#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_ORegAnno_bin	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
ABHD13	84945	genome.wustl.edu	37	13	108882113	108882113	+	Missense_Mutation	SNP	G	G	A			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr13:108882113G>A	ENST00000375898.3	+	2	848	c.547G>A	c.(547-549)Gat>Aat	p.D183N		NM_032859.2	NP_116248.2	Q7L211	ABHDD_HUMAN	abhydrolase domain containing 13	183						integral component of membrane (GO:0016021)|membrane (GO:0016020)	hydrolase activity (GO:0016787)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					ACCTGACCTTGATAAAACAAA	0.398																																					Pancreas(22;506 789 38166 45896 51596)	dbGAP											0													99.0	86.0	90.0					13																	108882113		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK027812	CCDS32007.1	13q33.2	2007-04-03	2006-03-10	2006-03-10	ENSG00000139826	ENSG00000139826		"""Abhydrolase domain containing"""	20293	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 6"""	C13orf6			Standard	NM_032859		Approved	bA153I24.2, FLJ14906, BEM46L1	uc001vqq.3	Q7L211	OTTHUMG00000017330	ENST00000375898.3:c.547G>A	13.37:g.108882113G>A	ENSP00000365063:p.Asp183Asn		B3KWE7|Q8NBW1|Q96JX9	Missense_Mutation	SNP	pfam_AB_hydrolase_1,pfam_AXE1	p.D183N	ENST00000375898.3	37	c.547	CCDS32007.1	13	.	.	.	.	.	.	.	.	.	.	G	20.4	3.981671	0.74474	.	.	ENSG00000139826	ENST00000375898	T	0.55588	0.51	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.55417	0.1919	L	0.31578	0.945	0.80722	D	1	P	0.44659	0.84	P	0.51415	0.669	T	0.43734	-0.9373	10	0.30078	T	0.28	-23.9234	19.5254	0.95203	0.0:0.0:1.0:0.0	.	183	Q7L211	ABHDD_HUMAN	N	183	ENSP00000365063:D183N	ENSP00000365063:D183N	D	+	1	0	ABHD13	107680114	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	9.745000	0.98856	2.857000	0.98124	0.650000	0.86243	GAT	ABHD13	-	pfam_AB_hydrolase_1,pfam_AXE1	ENSG00000139826		0.398	ABHD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ABHD13	HGNC	protein_coding	OTTHUMT00000045743.1	55	0.00	0	G	NM_032859		108882113	108882113	+1	no_errors	ENST00000375898	ensembl	human	known	69_37n	missense	68	19.05	16	SNP	1.000	A
ARID1B	57492	genome.wustl.edu	37	6	157528608	157528608	+	Frame_Shift_Del	DEL	C	C	-			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr6:157528608delC	ENST00000350026.5	+	19	6295	c.6294delC	c.(6292-6294)ttcfs	p.F2098fs	ARID1B_ENST00000275248.4_Frame_Shift_Del_p.F2093fs|ARID1B_ENST00000367148.1_Frame_Shift_Del_p.F2151fs|ARID1B_ENST00000346085.5_Frame_Shift_Del_p.F2111fs	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	2098					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		AGGAGAAATTCTATGCTACAT	0.483																																						dbGAP											0													185.0	195.0	191.0					6																	157528608		2203	4296	6499	-	-	-	SO:0001589	frameshift_variant	0			AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.6294delC	6.37:g.157528608delC	ENSP00000055163:p.Phe2098fs		Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Frame_Shift_Del	DEL	pfam_DUF3518,pfam_ARID/BRIGHT_DNA-bd,superfamily_ARID/BRIGHT_DNA-bd,superfamily_ARM-type_fold,smart_ARID/BRIGHT_DNA-bd,pfscan_ARID/BRIGHT_DNA-bd	p.Y2152fs	ENST00000350026.5	37	c.6453	CCDS5251.2	6																																																																																			ARID1B	-	pfam_DUF3518,superfamily_ARM-type_fold	ENSG00000049618		0.483	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	ARID1B	HGNC	protein_coding	OTTHUMT00000372723.1	28	0.00	0	C	NM_020732		157528608	157528608	+1	no_errors	ENST00000367148	ensembl	human	known	69_37n	frame_shift_del	28	32.61	15	DEL	1.000	-
C1orf86	199990	genome.wustl.edu	37	1	2129485	2129485	+	Frame_Shift_Del	DEL	G	G	-	rs561736453		TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr1:2129485delG	ENST00000378545.3	-	2	331	c.332delC	c.(331-333)ccgfs	p.P111fs	C1orf86_ENST00000487186.1_5'UTR	NM_001282670.1	NP_001269599.1	Q6NZ36	FAP20_HUMAN	chromosome 1 open reading frame 86	0					cellular response to DNA damage stimulus (GO:0006974)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	cell junction (GO:0030054)|chromosome (GO:0005694)|Fanconi anaemia nuclear complex (GO:0043240)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|metal ion binding (GO:0046872)|polyubiquitin binding (GO:0031593)|ubiquitin binding (GO:0043130)			central_nervous_system(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4	all_cancers(77;0.000134)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.09e-37)|OV - Ovarian serous cystadenocarcinoma(86;1.5e-23)|GBM - Glioblastoma multiforme(42;1.61e-08)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00437)|STAD - Stomach adenocarcinoma(132;0.0134)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)		ATGACACAGCGGTGCTGGTGA	0.507																																						dbGAP											0													249.0	213.0	224.0					1																	2129485		692	1591	2283	-	-	-	SO:0001589	frameshift_variant	0			AK126870	CCDS38.2, CCDS57965.1, CCDS72686.1, CCDS72687.1	1p36.33	2013-05-22			ENSG00000162585	ENSG00000162585			26428	protein-coding gene	gene with protein product		615183				14702039	Standard	NM_182533		Approved	FLJ31031, FAAP20	uc031pkt.1	Q6NZ36	OTTHUMG00000001404	ENST00000378545.3:c.332delC	1.37:g.2129485delG	ENSP00000367807:p.Pro111fs		A6PW39|A6PW40|A6PW41|A8MQT6|F2Z2L4|Q6ZT64|Q71M24|Q96ND7	Frame_Shift_Del	DEL	NULL	p.P111fs	ENST00000378545.3	37	c.332		1																																																																																			C1orf86	-	NULL	ENSG00000162585		0.507	C1orf86-201	KNOWN	basic|appris_candidate_longest	protein_coding	C1orf86	HGNC	protein_coding		98	0.00	0	G	NM_182533		2129485	2129485	-1	no_errors	ENST00000378545	ensembl	human	known	69_37n	frame_shift_del	93	45.20	80	DEL	0.000	-
C1orf146	388649	genome.wustl.edu	37	1	92709922	92709922	+	Silent	SNP	G	G	C			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr1:92709922G>C	ENST00000370375.3	+	4	457	c.309G>C	c.(307-309)ctG>ctC	p.L103L	C1orf146_ENST00000370373.2_Silent_p.L44L	NM_001012425.1	NP_001012425.1	Q5VVC0	CA146_HUMAN	chromosome 1 open reading frame 146	103										breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	8		all_lung(203;0.00528)|Lung NSC(277;0.0193)		all cancers(265;0.00846)|Epithelial(280;0.0952)		AATGGAAACTGATGTTCAGGA	0.308																																						dbGAP											0													47.0	47.0	47.0					1																	92709922		2201	4298	6499	-	-	-	SO:0001819	synonymous_variant	0				CCDS30772.1	1p22.1	2008-02-05			ENSG00000203910	ENSG00000203910			24032	protein-coding gene	gene with protein product						15496913	Standard	NM_001012425		Approved		uc001doq.3	Q5VVC0	OTTHUMG00000010285	ENST00000370375.3:c.309G>C	1.37:g.92709922G>C			Q5VVC4	Silent	SNP	NULL	p.L103	ENST00000370375.3	37	c.309	CCDS30772.1	1																																																																																			C1orf146	-	NULL	ENSG00000203910		0.308	C1orf146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C1orf146	HGNC	protein_coding	OTTHUMT00000028364.1	48	0.00	0	G	NM_001012425		92709922	92709922	+1	no_errors	ENST00000370375	ensembl	human	known	69_37n	silent	48	15.79	9	SNP	0.993	C
