#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
ABCA1	19	genome.wustl.edu	37	9	107550711	107550711	+	Missense_Mutation	SNP	C	C	G			TCGA-B6-A0RI-01A-11W-A071-09	TCGA-B6-A0RI-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	50d83050-b98c-4a1a-a673-91dbc67c37c6	71508273-8303-4261-bcf2-b5ace767bfe2	g.chr9:107550711C>G	ENST00000374736.3	-	45	6459	c.6065G>C	c.(6064-6066)gGc>gCc	p.G2022A		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	2022	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	CAGTACCTTGCCAACTTCTTT	0.493																																						dbGAP											0													161.0	159.0	160.0					9																	107550711		2203	4300	6503	-	-	-	SO:0001583	missense	0			AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"""ATP binding cassette transporters / subfamily A"""	29	protein-coding gene	gene with protein product	"""Tangier disease"""	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.6065G>C	9.37:g.107550711C>G	ENSP00000363868:p.Gly2022Ala	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	pfam_ABC_transporter-like,smart_AAA+_ATPase,pfscan_ABC_transporter-like	p.G2022A	ENST00000374736.3	37	c.6065	CCDS6762.1	9	.	.	.	.	.	.	.	.	.	.	C	7.856	0.725125	0.15439	.	.	ENSG00000165029	ENST00000374736	D	0.93488	-3.23	6.02	6.02	0.97574	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.091610	0.85682	D	0.000000	T	0.81602	0.4857	N	0.01257	-0.925	0.80722	D	1	B	0.02656	0.0	B	0.11329	0.006	T	0.78380	-0.2226	10	0.05620	T	0.96	.	20.6085	0.99466	0.0:1.0:0.0:0.0	.	2022	O95477	ABCA1_HUMAN	A	2022	ENSP00000363868:G2022A	ENSP00000363868:G2022A	G	-	2	0	ABCA1	106590532	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	4.043000	0.57354	2.866000	0.98385	0.650000	0.86243	GGC	ABCA1	-	pfam_ABC_transporter-like,smart_AAA+_ATPase,pfscan_ABC_transporter-like	ENSG00000165029		0.493	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	ABCA1	HGNC	protein_coding	OTTHUMT00000053491.1	291	0.00	0	C	NM_005502		107550711	107550711	-1	no_errors	ENST00000374736	ensembl	human	known	69_37n	missense	203	34.94	109	SNP	1.000	G
CTCF	10664	genome.wustl.edu	37	16	67645518	67645518	+	Splice_Site	SNP	T	T	G			TCGA-B6-A0RI-01A-11W-A071-09	TCGA-B6-A0RI-10A-01W-A071-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	50d83050-b98c-4a1a-a673-91dbc67c37c6	71508273-8303-4261-bcf2-b5ace767bfe2	g.chr16:67645518T>G	ENST00000264010.4	+	3	1225		c.e3+2		CTCF_ENST00000401394.1_Intron|AC009095.4_ENST00000388909.4_RNA	NM_006565.3	NP_006556.1	P49711	CTCF_HUMAN	CCCTC-binding factor (zinc finger protein)						chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|DNA methylation (GO:0006306)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome positioning (GO:0016584)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone acetylation (GO:0035065)|regulation of histone methylation (GO:0031060)|regulation of molecular function, epigenetic (GO:0040030)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin insulator sequence binding (GO:0043035)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(6)|central_nervous_system(2)|cervix(1)|endometrium(34)|haematopoietic_and_lymphoid_tissue(7)|kidney(3)|large_intestine(9)|liver(1)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	79		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		AAAAGAAAGGTAAAACGAGTT	0.358																																					Colon(175;1200 1966 6945 23069 27405)	dbGAP											0													43.0	48.0	46.0					16																	67645518		2184	4262	6446	-	-	-	SO:0001630	splice_region_variant	0			U25435	CCDS10841.1, CCDS54029.1	16q21-q22.3	2013-01-08			ENSG00000102974	ENSG00000102974		"""Zinc fingers, C2H2-type"""	13723	protein-coding gene	gene with protein product	"""11 zinc finger transcriptional repressor"""	604167				8649389, 18550811	Standard	NM_006565		Approved		uc002etl.3	P49711	OTTHUMG00000137539	ENST00000264010.4:c.781+2T>G	16.37:g.67645518T>G		Somatic		WXS	Illumina GAIIx	Phase_IV	B5MC38|Q53XI7|Q59EL8	Splice_Site	SNP	-	e1+2	ENST00000264010.4	37	c.781+2	CCDS10841.1	16	.	.	.	.	.	.	.	.	.	.	T	17.89	3.498912	0.64298	.	.	ENSG00000102974	ENST00000264010	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5974	0.76595	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	CTCF	66203019	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	4.122000	0.57910	2.271000	0.75665	0.533000	0.62120	.	CTCF	-	-	ENSG00000102974		0.358	CTCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CTCF	HGNC	protein_coding	OTTHUMT00000268870.2	155	0.00	0	T	NM_006565	Intron	67645518	67645518	+1	no_errors	ENST00000264010	ensembl	human	known	69_37n	splice_site	26	69.77	60	SNP	1.000	G
