT00000045326.1	195	0.00	0	T	NM_015057		77671946	77671946	-1	no_errors	ENST00000407578	ensembl	human	known	69_37n	missense	129	44.92	106	SNP	1.000	C
NACA	4666	genome.wustl.edu	37	12	57118242	57118242	+	Missense_Mutation	SNP	C	C	T			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr12:57118242C>T	ENST00000454682.1	-	2	345	c.64G>A	c.(64-66)Gag>Aag	p.E22K	NACA_ENST00000552540.1_Missense_Mutation_p.E22K|NACA_ENST00000550952.1_Missense_Mutation_p.E22K|NACA_ENST00000551793.1_5'UTR|NACA_ENST00000546392.1_Missense_Mutation_p.E22K|NACA_ENST00000393891.4_Missense_Mutation_p.E22K|NACA_ENST00000548563.1_5'UTR|NACA_ENST00000356769.3_Missense_Mutation_p.E22K	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	22					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						CTACCTGTCTCAGCCTGGGGC	0.488			T	BCL6	NHL																																	dbGAP		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	0													33.0	30.0	31.0					12																	57118242		2203	4300	6503	-	-	-	SO:0001583	missense	0			X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.64G>A	12.37:g.57118242C>T	ENSP00000403817:p.Glu22Lys	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Nas_poly-pep-assoc_cplx,superfamily_UBA-like,pfscan_Nas_poly-pep-assoc_cplx	p.E22K	ENST00000454682.1	37	c.64		12	.	.	.	.	.	.	.	.	.	.	C	22.3	4.269817	0.80469	.	.	ENSG00000196531	ENST00000454682;ENST00000550952;ENST00000356769;ENST00000552540;ENST00000393891;ENST00000546392;ENST00000549259;ENST00000552055;ENST00000549855	T;T;T;T;T;T;T;T;T	0.47528	1.54;1.54;0.92;0.92;0.92;0.92;0.93;0.84;0.9	5.15	5.15	0.70609	.	0.214824	0.38058	N	0.001833	T	0.67040	0.2851	M	0.63843	1.955	0.33498	D	0.589571	D;D;B	0.89917	1.0;1.0;0.001	D;D;B	0.85130	0.996;0.997;0.003	T	0.73151	-0.4073	10	0.52906	T	0.07	.	18.0099	0.89220	0.0:1.0:0.0:0.0	.	22;22;22	E9PAV3;F8VU71;Q13765	.;.;NACA_HUMAN	K	22	ENSP00000403817:E22K;ENSP00000448035:E22K;ENSP00000349212:E22K;ENSP00000447821:E22K;ENSP00000377469:E22K;ENSP00000446801:E22K;ENSP00000447133:E22K;ENSP00000450383:E22K;ENSP00000447764:E22K	ENSP00000349212:E22K	E	-	1	0	NACA	55404509	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	6.945000	0.75947	2.869000	0.98440	0.558000	0.71614	GAG	NACA	-	NULL	ENSG00000196531		0.488	NACA-201	KNOWN	basic	protein_coding	NACA	HGNC	protein_coding		32	0.00	0	C	NM_005594		57118242	57118242	-1	no_errors	ENST00000454682	ensembl	human	known	69_37n	missense	18	33.33	9	SNP	1.000	T
NBPF9	400818	genome.wustl.edu	37	1	144827878	144827879	+	In_Frame_Ins	INS	-	-	AGG			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr1:144827878_144827879insAGG	ENST00000440491.2	+	15	1757_1758	c.1757_1758insAGG	c.(1756-1761)gaagaa>gaAGGagaa	p.586_587EE>EGE	NBPF9_ENST00000281815.8_Intron|NBPF9_ENST00000338347.4_In_Frame_Ins_p.513_513R>RR|NBPF9_ENST00000468645.1_3'UTR	NM_001037675.2	NP_001032764.2	Q3BBW0	NBPF9_HUMAN	neuroblastoma breakpoint family, member 9	0	NBPF 3. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				NS(2)|prostate(1)	3						agaaggaaagaagaaggggaag	0.426																																						dbGAP											0																																										-	-	-	SO:0001652	inframe_insertion	0				CCDS72895.1, CCDS72896.1	1q21.1	2013-01-17			ENSG00000168614	ENSG00000269713		"""neuroblastoma breakpoint family"""	31991	protein-coding gene	gene with protein product		613999				16079250	Standard	NM_001037675		Approved	AE01		Q3BBW0	OTTHUMG00000013845	Exception_encountered	1.37:g.144827878_144827879insAGG	ENSP00000390934:p.Glu586_Glu587insGly	Somatic		WXS	Illumina GAIIx	Phase_IV		In_Frame_Ins	INS	pfam_NBPF_dom	p.587in_frame_insG	ENST00000440491.2	37	c.1757_1758		1																																																																																			NBPF9	-	NULL	ENSG00000168614		0.426	NBPF9-203	KNOWN	basic	protein_coding	NBPF9	HGNC	protein_coding		9	0.00	0	-	NM_001037675		144827878	144827879	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000375552	ensembl	human	known	69_37n	in_frame_ins	32	13.51	5	INS	0.025:0.025	AGG