CBFB	865	genome.wustl.edu	37	16	67070564	67070564	+	Missense_Mutation	SNP	A	A	G			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr16:67070564A>G	ENST00000290858.6	+	3	449	c.188A>G	c.(187-189)aAt>aGt	p.N63S	CBFB_ENST00000412916.2_Missense_Mutation_p.N63S|CBFB_ENST00000561924.2_5'UTR	NM_001755.2|NM_022845.2	NP_001746.1|NP_074036.1	Q13951	PEBB_HUMAN	core-binding factor, beta subunit	63					cell maturation (GO:0048469)|definitive hemopoiesis (GO:0060216)|lymphocyte differentiation (GO:0030098)|myeloid cell differentiation (GO:0030099)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(3)|large_intestine(1)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00189)|Epithelial(162;0.00755)|all cancers(182;0.066)		ACAGGAACCAATCTGTCTCTC	0.433			T	MYH11	AML																																	dbGAP		Dom	yes		16	16q22	865	"""core-binding factor, beta subunit"""		L	0													85.0	87.0	86.0					16																	67070564		2200	4300	6500	-	-	-	SO:0001583	missense	0			BC018509	CCDS10827.1, CCDS45508.1	16q22.1	2008-02-05			ENSG00000067955	ENSG00000067955			1539	protein-coding gene	gene with protein product		121360				8351518, 7587111	Standard	NM_001755		Approved	PEBP2B	uc002erb.3	Q13951	OTTHUMG00000137520	ENST00000290858.6:c.188A>G	16.37:g.67070564A>G	ENSP00000290858:p.Asn63Ser		A8K347|Q13124|Q9HCT2	Missense_Mutation	SNP	pfam_CBF_beta,superfamily_CBF_beta	p.N63S	ENST00000290858.6	37	c.188	CCDS10827.1	16	.	.	.	.	.	.	.	.	.	.	A	21.1	4.099850	0.76983	.	.	ENSG00000067955	ENST00000290858;ENST00000412916	.	.	.	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.76241	0.3960	M	0.70595	2.14	0.80722	D	1	P;P	0.42692	0.747;0.787	P;P	0.60236	0.855;0.871	T	0.78104	-0.2334	9	0.59425	D	0.04	-16.0905	13.9085	0.63850	1.0:0.0:0.0:0.0	.	63;63	Q13951-2;Q13951	.;PEBB_HUMAN	S	63	.	ENSP00000290858:N63S	N	+	2	0	CBFB	65628065	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.676000	0.91199	2.022000	0.59522	0.459000	0.35465	AAT	CBFB	-	pfam_CBF_beta,superfamily_CBF_beta	ENSG00000067955		0.433	CBFB-001	KNOWN	basic|CCDS	protein_coding	CBFB	HGNC	protein_coding	OTTHUMT00000268843.2	85	0.00	0	A	NM_001755		67070564	67070564	+1	no_errors	ENST00000290858	ensembl	human	known	69_37n	missense	31	49.18	30	SNP	1.000	G
CDK12	51755	genome.wustl.edu	37	17	37672031	37672031	+	Missense_Mutation	SNP	A	A	G			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr17:37672031A>G	ENST00000447079.4	+	9	2849	c.2816A>G	c.(2815-2817)aAt>aGt	p.N939S	CDK12_ENST00000430627.2_Missense_Mutation_p.N939S	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	939	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						TTTCAAGCCAATCTGGAACTG	0.403			"""Mis, N, F"""		serous ovarian					TCGA Ovarian(9;0.13)																												dbGAP		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	0													117.0	110.0	112.0					17																	37672031		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"""Cyclin-dependent kinases"""	24224	protein-coding gene	gene with protein product	"""CDC2 related protein kinase 7"""	615514	"""Cdc2-related kinase, arginine/serine-rich"""	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.2816A>G	17.37:g.37672031A>G	ENSP00000398880:p.Asn939Ser		A7E2B2|B4DYX4|B9EIQ6|O94978	Missense_Mutation	SNP	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	p.N939S	ENST00000447079.4	37	c.2816	CCDS11337.1	17	.	.	.	.	.	.	.	.	.	.	A	18.73	3.685461	0.68157	.	.	ENSG00000167258	ENST00000430627;ENST00000447079	T;T	0.64438	-0.1;-0.1	6.03	4.95	0.65309	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.48767	D	0.000173	T	0.44912	0.1316	N	0.11284	0.12	0.80722	D	1	P;B;B	0.38129	0.619;0.362;0.312	B;B;B	0.38921	0.285;0.185;0.116	T	0.51188	-0.8737	10	0.72032	D	0.01	-12.1634	11.8765	0.52550	0.9326:0.0:0.0674:0.0	.	938;939;939	E7EUM9;Q9NYV4;Q9NYV4-2	.;CDK12_HUMAN;.	S	939	ENSP00000407720:N939S;ENSP00000398880:N939S	ENSP00000407720:N939S	N	+	2	0	CDK12	34925557	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.503000	0.81632	1.113000	0.41760	0.533000	0.62120	AAT	CDK12	-	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	ENSG00000167258		0.403	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CDK12	HGNC	protein_coding	OTTHUMT00000256941.4	76	0.00	0	A	NM_016507		37672031	37672031	+1	no_errors	ENST00000447079	ensembl	human	known	69_37n	missense	101	19.84	25	SNP	1.000	G
CSTF3	1479	genome.wustl.edu	37	11	33129459	33129459	+	Missense_Mutation	SNP	G	G	A			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr11:33129459G>A	ENST00000323959.4	-	5	485	c.346C>T	c.(346-348)Cca>Tca	p.P116S	CSTF3_ENST00000524827.1_Missense_Mutation_p.P148S	NM_001326.2	NP_001317.1	Q12996	CSTF3_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kDa	116					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|stomach(1)	19						TTGTAACTTGGTAGTTTACCC	0.388																																						dbGAP											0													176.0	162.0	167.0					11																	33129459		2202	4298	6500	-	-	-	SO:0001583	missense	0			U15782	CCDS7883.1, CCDS44563.1, CCDS44564.1	11p13	2007-01-05	2002-08-29		ENSG00000176102	ENSG00000176102			2485	protein-coding gene	gene with protein product		600367	"""cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kD"""			7984242	Standard	XM_006718154		Approved	CstF-77	uc001muh.3	Q12996	OTTHUMG00000166268	ENST00000323959.4:c.346C>T	11.37:g.33129459G>A	ENSP00000315791:p.Pro116Ser		A8K471|D3DR04|E9PB40|Q32P22|Q96FQ8|Q96QD6|Q96QK4	Missense_Mutation	SNP	pfam_Suf,smart_HAT	p.P116S	ENST00000323959.4	37	c.346	CCDS7883.1	11	.	.	.	.	.	.	.	.	.	.	G	11.31	1.599652	0.28534	.	.	ENSG00000176102	ENST00000323959;ENST00000537832;ENST00000524827	T;T	0.20463	2.07;2.07	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.13713	0.0332	L	0.28274	0.84	0.80722	D	1	B	0.13594	0.008	B	0.09377	0.004	T	0.04551	-1.0943	10	0.05721	T	0.95	.	14.8002	0.69909	0.0:0.1438:0.8562:0.0	.	116	Q12996	CSTF3_HUMAN	S	116;49;148	ENSP00000315791:P116S;ENSP00000431355:P148S	ENSP00000315791:P116S	P	-	1	0	CSTF3	33086035	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	9.863000	0.99569	2.554000	0.86153	0.655000	0.94253	CCA	CSTF3	-	NULL	ENSG00000176102		0.388	CSTF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CSTF3	HGNC	protein_coding	OTTHUMT00000388801.1	143	0.00	0	G	NM_001326		33129459	33129459	-1	no_errors	ENST00000323959	ensembl	human	known	69_37n	missense	84	39.13	54	SNP	1.000	A