NDUFA6-AS1	100132273	genome.wustl.edu	37	22	42537329	42537329	+	RNA	SNP	C	C	T			TCGA-B6-A0RI-01A-11W-A071-09	TCGA-B6-A0RI-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	50d83050-b98c-4a1a-a673-91dbc67c37c6	71508273-8303-4261-bcf2-b5ace767bfe2	g.chr22:42537329C>T	ENST00000416037.2	+	0	8970				CYP2D7P1_ENST00000358097.4_RNA|RP4-669P10.16_ENST00000428786.1_RNA|CYP2D7P1_ENST00000433992.1_RNA|CYP2D7P1_ENST00000424775.1_RNA	NR_034118.1				NDUFA6 antisense RNA 1 (head to head)																		ATCACGTCGTCGATCTCCTGT	0.592																																						dbGAP											0																																										-	-	-			0			BC039542		22q13.2	2013-03-18	2013-03-18		ENSG00000237037	ENSG00000237037		"""Long non-coding RNAs"""	45273	non-coding RNA	RNA, long non-coding							Standard	NR_034118		Approved		uc003bcd.1		OTTHUMG00000150917		22.37:g.42537329C>T		Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	NULL	p.R355Q	ENST00000416037.2	37	c.1064		22	.	.	.	.	.	.	.	.	.	.	c	12.99	2.104459	0.37145	.	.	ENSG00000205702	ENST00000428297;ENST00000354609;ENST00000381321;ENST00000436260	.	.	.	3.91	3.91	0.45181	.	0.000000	0.85682	D	0.000000	T	0.44973	0.1319	.	.	.	0.80722	D	1	P	0.43607	0.812	B	0.36808	0.233	T	0.55585	-0.8118	8	0.59425	D	0.04	.	15.2436	0.73490	0.0:1.0:0.0:0.0	.	246	F5H167	.	N	335;284;282;246	.	ENSP00000442416:D284N	D	-	1	0	CYP2D7P1	40867273	0.974000	0.33945	0.966000	0.40874	0.684000	0.39900	2.500000	0.45381	2.156000	0.67533	0.508000	0.49915	GAC	CYP2D7P1	-	NULL	ENSG00000205702		0.592	NDUFA6-AS1-001	KNOWN	basic|exp_conf	antisense	CYP2D7P1	HGNC	processed_transcript	OTTHUMT00000320522.4	43	0.00	0	C	NR_034118		42537329	42537329	-1	pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000433992	ensembl	human	known	69_37n	missense	11	26.67	4	SNP	0.981	T
FAM49B	51571	genome.wustl.edu	37	8	130891697	130891697	+	Missense_Mutation	SNP	A	A	C			TCGA-B6-A0RI-01A-11W-A071-09	TCGA-B6-A0RI-10A-01W-A071-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	50d83050-b98c-4a1a-a673-91dbc67c37c6	71508273-8303-4261-bcf2-b5ace767bfe2	g.chr8:130891697A>C	ENST00000519824.2	-	3	284	c.11T>G	c.(10-12)cTt>cGt	p.L4R	FAM49B_ENST00000519540.1_Missense_Mutation_p.L4R|FAM49B_ENST00000517654.1_Missense_Mutation_p.L4R|FAM49B_ENST00000522250.1_Intron|FAM49B_ENST00000401979.2_Missense_Mutation_p.L4R|FAM49B_ENST00000522941.1_Intron|FAM49B_ENST00000523509.1_Missense_Mutation_p.L4R|FAM49B_ENST00000522746.1_Missense_Mutation_p.L4R|FAM49B_ENST00000519110.1_Missense_Mutation_p.L4R|FAM49B_ENST00000518879.1_Intron	NM_016623.4	NP_057707.3	Q9NUQ9	FA49B_HUMAN	family with sequence similarity 49, member B	4						cilium (GO:0005929)|extracellular vesicular exosome (GO:0070062)				kidney(1)|large_intestine(6)|lung(4)|prostate(1)	12	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)			AACTTTAAGAAGATTCCCCAT	0.328																																						dbGAP											0													79.0	81.0	81.0					8																	130891697		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF208851	CCDS6361.1	8q24	2004-08-20				ENSG00000153310			25216	protein-coding gene	gene with protein product							Standard	NM_001256763		Approved	BM-009	uc003ysu.4	Q9NUQ9		ENST00000519824.2:c.11T>G	8.37:g.130891697A>C	ENSP00000429150:p.Leu4Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	Q96AZ5|Q9NW21|Q9NZE7	Missense_Mutation	SNP	pfam_DUF1394	p.L4R	ENST00000519824.2	37	c.11	CCDS6361.1	8	.	.	.	.	.	.	.	.	.	.	A	17.22	3.333897	0.60853	.	.	ENSG00000153310	ENST00000522746;ENST00000523509;ENST00000401979;ENST00000519110;ENST00000519824;ENST00000517654;ENST00000519540;ENST00000519142;ENST00000520204;ENST00000518283;ENST00000523993;ENST00000520254;ENST00000519020;ENST00000518167;ENST00000517672;ENST00000519070;ENST00000522361	T;T;T;T;T;T;T	0.59224	0.28;0.28;0.28;0.28;0.28;0.28;0.28	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.79240	0.4412	M	0.87547	2.89	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.83168	-0.0095	10	0.87932	D	0	-12.4075	15.3479	0.74355	1.0:0.0:0.0:0.0	.	