PIK3CA	5290	genome.wustl.edu	37	3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	rs104886003		TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	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	126	0.00	0	G			178936091	178936091	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	72	29.41	30	SNP	1.000	A
PIP5K1C	23396	genome.wustl.edu	37	19	3656491	3656491	+	Missense_Mutation	SNP	T	T	C			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr19:3656491T>C	ENST00000335312.3	-	6	621	c.533A>G	c.(532-534)tAc>tGc	p.Y178C	PIP5K1C_ENST00000537021.1_Missense_Mutation_p.Y178C|PIP5K1C_ENST00000539785.1_Missense_Mutation_p.Y178C|PIP5K1C_ENST00000589578.1_Missense_Mutation_p.Y178C|PIP5K1C_ENST00000587482.1_5'UTR	NM_001195733.1|NM_012398.2	NP_001182662.1|NP_036530.1	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, gamma	178	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				actin cytoskeleton organization (GO:0030036)|adherens junction assembly (GO:0034333)|axon guidance (GO:0007411)|clathrin-mediated endocytosis (GO:0072583)|cytoskeletal anchoring at plasma membrane (GO:0007016)|neutrophil chemotaxis (GO:0030593)|phagocytosis (GO:0006909)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet aggregation (GO:0070527)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle exocytosis (GO:0016079)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			large_intestine(3)|ovary(1)|skin(3)|stomach(2)	9		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		GCTGGTGACGTAGAAGAGGGA	0.627																																					Esophageal Squamous(135;99 1744 12852 27186 39851)	dbGAP											0													76.0	77.0	77.0					19																	3656491		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB011161	CCDS32872.1, CCDS56074.1, CCDS74257.1	19p13.3	2012-10-02			ENSG00000186111	ENSG00000186111			8996	protein-coding gene	gene with protein product		606102				9535851	Standard	NM_001195733		Approved	PIP5Kgamma, KIAA0589, LCCS3	uc002lyj.2	O60331	OTTHUMG00000180870	ENST00000335312.3:c.533A>G	19.37:g.3656491T>C	ENSP00000335333:p.Tyr178Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z9E7|C6GIJ7|C6GIJ8|Q7LE07	Missense_Mutation	SNP	pfam_PInositol-4-P-5-kinase_core,smart_PInositol-4P-5-kinase_core_sub	p.Y178C	ENST00000335312.3	37	c.533	CCDS32872.1	19	.	.	.	.	.	.	.	.	.	.	T	16.63	3.175415	0.57692	.	.	ENSG00000186111	ENST00000335312;ENST00000539785;ENST00000537021	T;T;T	0.39056	1.1;1.1;1.1	4.22	4.22	0.49857	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.56321	0.1977	M	0.83384	2.64	0.58432	D	0.999994	P;P	0.42584	0.511;0.784	B;P	0.48921	0.281;0.595	T	0.64689	-0.6348	10	0.87932	D	0	-15.4266	12.7667	0.57396	0.0:0.0:0.0:1.0	.	178;178	O60331-3;O60331	.;PI51C_HUMAN	C	178	ENSP00000335333:Y178C;ENSP00000445992:Y178C;ENSP00000444779:Y178C	ENSP00000335333:Y178C	Y	-	2	0	PIP5K1C	3607491	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.896000	0.69822	1.679000	0.50963	0.459000	0.35465	TAC	PIP5K1C	-	pfam_PInositol-4-P-5-kinase_core,smart_PInositol-4P-5-kinase_core_sub	ENSG00000186111		0.627	PIP5K1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PIP5K1C	HGNC	protein_coding	OTTHUMT00000453432.2	9	0.00	0	T	NM_012398		3656491	3656491	-1	no_errors	ENST00000537021	ensembl	human	known	69_37n	missense	6	50.00	6	SNP	1.000	C