DHRS2	10202	genome.wustl.edu	37	14	24114451	24114451	+	Missense_Mutation	SNP	A	A	G			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr14:24114451A>G	ENST00000250383.6	+	9	1308	c.832A>G	c.(832-834)Act>Gct	p.T278A	DHRS2_ENST00000344777.7_Silent_p.P281P	NM_005794.3	NP_005785.1	Q13268	DHRS2_HUMAN	dehydrogenase/reductase (SDR family) member 2	278					C21-steroid hormone metabolic process (GO:0008207)|cellular response to oxidative stress (GO:0034599)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	carbonyl reductase (NADPH) activity (GO:0004090)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00659)		AGGCTACTCCACTCGGCTCTG	0.607																																						dbGAP											0													88.0	79.0	82.0					14																	24114451		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS9604.1, CCDS41927.1	14q11.2	2011-09-14			ENSG00000100867	ENSG00000100867		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18349	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 1"""	615194				7556196, 11944995, 16685466, 19027726	Standard	NM_182908		Approved	HEP27, SDR25C1	uc001wkt.4	Q13268	OTTHUMG00000028771	ENST00000250383.6:c.832A>G	14.37:g.24114451A>G	ENSP00000250383:p.Thr278Ala		D3DS54|Q53GS4|Q7Z789|Q9H2R2	Missense_Mutation	SNP	pfam_DH_sc/Rdtase_SDR,pfam_PKS_KR,prints_Glc/ribitol_DH,prints_DHB_DH,prints_DH_sc/Rdtase_SDR,prints_ADH_insect	p.T278A	ENST00000250383.6	37	c.832	CCDS9604.1	14	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	11.71|11.71	1.720482|1.720482	0.30503|0.30503	.|.	.|.	ENSG00000100867|ENSG00000100867	ENST00000557535|ENST00000250383	.|D	.|0.81821	.|-1.54	4.59|4.59	-0.567|-0.567	0.11763|0.11763	.|.	.|.	.|.	.|.	.|.	T|T	0.63745|0.63745	0.2537|0.2537	.|.	.|.	.|.	0.18873|0.18873	N|N	0.999984|0.999984	.|B	.|0.06786	.|0.001	.|B	.|0.04013	.|0.001	T|T	0.46871|0.46871	-0.9160|-0.9160	4|8	.|0.33940	.|T	.|0.23	.|.	3.783|3.783	0.08687|0.08687	0.1645:0.4544:0.0:0.3811|0.1645:0.4544:0.0:0.3811	.|.	.|278	.|D3DS54	.|.	R|A	177|278	.|ENSP00000250383:T278A	.|ENSP00000250383:T278A	H|T	+|+	2|1	0|0	DHRS2|DHRS2	23184291|23184291	0.000000|0.000000	0.05858|0.05858	0.012000|0.012000	0.15200|0.15200	0.018000|0.018000	0.09664|0.09664	-0.575000|-0.575000	0.05861|0.05861	-0.219000|-0.219000	0.10003|0.10003	-1.282000|-1.282000	0.01380|0.01380	CAC|ACT	DHRS2	-	NULL	ENSG00000100867		0.607	DHRS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	DHRS2	HGNC	protein_coding	OTTHUMT00000071842.2	40	0.00	0	A	NM_182908		24114451	24114451	+1	no_errors	ENST00000250383	ensembl	human	known	69_37n	missense	34	39.29	22	SNP	0.007	G
DNAH8	1769	genome.wustl.edu	37	6	38759340	38759340	+	Silent	SNP	T	T	C			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr6:38759340T>C	ENST00000359357.3	+	19	2394	c.2140T>C	c.(2140-2142)Ttg>Ctg	p.L714L	DNAH8_ENST00000449981.2_Silent_p.L931L|DNAH8_ENST00000441566.1_Silent_p.L714L			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	714					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						GATCAGTGACTTGTGTGAAAT	0.343																																						dbGAP											0													99.0	92.0	94.0					6																	38759340		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.2140T>C	6.37:g.38759340T>C			O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	pfam_Dynein_heavy,pfam_Dynein_heavy_dom-1,pfam_Dynein_heavy_dom-2,pfam_ATPase_dyneun-rel_AAA,smart_AAA+_ATPase	p.L714	ENST00000359357.3	37	c.2140		6																																																																																			DNAH8	-	NULL	ENSG00000124721		0.343	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	DNAH8	HGNC	protein_coding	OTTHUMT00000043574.1	86	0.00	0	T	NM_001206927		38759340	38759340	+1	no_errors	ENST00000359357	ensembl	human	known	69_37n	silent	105	33.12	52	SNP	0.998	C
GATA3	2625	genome.wustl.edu	37	10	8111433	8111434	+	Splice_Site	DEL	CA	CA	-	rs111853237		TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	CA	CA					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr10:8111433_8111434delCA	ENST00000346208.3	+	5	1376		c.e5-1		GATA3_ENST00000461472.1_Splice_Site|GATA3_ENST00000379328.3_Splice_Site			P23771	GATA3_HUMAN	GATA binding protein 3						anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cardiac right ventricle morphogenesis (GO:0003215)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|cellular response to interferon-alpha (GO:0035457)|cellular response to interleukin-4 (GO:0071353)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|developmental growth (GO:0048589)|ear development (GO:0043583)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|interferon-gamma secretion (GO:0072643)|interleukin-4 secretion (GO:0072602)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lymphocyte migration (GO:0072676)|male gonad development (GO:0008584)|mast cell differentiation (GO:0060374)|mesenchymal to epithelial transition (GO:0060231)|mesonephros development (GO:0001823)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell motility (GO:2000146)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in mesonephros development (GO:2000607)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation (GO:2000703)|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation (GO:2000734)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|nephric duct morphogenesis (GO:0072178)|neuron migration (GO:0001764)|norepinephrine biosynthetic process (GO:0042421)|otic vesicle development (GO:0071599)|parathyroid gland development (GO:0060017)|parathyroid hormone secretion (GO:0035898)|pharyngeal system development (GO:0060037)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of signal transduction (GO:0009967)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureteric bud formation (GO:0072107)|post-embryonic development (GO:0009791)|pro-T cell differentiation (GO:0002572)|regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043370)|regulation of cellular response to X-ray (GO:2000683)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of establishment of cell polarity (GO:2000114)|regulation of histone H3-K27 methylation (GO:0061085)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to virus (GO:0009615)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|T cell receptor signaling pathway (GO:0050852)|T-helper 2 cell differentiation (GO:0045064)|thymic T cell selection (GO:0045061)|thymus development (GO:0048538)|TOR signaling (GO:0031929)|transcription from RNA polymerase II promoter (GO:0006366)|type IV hypersensitivity (GO:0001806)|ureter maturation (GO:0035799)|ureteric bud formation (GO:0060676)|uterus development (GO:0060065)|ventricular septum development (GO:0003281)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer sequence-specific DNA binding (GO:0001158)|HMG box domain binding (GO:0071837)|nucleic acid binding transcription factor activity (GO:0001071)|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 core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)	p.?(7)		NS(1)|breast(44)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(24)|ovary(3)|skin(2)	87						TCCCCACTCTCAGTCTGCAGCC	0.48			"""F, N, S"""		breast		"""HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"""																															dbGAP		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	7	Unknown(7)	breast(7)																																								-	-	-	SO:0001630	splice_region_variant	0			X55122	CCDS7083.1, CCDS31143.1	10p15	2013-01-25	2001-11-28		ENSG00000107485	ENSG00000107485		"""GATA zinc finger domain containing"""	4172	protein-coding gene	gene with protein product		131320	"""GATA-binding protein 3"""			2050118, 15087456	Standard	NM_002051		Approved	HDR	uc001ijz.3	P23771	OTTHUMG00000017640	ENST00000346208.3:c.922-1CA>-	10.37:g.8111433_8111434delCA			Q5VWG7|Q5VWG8|Q96J16	Splice_Site	DEL	-	e4-2	ENST00000346208.3	37	c.925-3_925-2	CCDS7083.1	10																																																																																			GATA3	-	-	ENSG00000107485		0.480	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	GATA3	HGNC	protein_coding	OTTHUMT00000046719.1	61	0	0	CA	NM_001002295	Intron	8111433	8111434	+1	no_errors	ENST00000379328	ensembl	human	known	69_37n	splice_site_del	63	31.52	29	DEL	1.000:1.000	-
IL7R	3575	genome.wustl.edu	37	5	35873588	35873588	+	Missense_Mutation	SNP	A	A	T			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr5:35873588A>T	ENST00000303115.3	+	5	673	c.544A>T	c.(544-546)Aat>Tat	p.N182Y	IL7R_ENST00000506850.1_Missense_Mutation_p.N182Y|IL7R_ENST00000343305.4_Missense_Mutation_p.N182Y	NM_002185.3	NP_002176.2	P16871	IL7RA_HUMAN	interleukin 7 receptor	182	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				B cell proliferation (GO:0042100)|cell growth (GO:0016049)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|immune response (GO:0006955)|immunoglobulin production (GO:0002377)|interleukin-7-mediated signaling pathway (GO:0038111)|lymph node development (GO:0048535)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of gene expression (GO:0010628)|positive regulation of T cell differentiation in thymus (GO:0033089)|regulation of cell size (GO:0008361)|regulation of DNA recombination (GO:0000018)|signal transduction (GO:0007165)|T cell differentiation (GO:0030217)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|interleukin-7 receptor activity (GO:0004917)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(78)|kidney(2)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|skin(5)|stomach(3)	126	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			CTAGCATGTGAATTTATCCAG	0.418			"""Mis, O"""		"""ALL, ETP ALL"""		Severe combined immune deficiency																															dbGAP		Dom	yes		5	5p13	146661	interleukin 7 receptor	yes	L	0													47.0	46.0	46.0					5																	35873588		2203	4300	6503	-	-	-	SO:0001583	missense	0			M29696	CCDS3911.1	5p13	2014-09-17			ENSG00000168685	ENSG00000168685		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	6024	protein-coding gene	gene with protein product		146661				2317865	Standard	NM_002185		Approved	CD127	uc003jjs.4	P16871	OTTHUMG00000090791	ENST00000303115.3:c.544A>T	5.37:g.35873588A>T	ENSP00000306157:p.Asn182Tyr		B2RCS6|B4DVT1|Q05CU8|Q6NSP4|Q6NWM0|Q6NWM1|Q6NWM2|Q6NWM3|Q6SV45|Q9UPC1	Missense_Mutation	SNP	pfam_Fibronectin_type3,superfamily_Fibronectin_type3	p.N182Y	ENST00000303115.3	37	c.544	CCDS3911.1	5	.	.	.	.	.	.	.	.	.	.	A	10.17	1.277830	0.23307	.	.	ENSG00000168685	ENST00000303115;ENST00000343305;ENST00000506850	T;T;T	0.59502	0.26;0.26;0.26	5.83	4.65	0.58169	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.714254	0.14469	N	0.317665	T	0.51736	0.1692	L	0.48362	1.52	0.09310	N	1	B;B	0.18741	0.03;0.007	B;B	0.27076	0.076;0.023	T	0.48948	-0.8989	10	0.52906	T	0.07	-2.3828	8.9034	0.35507	0.8279:0.0:0.0:0.1721	.	182;182	D6RGV2;P16871	.;IL7RA_HUMAN	Y	182	ENSP00000306157:N182Y;ENSP00000345819:N182Y;ENSP00000421207:N182Y	ENSP00000306157:N182Y	N	+	1	0	IL7R	35909345	0.032000	0.19561	0.343000	0.25615	0.565000	0.35776	1.006000	0.29847	0.986000	0.38683	0.459000	0.35465	AAT	IL7R	-	pfam_Fibronectin_type3,superfamily_Fibronectin_type3	ENSG00000168685		0.418	IL7R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IL7R	HGNC	protein_coding	OTTHUMT00000207577.2	40	0.00	0	A			35873588	35873588	+1	no_errors	ENST00000303115	ensembl	human	known	69_37n	missense	37	36.21	21	SNP	0.027	T
ITGB8	3696	genome.wustl.edu	37	7	20418798	20418798	+	Silent	SNP	C	C	T	rs574544273	byFrequency	TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr7:20418798C>T	ENST00000222573.4	+	4	1197	c.513C>T	c.(511-513)aaC>aaT	p.N171N	SNORD56_ENST00000363883.1_RNA|ITGB8_ENST00000537992.1_Silent_p.N36N	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	171	VWFA.				cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						CCGTTGGAAACGATTTATCTA	0.358													C|||	5	0.000998403	0.0	0.0	5008	,	,		12413	0.005		0.0	False		,,,				2504	0.0					dbGAP											0													90.0	94.0	93.0					7																	20418798		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"""Integrins"""	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.513C>T	7.37:g.20418798C>T			A4D133|B4DHD4	Silent	SNP	pirsf_Integrin_bsu,pfam_Integrin_bsu_N,pfam_EGF_extracell,superfamily_Plexin-like_fold,smart_Plexin-like,smart_Integrin_bsu_N,prints_Integrin_bsu	p.N171	ENST00000222573.4	37	c.513	CCDS5370.1	7																																																																																			ITGB8	-	pirsf_Integrin_bsu,pfam_Integrin_bsu_N,smart_Integrin_bsu_N	ENSG00000105855		0.358	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ITGB8	HGNC	protein_coding	OTTHUMT00000059915.3	107	0.00	0	C	NM_002214		20418798	20418798	+1	no_errors	ENST00000222573	ensembl	human	known	69_37n	silent	96	35.14	52	SNP	1.000	T
KIR3DL1	3811	genome.wustl.edu	37	19	55344245	55344245	+	IGR	SNP	C	C	T	rs575946275		TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr19:55344245C>T	ENST00000391728.4	+	0	1871				KIR2DS4_ENST00000339924.8_RNA|KIR3DL1_ENST00000402254.2_Intron	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1						immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		ATCATCATGGCGTGTGTTGGT	0.622													.|||	1	0.000199681	0.0	0.0	5008	,	,		15048	0.001		0.0	False		,,,				2504	0.0					dbGAP											0													175.0	161.0	166.0					19																	55344245		2172	4175	6347	-	-	-	SO:0001628	intergenic_variant	0			L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933		19.37:g.55344245C>T			O43473|Q14946|Q16541	Missense_Mutation	SNP	NULL	p.A9V	ENST00000391728.4	37	c.26	CCDS42621.1	19																																																																																			KIR2DS4	-	NULL	ENSG00000221957		0.622	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	KIR2DS4	HGNC	protein_coding	OTTHUMT00000141238.1	252	0.00	0	C	NM_013289		55344245	55344245	+1	pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000339924	ensembl	human	known	69_37n	missense	380	14.13	63	SNP	0.304	T