POGK	57645	genome.wustl.edu	37	1	166810249	166810249	+	Frame_Shift_Del	DEL	A	A	-			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr1:166810249delA	ENST00000367875.1	+	2	416	c.56delA	c.(55-57)gaafs	p.E20fs	POGK_ENST00000537173.1_5'UTR|POGK_ENST00000536514.1_5'UTR|POGK_ENST00000367876.4_Frame_Shift_Del_p.E20fs			Q9P215	POGK_HUMAN	pogo transposable element with KRAB domain	20	Poly-Glu.				multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	22						GAAGAGGAAGAAGAGATTCAG	0.512																																					GBM(76;192 1530 30153 48742)	dbGAP											0													103.0	104.0	104.0					1																	166810249		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			AB040946	CCDS1254.1	1q23.2	2013-01-08			ENSG00000143157	ENSG00000143157		"""-"""	18800	protein-coding gene	gene with protein product	"""KRAB box domain containing 2"""						Standard	NM_017542		Approved	KIAA15131, LST003, BASS2, KRBOX2	uc001gdt.1	Q9P215	OTTHUMG00000034325	ENST00000367875.1:c.56delA	1.37:g.166810249delA	ENSP00000356849:p.Glu20fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5TIJ1|Q8TE07	Frame_Shift_Del	DEL	pfam_DDE_SF_endonuclease_CENPB-like,pfam_Brinker_DNA-bd,pfam_HTH_CenpB_DNA-bd_dom,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,superfamily_Homeodomain-like,smart_Krueppel-associated_box,smart_HTH_CenpB_DNA-bd_dom,pfscan_Krueppel-associated_box,pfscan_Krueppel-associated_box-rel	p.E20fs	ENST00000367875.1	37	c.56	CCDS1254.1	1																																																																																			POGK	-	NULL	ENSG00000143157		0.512	POGK-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	POGK	HGNC	protein_coding	OTTHUMT00000082888.1	92	0.00	0	A	NM_017542		166810249	166810249	+1	no_errors	ENST00000367875	ensembl	human	known	69_37n	frame_shift_del	34	52.78	38	DEL	1.000	-
POLQ	10721	genome.wustl.edu	37	3	121207309	121207309	+	Missense_Mutation	SNP	A	A	G			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr3:121207309A>G	ENST00000264233.5	-	16	4597	c.4469T>C	c.(4468-4470)cTa>cCa	p.L1490P		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1490					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		GCTATCAAATAGTAAACTATC	0.358								DNA polymerases (catalytic subunits)																													Pancreas(152;907 1925 26081 31236 36904)	dbGAP											0													80.0	81.0	81.0					3																	121207309		2203	4299	6502	-	-	-	SO:0001583	missense	0			AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.4469T>C	3.37:g.121207309A>G	ENSP00000264233:p.Leu1490Pro	Somatic		WXS	Illumina GAIIx	Phase_IV	O95160|Q6VMB5	Missense_Mutation	SNP	pfam_DNA-dir_DNA_pol_A_palm_dom,pfam_DNA/RNA_helicase_DEAD/DEAH_N,pfam_Helicase_C,superfamily_RNaseH-like_dom,smart_Helicase_ATP-bd,smart_Helicase_C,smart_DNA-dir_DNA_pol_A_palm_dom,pfscan_Helicase_ATP-bd,pfscan_Helicase_C,prints_DNA_polymerase_A	p.L1490P	ENST00000264233.5	37	c.4469	CCDS33833.1	3	.	.	.	.	.	.	.	.	.	.	A	19.14	3.769910	0.69992	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.71934	-0.61	6.11	6.11	0.99139	.	0.000000	0.64402	D	0.000001	T	0.79064	0.4383	L	0.36672	1.1	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.975;0.999	T	0.80939	-0.1158	10	0.87932	D	0	.	16.7021	0.85357	1.0:0.0:0.0:0.0	.	1490;662	O75417;O75417-2	DPOLQ_HUMAN;.	P	1113;1490;1626	ENSP00000264233:L1490P	ENSP00000264233:L1490P	L	-	2	0	POLQ	122689999	0.998000	0.40836	0.897000	0.35233	0.818000	0.46254	7.431000	0.80335	2.343000	0.79666	0.533000	0.62120	CTA	POLQ	-	NULL	ENSG00000051341		0.358	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	POLQ	HGNC	protein_coding	OTTHUMT00000355097.1	229	0.00	0	A	NM_199420		121207309	121207309	-1	no_errors	ENST00000264233	ensembl	human	known	69_37n	missense	203	10.96	25	SNP	0.993	G