LINC00200	399706	genome.wustl.edu	37	10	1205736	1205736	+	lincRNA	SNP	A	A	G	rs60415666		TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr10:1205736A>G	ENST00000425630.1	+	0	29					NR_015376.2				long intergenic non-protein coding RNA 200																		ATGAGGGATGACGCAGGCACA	0.667																																						dbGAP											0													15.0	18.0	17.0					10																	1205736		687	1591	2278	-	-	-			0			AK097673		10p15.3	2012-10-12	2011-08-11	2011-08-11	ENSG00000229205	ENSG00000229205		"""Long non-coding RNAs"""	30974	non-coding RNA	RNA, long non-coding			"""chromosome 10 open reading frame 139"", ""non-protein coding RNA 200"""	C10orf139, NCRNA00200			Standard	NR_015376		Approved	FLJ40354	uc010qag.1		OTTHUMG00000017539		10.37:g.1205736A>G				RNA	SNP	-	NULL	ENST00000425630.1	37	NULL		10																																																																																			LINC00200	-	-	ENSG00000229205		0.667	LINC00200-001	KNOWN	basic	lincRNA	LINC00200	HGNC	lincRNA	OTTHUMT00000046417.2	29	0.00	0	A	NR_015376		1205736	1205736	+1	no_errors	ENST00000425630	ensembl	human	known	69_37n	rna	25	16.67	5	SNP	0.155	G
ZFP91	80829	genome.wustl.edu	37	11	58345513	58345513	+	5'Flank	SNP	T	T	C			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr11:58345513T>C	ENST00000316059.6	+	0	0				LPXN_ENST00000528954.1_Missense_Mutation_p.T3A|LPXN_ENST00000395074.2_5'Flank|ZFP91-CNTF_ENST00000389919.4_5'Flank|LPXN_ENST00000528489.1_5'UTR	NM_001197051.1|NM_053023.4	NP_001183980.1|NP_444251.1	Q96JP5	ZFP91_HUMAN	ZFP91 zinc finger protein						activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein K63-linked ubiquitination (GO:0070534)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	26		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				atcaataatgtagacatgaac	0.552																																						dbGAP											0													46.0	45.0	45.0					11																	58345513		692	1591	2283	-	-	-	SO:0001631	upstream_gene_variant	0			AB056107	CCDS31553.1	11q12	2012-11-27	2012-11-27		ENSG00000186660	ENSG00000186660		"""Zinc fingers, C2H2-type"""	14983	protein-coding gene	gene with protein product			"""zinc finger protein homologous to Zfp91 in mouse"", ""zinc finger protein 91 homolog (mouse)"""			12738986, 20682767	Standard	NM_053023		Approved	PZF, ZNF757	uc001nmx.4	Q96JP5	OTTHUMG00000137391		11.37:g.58345513T>C	Exception_encountered		A6NHC4|A8MSG7|Q86V47|Q96JP4|Q96QA3	Missense_Mutation	SNP	pfam_Znf_LIM,smart_Znf_LIM,pirsf_Leupaxin,pfscan_Znf_LIM	p.T3A	ENST00000316059.6	37	c.7	CCDS31553.1	11	.	.	.	.	.	.	.	.	.	.	T	10.66	1.411852	0.25465	.	.	ENSG00000110031	ENST00000528954	T	0.28454	1.61	3.89	-6.82	0.01698	.	.	.	.	.	T	0.10937	0.0267	N	0.08118	0	0.21604	N	0.999621	B	0.02656	0.0	B	0.01281	0.0	T	0.22800	-1.0206	9	0.56958	D	0.05	.	1.0665	0.01611	0.2275:0.2029:0.1192:0.4503	.	3	B4DV71	.	A	3	ENSP00000431284:T3A	ENSP00000431284:T3A	T	-	1	0	LPXN	58102089	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.541000	0.06099	-1.628000	0.01548	-0.379000	0.06801	ACA	LPXN	-	pirsf_Leupaxin	ENSG00000110031		0.552	ZFP91-003	KNOWN	basic|appris_principal|CCDS	protein_coding	LPXN	HGNC	protein_coding	OTTHUMT00000268674.1	13	0.00	0	T	NM_053023		58345513	58345513	-1	no_errors	ENST00000528954	ensembl	human	known	69_37n	missense	11	56.00	14	SNP	0.000	C
MAP4K1	11184	genome.wustl.edu	37	19	39103372	39103372	+	Frame_Shift_Del	DEL	C	C	-			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr19:39103372delC	ENST00000591517.1	-	9	572	c.544delG	c.(544-546)gaafs	p.E182fs	MAP4K1_ENST00000589002.1_5'UTR|MAP4K1_ENST00000423454.2_5'UTR|MAP4K1_ENST00000589130.1_Frame_Shift_Del_p.E178fs|MAP4K1_ENST00000396857.2_Frame_Shift_Del_p.E182fs|MAP4K1_ENST00000586296.1_Frame_Shift_Del_p.E182fs	NM_007181.4	NP_009112.1	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase kinase 1	182	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|cell proliferation (GO:0008283)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)	membrane (GO:0016020)	ATP binding (GO:0005524)|MAP kinase kinase kinase kinase activity (GO:0008349)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(24)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	44	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			GCTGCCACTTCCGGAGCCATC	0.622																																						dbGAP											0													47.0	51.0	50.0					19																	39103372		2123	4266	6389	-	-	-	SO:0001589	frameshift_variant	0			U66464	CCDS42564.1, CCDS59385.1	19q13.1-q13.4	2011-06-09				ENSG00000104814	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6863	protein-coding gene	gene with protein product	"""hematopoietic progenitor kinase 1"""	601983				8824585	Standard	NM_001042600		Approved	HPK1	uc002oix.1	Q92918		ENST00000591517.1:c.544delG	19.37:g.39103372delC	ENSP00000465039:p.Glu182fs			Frame_Shift_Del	DEL	pfam_Prot_kinase_cat_dom,pfam_Citron,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_Citron,pfscan_Prot_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	p.E182fs	ENST00000591517.1	37	c.544	CCDS59385.1	19																																																																																			MAP4K1	-	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	ENSG00000104814		0.622	MAP4K1-002	KNOWN	basic|CCDS	protein_coding	MAP4K1	HGNC	protein_coding	OTTHUMT00000453390.1	29	0.00	0	C	NM_001042600		39103372	39103372	-1	no_errors	ENST00000591517	ensembl	human	known	69_37n	frame_shift_del	30	41.18	21	DEL	1.000	-