PRICKLE3	4007	genome.wustl.edu	37	X	49040116	49040117	+	Intron	DEL	GT	GT	-			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	GT	GT					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chrX:49040116_49040117delGT	ENST00000376317.3	-	3	407				PRICKLE3_ENST00000376310.3_Intron|PRICKLE3_ENST00000536904.1_Frame_Shift_Del_p.T60fs|PRICKLE3_ENST00000540849.1_Intron|PRICKLE3_ENST00000538114.1_Frame_Shift_Del_p.T128fs	NM_006150.3	NP_006141.2	O43900	PRIC3_HUMAN	prickle homolog 3 (Drosophila)								zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|skin(2)	22						TCCCACCTGAGTGTGTGTGTGT	0.604																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			BC016856	CCDS14320.1	Xp11.23	2008-02-05	2007-09-18	2007-09-18	ENSG00000012211	ENSG00000012211			6645	protein-coding gene	gene with protein product		300111	"""LIM domain only 6"""	LMO6		9344658	Standard	XM_005272605		Approved		uc004dmy.1	O43900	OTTHUMG00000024134	ENST00000376317.3:c.312+69AC>-	X.37:g.49040126_49040127delGT		Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z8F2|O76007|Q53XR5	Frame_Shift_Del	DEL	pfam_Znf_LIM,pfam_PET_domain,smart_Znf_LIM,pfscan_Znf_LIM	p.T60fs	ENST00000376317.3	37	c.179_178	CCDS14320.1	X																																																																																			PRICKLE3	-	NULL	ENSG00000012211		0.604	PRICKLE3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PRICKLE3	HGNC	protein_coding	OTTHUMT00000060811.1	32	0.00	0	GT	NM_006150		49040116	49040117	-1	no_errors	ENST00000536904	ensembl	human	known	69_37n	frame_shift_del	12	20.00	3	DEL	0.149:0.119	-
PTCHD1	139411	genome.wustl.edu	37	X	23412005	23412005	+	Silent	SNP	C	C	T	rs371092709		TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chrX:23412005C>T	ENST00000379361.4	+	3	3230	c.2370C>T	c.(2368-2370)gcC>gcT	p.A790A		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	790					cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						TAAAAAATGCCCTGGAAGTGC	0.388																																						dbGAP											0													146.0	121.0	129.0					X																	23412005		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.2370C>T	X.37:g.23412005C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B4DQH0|Q0IJ60|Q6P6B8	Silent	SNP	pfam_Patched,pfscan_SSD	p.A790	ENST00000379361.4	37	c.2370	CCDS35215.2	X																																																																																			PTCHD1	-	pfam_Patched	ENSG00000165186		0.388	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	PTCHD1	HGNC	protein_coding	OTTHUMT00000056047.2	166	0.00	0	C	NM_173495		23412005	23412005	+1	no_errors	ENST00000379361	ensembl	human	known	69_37n	silent	150	14.29	25	SNP	1.000	T
RAB40C	57799	genome.wustl.edu	37	16	677579	677580	+	Frame_Shift_Ins	INS	-	-	C			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr16:677579_677580insC	ENST00000248139.3	+	6	1006_1007	c.803_804insC	c.(802-807)agccccfs	p.SP268fs	RAB40C_ENST00000535977.1_Frame_Shift_Ins_p.SP268fs|RAB40C_ENST00000539661.1_Frame_Shift_Ins_p.SP268fs|RAB40C_ENST00000538492.1_Frame_Shift_Ins_p.SP268fs	NM_021168.4	NP_066991.3	Q96S21	RB40C_HUMAN	RAB40C, member RAS oncogene family	268					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)	p.Q271fs*7(1)		NS(1)|endometrium(2)|large_intestine(1)|lung(1)|prostate(1)	6		Hepatocellular(780;0.0218)				CCACCCCAGAGCCCCCCCCAGA	0.678																																					Melanoma(123;1631 1690 28262 44104 44957)	dbGAP											1	Insertion - Frameshift(1)	large_intestine(1)																																								-	-	-	SO:0001589	frameshift_variant	0			Z84779	CCDS10413.1	16p13.3	2008-07-28	2003-10-14		ENSG00000197562	ENSG00000197562		"""RAB, member RAS oncogene"""	18285	protein-coding gene	gene with protein product			"""RAS-like, family 8, member C"""	RASL8C		11697911, 18485483	Standard	NM_021168		Approved	RARL	uc021szv.1	Q96S21	OTTHUMG00000047854	ENST00000248139.3:c.811dupC	16.37:g.677587_677587dupC	ENSP00000248139:p.Ser268fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A2IDE2|D3DU54|O60795|Q4TT41|Q5PXE8|Q6PIU5	Frame_Shift_Ins	INS	pfam_Small_GTPase,pfam_MIRO-like,pfam_SOCS_C,pfam_Small_GTPase_ARF/SAR,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,smart_Ran_GTPase,smart_SOCS_C,prints_Small_GTPase,pfscan_SOCS_C,tigrfam_Small_GTP-bd_dom	p.Q271fs	ENST00000248139.3	37	c.803_804	CCDS10413.1	16																																																																																			RAB40C	-	NULL	ENSG00000197562		0.678	RAB40C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RAB40C	HGNC	protein_coding	OTTHUMT00000109079.4	13	0.00	0	-	NM_021168		677579	677580	+1	no_errors	ENST00000248139	ensembl	human	known	69_37n	frame_shift_ins	10	23.08	3	INS	1.000:1.000	C
SMTNL1	219537	genome.wustl.edu	37	11	57311158	57311158	+	Missense_Mutation	SNP	C	C	A			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr11:57311158C>A	ENST00000399154.2	+	3	683	c.683C>A	c.(682-684)gCa>gAa	p.A228E	SMTNL1_ENST00000457912.1_Missense_Mutation_p.A283E|SMTNL1_ENST00000527972.1_Missense_Mutation_p.A265E			A8MU46	SMTL1_HUMAN	smoothelin-like 1	228	Glu-rich.				negative regulation of vasodilation (GO:0045908)|positive regulation of vasoconstriction (GO:0045907)	contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	8						GAGGGAGGGGCAGGGGTGATT	0.622																																						dbGAP											0													18.0	23.0	21.0					11																	57311158		1982	4162	6144	-	-	-	SO:0001583	missense	0			BX116227		11q12.1	2006-02-02				ENSG00000214872			32394	protein-coding gene	gene with protein product	"""calponin homology-associated smooth muscle protein"""	613664				15327999	Standard	NM_001105565		Approved	CHASM	uc021qjh.1	A8MU46		ENST00000399154.2:c.683C>A	11.37:g.57311158C>A	ENSP00000382108:p.Ala228Glu	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_CH-domain,pfam_CAMSAP_CH,superfamily_CH-domain,smart_CH-domain,pfscan_CH-domain	p.A283E	ENST00000399154.2	37	c.848		11	.	.	.	.	.	.	.	.	.	.	C	20.3	3.969076	0.74131	.	.	ENSG00000214872	ENST00000457912;ENST00000527972;ENST00000399154	D;D;D	0.92965	-3.14;-3.12;-3.12	5.05	3.16	0.36331	.	0.270906	0.19502	U	0.112710	D	0.88962	0.6580	L	0.34521	1.04	0.19300	N	0.999979	D	0.54047	0.964	P	0.50314	0.637	T	0.79720	-0.1685	10	0.22706	T	0.39	-3.9647	10.6736	0.45772	0.0:0.8386:0.0:0.1614	.	283	C9J621	.	E	283;265;228	ENSP00000406485:A283E;ENSP00000432651:A265E;ENSP00000382108:A228E	ENSP00000382108:A228E	A	+	2	0	SMTNL1	57067734	0.000000	0.05858	0.728000	0.30774	0.415000	0.31203	0.406000	0.21032	0.535000	0.28714	0.462000	0.41574	GCA	SMTNL1	-	NULL	ENSG00000214872		0.622	SMTNL1-201	KNOWN	basic|appris_candidate	protein_coding	SMTNL1	HGNC	protein_coding		10	0.00	0	C	XM_166203		57311158	57311158	+1	no_errors	ENST00000457912	ensembl	human	known	69_37n	missense	9	35.71	5	SNP	0.446	A
SUFU	51684	genome.wustl.edu	37	10	104356980	104356981	+	Frame_Shift_Ins	INS	-	-	C			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr10:104356980_104356981insC	ENST00000369902.3	+	7	1006_1007	c.840_841insC	c.(841-843)cccfs	p.P281fs	SUFU_ENST00000369899.2_Frame_Shift_Ins_p.P281fs|SUFU_ENST00000423559.2_Frame_Shift_Ins_p.P281fs|SUFU_ENST00000471000.1_3'UTR	NM_016169.3	NP_057253.2	Q9UMX1	SUFU_HUMAN	suppressor of fused homolog (Drosophila)	281					cytoplasmic sequestering of transcription factor (GO:0042994)|heart looping (GO:0001947)|multicellular organismal development (GO:0007275)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of transcription factor import into nucleus (GO:0042992)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|skin development (GO:0043588)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|primary cilium (GO:0072372)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.P281T(1)		breast(2)|central_nervous_system(7)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(2)	24		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)		ACCTGAGCCGGCCCCCCGAGGA	