PAPPA	5069	genome.wustl.edu	37	9	119097220	119097220	+	Nonsense_Mutation	SNP	C	C	T			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr9:119097220C>T	ENST00000328252.3	+	13	3847	c.3478C>T	c.(3478-3480)Cag>Tag	p.Q1160*	PAPPA_ENST00000534838.1_Nonsense_Mutation_p.Q198*	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	1160					cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						CTACCACAGCCAGGCGGTACG	0.617																																						dbGAP											0													106.0	87.0	93.0					9																	119097220		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0				CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"""insulin-like growth factor-dependent IGF binding protein-4 protease"", ""aspecific BCL2 ARE-binding protein 2"", ""differentially placenta 1 expressed protein"""	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.3478C>T	9.37:g.119097220C>T	ENSP00000330658:p.Gln1160*		B1AMF9|Q08371|Q68G52|Q9UDK7	Nonsense_Mutation	SNP	pfam_Sushi_SCR_CCP,pfam_Notch_dom,pfam_Peptidase_M43,superfamily_ConA-like_lec_gl,superfamily_Complement_control_module,superfamily_Fibronectin_type3,superfamily_Notch_dom,smart_LamG-like,smart_Notch_dom,smart_Sushi_SCR_CCP,pfscan_Sushi_SCR_CCP,tigrfam_Myxo_disulph_rpt	p.Q1160*	ENST00000328252.3	37	c.3478	CCDS6813.1	9	.	.	.	.	.	.	.	.	.	.	C	45	11.716299	0.99594	.	.	ENSG00000182752	ENST00000328252;ENST00000534838	.	.	.	5.86	5.86	0.93980	.	0.196564	0.53938	D	0.000046	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.4409	20.1865	0.98220	0.0:1.0:0.0:0.0	.	.	.	.	X	1160;198	.	ENSP00000330658:Q1160X	Q	+	1	0	PAPPA	118137041	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.574000	0.53863	2.775000	0.95449	0.655000	0.94253	CAG	PAPPA	-	NULL	ENSG00000182752		0.617	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PAPPA	HGNC	protein_coding	OTTHUMT00000055546.1	30	0.00	0	C	NM_002581		119097220	119097220	+1	no_errors	ENST00000328252	ensembl	human	known	69_37n	nonsense	30	33.33	15	SNP	1.000	T
PCCA	5095	genome.wustl.edu	37	13	101167710	101167710	+	Silent	SNP	C	C	T			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr13:101167710C>T	ENST00000376285.1	+	22	1967	c.1929C>T	c.(1927-1929)gcC>gcT	p.A643A	PCCA_ENST00000376286.4_Silent_p.A617A|PCCA_ENST00000376279.3_Intron	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide	643					biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|propionyl-CoA carboxylase activity (GO:0004658)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|prostate(1)|skin(2)	26	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	CCAGACTTGCCGCAGAATTGA	0.418											OREG0022490	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											0													76.0	71.0	73.0					13																	101167710		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			X14608	CCDS9496.2, CCDS45065.1, CCDS53878.1	13q32	2011-01-14	2010-04-30		ENSG00000175198	ENSG00000175198	6.4.1.3		8653	protein-coding gene	gene with protein product		232000	"""propionyl Coenzyme A carboxylase, alpha polypeptide"""			1427880	Standard	NM_000282		Approved		uc001voo.3	P05165	OTTHUMG00000017284	ENST00000376285.1:c.1929C>T	13.37:g.101167710C>T		1356	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	Silent	SNP	pfam_CbamoylP_synth_lsu-like_ATP-bd,pfam_CarbamoylP_synth_lsu_N,pfam_Biotin_COase_C,pfam_Biotin_lipoyl,pfam_Dala_Dala_lig_C,pfam_ATP-grasp_RimK-type,pfam_ATP-grasp_carboxylate-amine,superfamily_PreATP-grasp_fold,superfamily_Rudment_hybrid_motif,superfamily_Single_hybrid_motif,smart_Biotin_COase_C,pfscan_ATP-grasp,pfscan_Biotin_carboxylation_dom,pfscan_Biotin_lipoyl	p.A643	ENST00000376285.1	37	c.1929	CCDS9496.2	13																																																																																			PCCA	-	NULL	ENSG00000175198		0.418	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCCA	HGNC	protein_coding	OTTHUMT00000045627.2	66	0.00	0	C			101167710	101167710	+1	no_errors	ENST00000376285	ensembl	human	known	69_37n	silent	59	18.06	13	SNP	0.296	T
PIK3CA	5290	genome.wustl.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279		TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr3:178952085A>G	ENST00000263967.3	+	21	3297	c.3140A>G	c.(3139-3141)cAt>cGt	p.H1047R	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1047	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (in BC; unknown pathological significance). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16353168}.|H -> R (in CLOVE, KERSEB, CRC, BC and OC; also found in an endometrial carcinoma sample; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane). {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|H -> Y (in MCAP; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:16322209, 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.H1047R(1387)|p.H1047L(194)|p.H1047P(1)		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)	AATGATGCACATCATGGTGGC	0.378	H1047L(EFM19_BREAST)|H1047R(BT20_BREAST)|H1047R(CAL29_URINARY_TRACT)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(HCC1954_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(MCAS_OVARY)|H1047R(MDAMB453_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(RKO_LARGE_INTESTINE)|H1047R(SKOV3_OVARY)|H1047R(T47D_BREAST)	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"""	1582	Substitution - Missense(1582)	breast(961)|large_intestine(245)|endometrium(114)|ovary(77)|urinary_tract(36)|upper_aerodigestive_tract(26)|lung(19)|central_nervous_system(19)|stomach(19)|haematopoietic_and_lymphoid_tissue(11)|thyroid(10)|NS(9)|liver(7)|kidney(6)|soft_tissue(6)|skin(4)|prostate(4)|pituitary(3)|pancreas(3)|meninges(1)|cervix(1)|bone(1)											99.0	89.0	92.0					3																	178952085		1912	4130	6042	-	-	-	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.3140A>G	3.37:g.178952085A>G	ENSP00000263967:p.His1047Arg		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.H1047R	ENST00000263967.3	37	c.3140	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506328	0.44558	.	.	ENSG00000121879	ENST00000263967	T	0.80214	-1.35	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.62466	0.2430	N	0.08118	0	0.80722	D	1	P	0.38597	0.639	B	0.28011	0.085	T	0.67526	-0.5648	10	0.40728	T	0.16	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	R	1047	ENSP00000263967:H1047R	ENSP00000263967:H1047R	H	+	2	0	PIK3CA	180434779	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	CAT	PIK3CA	-	superfamily_Kinase-like_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	ENSG00000121879		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	62	0.00	0	A			178952085	178952085	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	50	60.63	77	SNP	1.000	G
PLIN4	729359	genome.wustl.edu	37	19	4512292	4512292	+	Silent	SNP	C	C	T			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr19:4512292C>T	ENST00000301286.3	-	3	1637	c.1638G>A	c.(1636-1638)gtG>gtA	p.V546V		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	546	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						TACCTATGACCACAGACTTGG	0.617																																						dbGAP											0													98.0	106.0	103.0					19																	4512292		1984	4155	6139	-	-	-	SO:0001819	synonymous_variant	0			AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.1638G>A	19.37:g.4512292C>T			A6NEI2	Silent	SNP	pfam_Perilipin,superfamily_Ankyrin_rpt-contain_dom	p.V546	ENST00000301286.3	37	c.1638	CCDS45927.1	19																																																																																			PLIN4	-	NULL	ENSG00000167676		0.617	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	PLIN4	HGNC	protein_coding	OTTHUMT00000395095.1	94	0.00	0	C	XM_170901		4512292	4512292	-1	no_errors	ENST00000301286	ensembl	human	novel	69_37n	silent	74	34.51	39	SNP	0.000	T