0.599			"""D, F, S"""		medulloblastoma	medulloblastoma			Medulloblastoma, associated with Germline SUFU Mutation		OREG0020482	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP	yes	Rec	yes	Medulloblastoma predisposition	10	10q24.32	51684	suppressor of fused homolog (Drosophila)		O	1	Substitution - Missense(1)	kidney(1)																																								-	-	-	SO:0001589	frameshift_variant	0	Familial Cancer Database		AF175770	CCDS7537.1, CCDS53571.1	10q24.32	2014-09-17			ENSG00000107882	ENSG00000107882			16466	protein-coding gene	gene with protein product		607035				15367681	Standard	NM_016169		Approved	SUFUH, SUFUXL, PRO1280	uc001kvy.2	Q9UMX1	OTTHUMG00000018966	ENST00000369902.3:c.846dupC	10.37:g.104356986_104356986dupC	ENSP00000358918:p.Pro281fs	Somatic	1381	WXS	Illumina GAIIx	Phase_IV	Q7LCP7|Q9NT90|Q9NZ07|Q9UHK2|Q9UHM8|Q9UMY0	Frame_Shift_Ins	INS	pfam_SUFU_C,pfam_SUFU_domain,pirsf_Suppressor_of_fused_protein	p.E282fs	ENST00000369902.3	37	c.840_841	CCDS7537.1	10																																																																																			SUFU	-	pfam_SUFU_C,pirsf_Suppressor_of_fused_protein	ENSG00000107882		0.599	SUFU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SUFU	HGNC	protein_coding	OTTHUMT00000050089.1	57	0.00	0	-	NM_016169		104356980	104356981	+1	no_errors	ENST00000369902	ensembl	human	known	69_37n	frame_shift_ins	11	21.43	3	INS	0.594:1.000	C
TCF19	6941	genome.wustl.edu	37	6	31127397	31127398	+	Frame_Shift_Ins	INS	-	-	A			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr6:31127397_31127398insA	ENST00000376257.3	+	2	905_906	c.151_152insA	c.(151-153)ggcfs	p.G51fs	CCHCR1_ENST00000480060.1_5'Flank|CCHCR1_ENST00000396268.3_5'Flank|CCHCR1_ENST00000396263.2_5'Flank|CCHCR1_ENST00000376266.5_5'Flank|TCF19_ENST00000376255.4_Frame_Shift_Ins_p.G51fs|CCHCR1_ENST00000451521.2_5'Flank	NM_007109.2	NP_009040.2	Q9Y242	TCF19_HUMAN	transcription factor 19	51	FHA. {ECO:0000255|PROSITE- ProRule:PRU00086}.				cell proliferation (GO:0008283)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	9						GCAGGAGCCTGGCCTCATCTCT	0.658																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			U25826	CCDS43446.1	6p21.3	2013-01-28	2009-02-05		ENSG00000137310	ENSG00000137310		"""Zinc fingers, PHD-type"""	11629	protein-coding gene	gene with protein product		600912				1868030, 8595903	Standard	NM_001077511		Approved	SC1	uc003nss.3	Q9Y242	OTTHUMG00000031274	Exception_encountered	6.37:g.31127397_31127398insA	ENSP00000365433:p.Gly51fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NCT8|B0UY11|Q0EFA8|Q13176|Q15967|Q5SQ89|Q5STD6|Q5STF5|Q9BUM2|Q9UBH7	Frame_Shift_Ins	INS	pfam_FHA_dom,pfam_Znf_PHD-finger,superfamily_SMAD_FHA_domain,superfamily_Znf_FYVE_PHD,smart_FHA_dom,smart_Znf_PHD,pfscan_FHA_dom	p.G51fs	ENST00000376257.3	37	c.151_152	CCDS43446.1	6																																																																																			TCF19	-	pfam_FHA_dom,superfamily_SMAD_FHA_domain,smart_FHA_dom,pfscan_FHA_dom	ENSG00000137310		0.658	TCF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TCF19	HGNC	protein_coding	OTTHUMT00000076595.2	10	0.00	0	-	NM_007109		31127397	31127398	+1	no_errors	ENST00000376255	ensembl	human	known	69_37n	frame_shift_ins	11	21.43	3	INS	0.800:0.937	A
SYNCRIP	10492	genome.wustl.edu	37	6	86350199	86350199	+	Nonsense_Mutation	SNP	G	G	A			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr6:86350199G>A	ENST00000369622.3	-	3	732	c.232C>T	c.(232-234)Caa>Taa	p.Q78*	SYNCRIP_ENST00000355238.6_Nonsense_Mutation_p.Q78*	NM_001159675.1|NM_006372.4	NP_001153147.1|NP_006363.4	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA interacting protein	78					cellular response to interferon-gamma (GO:0071346)|CRD-mediated mRNA stabilization (GO:0070934)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of translation (GO:0017148)|osteoblast differentiation (GO:0001649)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|CRD-mediated mRNA stability complex (GO:0070937)|endoplasmic reticulum (GO:0005783)|GAIT complex (GO:0097452)|histone pre-mRNA 3'end processing complex (GO:0071204)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)		TTAAACTGTTGAAGAACTGCC	0.313																																						dbGAP											0													86.0	86.0	86.0					6																	86350199		2203	4299	6502	-	-	-	SO:0001587	stop_gained	0			AF037448	CCDS5005.1, CCDS55041.1, CCDS75491.1	6q14-q15	2013-05-23			ENSG00000135316	ENSG00000135316		"""RNA binding motif (RRM) containing"""	16918	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein Q"""					9847309, 11352648	Standard	NM_006372		Approved	NSAP1, GRY-RBP, dJ3J17.2, HNRPQ1, hnRNP-Q, HNRNPQ	uc003pla.2	O60506	OTTHUMG00000015141	ENST00000369622.3:c.232C>T	6.37:g.86350199G>A	ENSP00000358635:p.Gln78*	Somatic		WXS	Illumina GAIIx	Phase_IV	E1P501|E1P502|Q53H05|Q5TCG2|Q5TCG3|Q8IW78|Q8N599|Q96LC1|Q96LC2|Q9Y583	Nonsense_Mutation	SNP	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom,tigrfam_HnRNP_R/Q_splicing_fac	p.Q78*	ENST00000369622.3	37	c.232	CCDS5005.1	6	.	.	.	.	.	.	.	.	.	.	G	36	5.619480	0.96649	.	.	ENSG00000135316	ENST00000355238;ENST00000369622;ENST00000444272	.	.	.	5.07	5.07	0.68467	.	0.326738	0.33875	N	0.004479	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.4659	0.90755	0.0:0.0:1.0:0.0	.	.	.	.	X	78	.	ENSP00000347380:Q78X	Q	-	1	0	SYNCRIP	86406918	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.003000	0.70701	2.329000	0.79093	0.655000	0.94253	CAA	SYNCRIP	-	NULL	ENSG00000135316		0.313	SYNCRIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SYNCRIP	HGNC	protein_coding	OTTHUMT00000041396.1	220	0.00	0	G	NM_006372		86350199	86350199	-1	no_errors	ENST00000369622	ensembl	human	known	69_37n	nonsense	195	26.14	69	SNP	1.000	A
TPCN2	219931	genome.wustl.edu	37	11	68822752	68822753	+	Frame_Shift_Ins	INS	-	-	CT			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr11:68822752_68822753insCT	ENST00000294309.3	+	4	462_463	c.361_362insCT	c.(361-363)cccfs	p.P121fs	TPCN2_ENST00000442692.2_3'UTR|TPCN2_ENST00000542467.1_Frame_Shift_Ins_p.P121fs	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	121					calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|release of sequestered calcium ion into cytosol (GO:0051209)|smooth muscle contraction (GO:0006939)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|protein kinase binding (GO:0019901)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	32			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			CTGGGAGCCGCCCTGCGGCCTG	0.639																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AK023366	CCDS8189.1	11q13.1	2011-07-05			ENSG00000162341	ENSG00000162341		"""Voltage-gated ion channels / Two-pore channels"""	20820	protein-coding gene	gene with protein product		612163				16382101	Standard	NM_139075		Approved	TPC2	uc001oos.2	Q8NHX9	OTTHUMG00000167898	Exception_encountered	11.37:g.68822752_68822753insCT	ENSP00000294309:p.Pro121fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q9NT82	Frame_Shift_Ins	INS	pfam_Ion_trans_dom	p.C122fs	ENST00000294309.3	37	c.361_362	CCDS8189.1	11																																																																																			TPCN2	-	NULL	ENSG00000162341		0.639	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TPCN2	HGNC	protein_coding	OTTHUMT00000396878.2	52	0.00	0	-	NM_139075		68822752	68822753	+1	no_errors	ENST00000294309	ensembl	human	known	69_37n	frame_shift_ins	38	11.63	5	INS	0.999:1.000	CT