SLC30A6	55676	genome.wustl.edu	37	2	32445456	32445456	+	Missense_Mutation	SNP	T	T	G			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr2:32445456T>G	ENST00000282587.5	+	14	1097	c.1060T>G	c.(1060-1062)Tca>Gca	p.S354A	SLC30A6_ENST00000538303.1_Missense_Mutation_p.S325A|SLC30A6_ENST00000357055.3_Missense_Mutation_p.S157A|SLC30A6_ENST00000406369.1_Missense_Mutation_p.S280A|SLC30A6_ENST00000379343.2_Missense_Mutation_p.S394A|SLC30A6_ENST00000435660.1_Missense_Mutation_p.S331A	NM_017964.3	NP_060434.2	Q6NXT4	ZNT6_HUMAN	solute carrier family 30 (zinc transporter), member 6	354					cellular protein metabolic process (GO:0044267)|Golgi to endosome transport (GO:0006895)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(4)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					CCTAAACTTTTCAGATCATCA	0.423																																						dbGAP											0													148.0	132.0	137.0					2																	32445456		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK055663	CCDS1780.1, CCDS54341.1, CCDS54342.1, CCDS54343.1	2p22.3	2013-05-22			ENSG00000152683	ENSG00000152683		"""Solute carriers"""	19305	protein-coding gene	gene with protein product		611148					Standard	NM_017964		Approved	FLJ31101, ZNT6	uc002rof.2	Q6NXT4	OTTHUMG00000128456	ENST00000282587.5:c.1060T>G	2.37:g.32445456T>G	ENSP00000282587:p.Ser354Ala		A5YM45|B7Z901|Q8N5C9|Q96NC3	Missense_Mutation	SNP	pfam_Cation_efflux,tigrfam_Cation_efflux	p.S354A	ENST00000282587.5	37	c.1060	CCDS1780.1	2	.	.	.	.	.	.	.	.	.	.	T	9.866	1.197522	0.22037	.	.	ENSG00000152683	ENST00000379343;ENST00000282587;ENST00000435660;ENST00000538303;ENST00000357055;ENST00000406369	T;T	0.76448	-1.02;-1.02	5.74	-0.962	0.10333	.	0.585659	0.18336	N	0.144333	T	0.58119	0.2100	L	0.27053	0.805	0.22989	N	0.998462	B;B;B;B	0.10296	0.002;0.003;0.001;0.002	B;B;B;B	0.13407	0.002;0.004;0.009;0.002	T	0.38090	-0.9677	10	0.28530	T	0.3	-8.0735	5.127	0.14890	0.2009:0.242:0.0:0.5571	.	325;331;394;354	B7Z901;Q6NXT4-3;Q6NXT4-2;Q6NXT4	.;.;.;ZNT6_HUMAN	A	394;354;331;325;157;280	ENSP00000282587:S354A;ENSP00000440678:S325A	ENSP00000282587:S354A	S	+	1	0	SLC30A6	32298960	0.996000	0.38824	0.976000	0.42696	0.614000	0.37383	0.645000	0.24782	-0.394000	0.07727	-2.979000	0.00080	TCA	SLC30A6	-	NULL	ENSG00000152683		0.423	SLC30A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC30A6	HGNC	protein_coding	OTTHUMT00000250254.2	85	0.00	0	T			32445456	32445456	+1	no_errors	ENST00000282587	ensembl	human	known	69_37n	missense	94	30.37	41	SNP	0.973	G
SMARCD1	6602	genome.wustl.edu	37	12	50480656	50480656	+	Missense_Mutation	SNP	A	A	G			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr12:50480656A>G	ENST00000394963.4	+	4	924	c.526A>G	c.(526-528)Atc>Gtc	p.I176V	SMARCD1_ENST00000381513.4_Missense_Mutation_p.I176V|SMARCD1_ENST00000548573.1_5'Flank	NM_003076.4	NP_003067.3			SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1											NS(1)|breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	18						GAAACGTCCCATCAAGGTAAC	0.468																																						dbGAP											0													68.0	65.0	66.0					12																	50480656		2203	4300	6503	-	-	-	SO:0001583	missense	0			U66617	CCDS8797.2, CCDS8798.2	12q13-q14	2008-08-05			ENSG00000066117	ENSG00000066117			11106	protein-coding gene	gene with protein product		601735				8804307, 9693044, 12917342	Standard	NM_003076		Approved	BAF60A, Rsc6p, CRACD1	uc001rvx.4	Q96GM5	OTTHUMG00000150194	ENST00000394963.4:c.526A>G	12.37:g.50480656A>G	ENSP00000378414:p.Ile176Val			Missense_Mutation	SNP	pfam_SWIB_MDM2_domain,superfamily_SWIB_MDM2_domain,smart_SWIB_domain	p.I176V	ENST00000394963.4	37	c.526	CCDS8797.2	12	.	.	.	.	.	.	.	.	.	.	A	4.408	0.075407	0.08485	.	.	ENSG00000066117	ENST00000394963;ENST00000381513;ENST00000551966;ENST00000550477	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.29458	0.0734	N	0.19112	0.55	0.80722	D	1	B;B;B	0.29162	0.235;0.006;0.004	B;B;B	0.36186	0.219;0.01;0.009	T	0.06215	-1.0839	10	0.02654	T	1	-12.0705	15.2591	0.73606	1.0:0.0:0.0:0.0	.	176;176;176	B4DF50;Q96GM5-2;Q96GM5	.;.;SMRD1_HUMAN	V	176	ENSP00000378414:I176V;ENSP00000370924:I176V;ENSP00000447386:I176V;ENSP00000448030:I176V	ENSP00000370924:I176V	I	+	1	0	SMARCD1	48766923	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	9.047000	0.93823	2.248000	0.74166	0.459000	0.35465	ATC	SMARCD1	-	NULL	ENSG00000066117		0.468	SMARCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SMARCD1	HGNC	protein_coding	OTTHUMT00000316759.2	67	0.00	0	A	NM_003076		50480656	50480656	+1	no_errors	ENST00000394963	ensembl	human	known	69_37n	missense	75	21.65	21	SNP	1.000	G
TLN1	7094	genome.wustl.edu	37	9	35724267	35724267	+	Silent	SNP	C	C	T			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr9:35724267C>T	ENST00000314888.9	-	6	929	c.576G>A	c.(574-576)ctG>ctA	p.L192L	TLN1_ENST00000540444.1_Silent_p.L192L	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	192	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TCCTCCGCAGCAGCAGCGTCT	0.577																																						dbGAP											0													90.0	78.0	82.0					9																	35724267		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.576G>A	9.37:g.35724267C>T			A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Silent	SNP	pfam_Talin_cent,pfam_Vinculin-bd_dom,pfam_ILWEQ,pfam_FERM_N,pfam_FERM_central,pfam_Insln_rcpt_S1,superfamily_Talin_cent,superfamily_Vinculin/catenin,superfamily_FERM_central,smart_Band_41_domain,smart_ILWEQ,pfscan_FERM_domain,pfscan_ILWEQ	p.L192	ENST00000314888.9	37	c.576	CCDS35009.1	9																																																																																			TLN1	-	pfam_FERM_N,smart_Band_41_domain,pfscan_FERM_domain	ENSG00000137076		0.577	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TLN1	HGNC	protein_coding	OTTHUMT00000052353.2	46	0.00	0	C	NM_006289		35724267	35724267	-1	no_errors	ENST00000314888	ensembl	human	known	69_37n	silent	36	35.71	20	SNP	0.998	T
TMEM132B	114795	genome.wustl.edu	37	12	125834300	125834300	+	Missense_Mutation	SNP	A	A	G			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr12:125834300A>G	ENST00000299308.3	+	2	363	c.355A>G	c.(355-357)Aaa>Gaa	p.K119E	TMEM132B_ENST00000418253.2_3'UTR	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	119						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		CTTCAACTGGAAATTGAAATC	0.478																																						dbGAP											0													114.0	112.0	113.0					12																	125834300		1922	4145	6067	-	-	-	SO:0001583	missense	0			AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.355A>G	12.37:g.125834300A>G	ENSP00000299308:p.Lys119Glu		A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	NULL	p.K119E	ENST00000299308.3	37	c.355	CCDS41859.1	12	.	.	.	.	.	.	.	.	.	.	A	17.07	3.294785	0.60086	.	.	ENSG00000139364	ENST00000299308	T	0.15017	2.46	5.49	5.49	0.81192	.	.	.	.	.	T	0.22820	0.0551	L	0.60067	1.865	0.80722	D	1	P	0.44521	0.837	P	0.45276	0.475	T	0.01162	-1.1432	9	0.48119	T	0.1	.	11.575	0.50856	0.851:0.149:0.0:0.0	.	119	Q14DG7	T132B_HUMAN	E	119	ENSP00000299308:K119E	ENSP00000299308:K119E	K	+	1	0	TMEM132B	124400253	1.000000	0.71417	0.963000	0.40424	0.970000	0.65996	5.695000	0.68279	2.068000	0.61886	0.482000	0.46254	AAA	TMEM132B	-	NULL	ENSG00000139364		0.478	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TMEM132B	HGNC	protein_coding	OTTHUMT00000400043.1	40	0.00	0	A	NM_052907		125834300	125834300	+1	no_errors	ENST00000299308	ensembl	human	known	69_37n	missense	60	21.05	16	SNP	1.000	G