TRIM28	10155	genome.wustl.edu	37	19	59061549	59061549	+	Silent	SNP	C	C	T			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr19:59061549C>T	ENST00000253024.5	+	16	2518	c.2229C>T	c.(2227-2229)atC>atT	p.I743I	TRIM28_ENST00000341753.6_Silent_p.I661I	NM_005762.2	NP_005753.1	Q13263	TIF1B_HUMAN	tripartite motif containing 28	743	Bromo.				convergent extension involved in axis elongation (GO:0060028)|DNA repair (GO:0006281)|embryonic placenta morphogenesis (GO:0060669)|epithelial to mesenchymal transition (GO:0001837)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|Krueppel-associated box domain binding (GO:0035851)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		TGACCCTGATCCGTGCCCGCC	0.557																																						dbGAP											0													50.0	44.0	46.0					19																	59061549		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS12985.1	19q13.4	2014-06-13	2011-01-25			ENSG00000130726		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	16384	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 157"""	601742	"""tripartite motif-containing 28"""			11331580, 11226167	Standard	NM_005762		Approved	TIF1B, KAP1, TF1B, RNF96, PPP1R157	uc002qtg.1	Q13263		ENST00000253024.5:c.2229C>T	19.37:g.59061549C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	O00677|Q7Z632|Q93040|Q96IM1	Silent	SNP	pfam_Znf_B-box,pfam_Znf_PHD-finger,superfamily_Znf_FYVE_PHD,superfamily_Bromodomain,smart_Znf_RING,smart_Znf_B-box,smart_Bbox_C,smart_Znf_PHD,smart_Bromodomain,pfscan_Znf_B-box,pfscan_Znf_PHD-finger,pfscan_Znf_RING	p.I743	ENST00000253024.5	37	c.2229	CCDS12985.1	19																																																																																			TRIM28	-	superfamily_Bromodomain,smart_Bromodomain	ENSG00000130726		0.557	TRIM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TRIM28	HGNC	protein_coding	OTTHUMT00000467074.1	11	0.00	0	C	NM_005762		59061549	59061549	+1	no_errors	ENST00000253024	ensembl	human	known	69_37n	silent	22	48.84	21	SNP	0.962	T
UROD	7389	genome.wustl.edu	37	1	45478691	45478691	+	Splice_Site	DEL	G	G	-			TCGA-A8-A06P-01A-11W-A019-09	TCGA-A8-A06P-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	239b3d55-c5d6-4478-9b7b-1cbad3c03c81	f8f99cc8-0355-4bf9-b26e-65603682d0f9	g.chr1:45478691delG	ENST00000246337.4	+	2	252	c.133delG	c.(133-135)gag>ag	p.E45fs	HECTD3_ENST00000372172.4_5'Flank|UROD_ENST00000494399.1_3'UTR	NM_000374.4	NP_000365.3	P06132	DCUP_HUMAN	uroporphyrinogen decarboxylase	45					heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	uroporphyrinogen decarboxylase activity (GO:0004853)			endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	4	Acute lymphoblastic leukemia(166;0.155)					TTACTTACCAGGTAAGAGTCA	0.567									Porphyria Cutanea Tarda, Type II																													dbGAP											0													39.0	41.0	41.0					1																	45478691		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0	Familial Cancer Database	PCT-II	BC001778	CCDS518.1	1p34	2012-10-02			ENSG00000126088	ENSG00000126088	4.1.1.37		12591	protein-coding gene	gene with protein product		613521				3015909, 3460962	Standard	NM_000374		Approved		uc001cna.2	P06132	OTTHUMG00000008949	ENST00000246337.4:c.133+1G>-	1.37:g.45478691delG		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K762|Q16863|Q16883|Q53YB8|Q53ZP6|Q6IB28|Q9BUZ0	Frame_Shift_Del	DEL	pfam_Uroporphyrinogen_deCOase,tigrfam_Uroporphyrinogen_deCO2ase_HemE	p.E45fs	ENST00000246337.4	37	c.133	CCDS518.1	1																																																																																			UROD	-	pfam_Uroporphyrinogen_deCOase,tigrfam_Uroporphyrinogen_deCO2ase_HemE	ENSG00000126088		0.567	UROD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	UROD	HGNC	protein_coding	OTTHUMT00000024803.1	42	0.00	0	G	NM_000374	Frame_Shift_Del	45478691	45478691	+1	no_errors	ENST00000246337	ensembl	human	known	69_37n	frame_shift_del	20	59.18	29	DEL	1.000	-