WAS	7454	genome.wustl.edu	37	X	48545241	48545241	+	Nonsense_Mutation	SNP	C	C	T			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chrX:48545241C>T	ENST00000376701.4	+	7	706	c.631C>T	c.(631-633)Cga>Tga	p.R211*	WAS_ENST00000483750.1_3'UTR	NM_000377.2	NP_000368.1	P42768	WASP_HUMAN	Wiskott-Aldrich syndrome	211					actin filament polymerization (GO:0030041)|actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|blood coagulation (GO:0007596)|defense response (GO:0006952)|endosomal transport (GO:0016197)|epidermis development (GO:0008544)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|protein complex assembly (GO:0006461)|regulation of catalytic activity (GO:0050790)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|phospholipase binding (GO:0043274)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28		all_lung(315;1.27e-10)				CACGAGTTCACGATACCGTGG	0.567			"""Mis, N, F, S"""			lymphoma																																dbGAP		X-linked recessive		Wiskott-Aldrich syndrome	X	Xp11.23-p11.22	7454	Wiskott-Aldrich syndrome		L	0			GRCh37	CM951331	WAS	M							89.0	70.0	76.0					X																	48545241		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AF115548	CCDS14303.1	Xp11.4-p11.21	2014-09-17	2012-07-12		ENSG00000015285	ENSG00000015285			12731	protein-coding gene	gene with protein product	"""eczema-thrombocytopenia"""	300392	"""thrombocytopenia 1 (X-linked)"", ""Wiskott-Aldrich syndrome (eczema-thrombocytopenia)"""	IMD2, THC		7795648	Standard	NM_000377		Approved	WASP	uc004dkm.4	P42768	OTTHUMG00000034483	ENST00000376701.4:c.631C>T	X.37:g.48545241C>T	ENSP00000365891:p.Arg211*		Q9BU11|Q9UNJ9	Nonsense_Mutation	SNP	pfam_EVH1,pfam_PAK_box_Rho-bd,pfam_WH2_dom,superfamily_WASP_C,smart_EVH1,smart_PAK_box_Rho-bd,smart_WH2_dom,pfscan_PAK_box_Rho-bd,pfscan_EVH1,pfscan_WH2_dom	p.R211*	ENST00000376701.4	37	c.631	CCDS14303.1	X	.	.	.	.	.	.	.	.	.	.	C	34	5.372758	0.95923	.	.	ENSG00000015285	ENST00000450772;ENST00000376701	.	.	.	4.39	1.22	0.21188	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.7992	10.8443	0.46735	0.6414:0.3586:0.0:0.0	.	.	.	.	X	211	.	ENSP00000365891:R211X	R	+	1	2	WAS	48430185	0.943000	0.32029	0.997000	0.53966	0.781000	0.44180	1.363000	0.34159	0.124000	0.18369	0.279000	0.19357	CGA	WAS	-	NULL	ENSG00000015285		0.567	WAS-007	KNOWN	basic|appris_principal|CCDS	protein_coding	WAS	HGNC	protein_coding	OTTHUMT00000083379.1	51	0.00	0	C	NM_000377		48545241	48545241	+1	no_errors	ENST00000376701	ensembl	human	known	69_37n	nonsense	60	22.08	17	SNP	0.953	T
ZC3H6	376940	genome.wustl.edu	37	2	113088873	113088873	+	Missense_Mutation	SNP	G	G	A			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr2:113088873G>A	ENST00000409871.1	+	12	2779	c.2378G>A	c.(2377-2379)aGt>aAt	p.S793N	AC115115.2_ENST00000607612.1_RNA|ZC3H6_ENST00000343936.4_Missense_Mutation_p.S793N	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	793							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						GGGAATGGAAGTGGTCACATA	0.458																																						dbGAP											0													104.0	100.0	101.0					2																	113088873		1898	4141	6039	-	-	-	SO:0001583	missense	0			AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"""Zinc fingers, CCCH-type domain containing"""	24762	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 6"""	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.2378G>A	2.37:g.113088873G>A	ENSP00000386764:p.Ser793Asn		A9JR71|Q6ZW96	Missense_Mutation	SNP	pfam_Znf_CCCH,smart_Znf_CCCH	p.S793N	ENST00000409871.1	37	c.2378	CCDS46393.1	2	.	.	.	.	.	.	.	.	.	.	G	16.84	3.234383	0.58886	.	.	ENSG00000188177	ENST00000409871;ENST00000343936;ENST00000542974	T;T	0.15372	2.43;2.43	5.7	5.7	0.88788	.	0.582566	0.20679	N	0.087692	T	0.14570	0.0352	L	0.38175	1.15	0.26360	N	0.977066	P	0.38922	0.651	B	0.32677	0.15	T	0.16217	-1.0410	10	0.56958	D	0.05	-8.3092	14.6543	0.68823	0.0:0.0:0.8546:0.1454	.	793	P61129	ZC3H6_HUMAN	N	793;793;770	ENSP00000386764:S793N;ENSP00000340298:S793N	ENSP00000340298:S793N	S	+	2	0	ZC3H6	112805344	0.980000	0.34600	0.994000	0.49952	0.960000	0.62799	3.040000	0.49799	2.691000	0.91804	0.655000	0.94253	AGT	ZC3H6	-	NULL	ENSG00000188177		0.458	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZC3H6	HGNC	protein_coding	OTTHUMT00000330551.1	51	0.00	0	G	NM_198581		113088873	113088873	+1	no_errors	ENST00000343936	ensembl	human	known	69_37n	missense	51	32.47	25	SNP	0.997	A
ZNF235	9310	genome.wustl.edu	37	19	44792859	44792859	+	Silent	SNP	T	T	C			TCGA-E9-A1NH-01A-11D-A14G-09	TCGA-E9-A1NH-11A-33D-A14G-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	13c312ec-0add-4758-ab8d-c193e2e08c6d	0ee95056-a7cc-415c-a487-3ad08604dfc0	g.chr19:44792859T>C	ENST00000291182.4	-	5	831	c.729A>G	c.(727-729)aaA>aaG	p.K243K	ZNF235_ENST00000589799.1_Intron|ZNF235_ENST00000589248.1_Intron	NM_004234.4	NP_004225.3	Q14590	ZN235_HUMAN	zinc finger protein 235	243					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29		Prostate(69;0.0352)|all_neural(266;0.116)				TTAGGGTATCTTTACCACAAT	0.383																																						dbGAP											0													109.0	110.0	110.0					19																	44792859		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			X78929	CCDS33048.1	19q13.2	2013-01-08	2002-11-04	2002-11-08	ENSG00000159917	ENSG00000159917		"""Zinc fingers, C2H2-type"", ""-"""	12866	protein-coding gene	gene with protein product		604749	"""zinc finger protein homologous to Zfp93 in mouse"""	ZNF270, ZFP93		7865130, 9570955	Standard	NM_004234		Approved	HZF6, ANF270	uc002oza.4	Q14590		ENST00000291182.4:c.729A>G	19.37:g.44792859T>C			B4DTQ7|O14898|O14899|Q17RR8	Silent	SNP	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.K243	ENST00000291182.4	37	c.729	CCDS33048.1	19																																																																																			ZNF235	-	NULL	ENSG00000159917		0.383	ZNF235-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF235	HGNC	protein_coding	OTTHUMT00000460732.1	95	0.00	0	T			44792859	44792859	-1	no_errors	ENST00000291182	ensembl	human	known	69_37n	silent	87	36.03	49	SNP	0.000	C