4	Q9NUQ9	FA49B_HUMAN	R	4	ENSP00000428117:L4R;ENSP00000429802:L4R;ENSP00000384880:L4R;ENSP00000429078:L4R;ENSP00000429150:L4R;ENSP00000430674:L4R;ENSP00000429499:L4R	ENSP00000384880:L4R	L	-	2	0	FAM49B	130960879	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.701000	0.91331	2.210000	0.71456	0.533000	0.62120	CTT	FAM49B	-	NULL	ENSG00000153310		0.328	FAM49B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM49B	HGNC	protein_coding	OTTHUMT00000380390.2	229	0.00	0	A	NM_016623		130891697	130891697	-1	no_errors	ENST00000401979	ensembl	human	known	69_37n	missense	127	40.93	88	SNP	1.000	C
FTMT	94033	genome.wustl.edu	37	5	121187814	121187814	+	Silent	SNP	C	C	T			TCGA-B6-A0RI-01A-11W-A071-09	TCGA-B6-A0RI-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	50d83050-b98c-4a1a-a673-91dbc67c37c6	71508273-8303-4261-bcf2-b5ace767bfe2	g.chr5:121187814C>T	ENST00000321339.1	+	1	165	c.156C>T	c.(154-156)gcC>gcT	p.A52A		NM_177478.1	NP_803431.1	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial	52					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lyase activity (GO:0051349)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of transferase activity (GO:0051347)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ferric iron binding (GO:0008199)|ferroxidase activity (GO:0004322)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	33		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)		TGGCCGCAGCCGCCTCCTCCC	0.771																																						dbGAP											0													6.0	8.0	8.0					5																	121187814		2092	4126	6218	-	-	-	SO:0001819	synonymous_variant	0			BC034419	CCDS4128.1	5q23.1	2008-02-05			ENSG00000181867	ENSG00000181867			17345	protein-coding gene	gene with protein product		608847				11323407	Standard	NM_177478		Approved	MtF	uc003kss.3	Q8N4E7	OTTHUMG00000128912	ENST00000321339.1:c.156C>T	5.37:g.121187814C>T		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	pfam_Ferritin_DPS_dom,superfamily_Ferritin/RR-like,pfscan_Ferritin-like_diiron	p.A52	ENST00000321339.1	37	c.156	CCDS4128.1	5																																																																																			FTMT	-	NULL	ENSG00000181867		0.771	FTMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FTMT	HGNC	protein_coding	OTTHUMT00000250884.1	21	0.00	0	C	NM_177478		121187814	121187814	+1	no_errors	ENST00000321339	ensembl	human	known	69_37n	silent	15	28.57	6	SNP	0.000	T
IL21	59067	genome.wustl.edu	37	4	123536991	123536991	+	Splice_Site	SNP	G	G	T			TCGA-B6-A0RI-01A-11W-A071-09	TCGA-B6-A0RI-10A-01W-A071-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	50d83050-b98c-4a1a-a673-91dbc67c37c6	71508273-8303-4261-bcf2-b5ace767bfe2	g.chr4:123536991G>T	ENST00000264497.3	-	3	263	c.206C>A	c.(205-207)aCa>aAa	p.T69K		NM_001207006.2|NM_021803.3	NP_001193935.1|NP_068575.1	Q9HBE4	IL21_HUMAN	interleukin 21	62					cell maturation (GO:0048469)|immune response (GO:0006955)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of natural killer cell cytokine production (GO:0002729)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tissue remodeling (GO:0034105)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	cytokine receptor binding (GO:0005126)|interleukin-2 receptor binding (GO:0005134)			NS(1)|kidney(1)|large_intestine(2)|liver(1)|lung(3)	8						CTCACAGTTTGTCTGAAAGAT	0.328																																						dbGAP											0													90.0	89.0	89.0					4																	123536991		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0			AF254069	CCDS3727.1, CCDS75189.1	4q26-q27	2011-07-15			ENSG00000138684	ENSG00000138684		"""Interleukins and interleukin receptors"""	6005	protein-coding gene	gene with protein product		605384				11081504, 17947662	Standard	NM_001207006		Approved	Za11, IL-21	uc003ies.3	Q9HBE4	OTTHUMG00000133073	ENST00000264497.3:c.205-1C>A	4.37:g.123536991G>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A5J0L4	Missense_Mutation	SNP	pfam_Interleukin_15-like	p.T69K	ENST00000264497.3	37	c.206	CCDS3727.1	4	.	.	.	.	.	.	.	.	.	.	G	1.796	-0.478179	0.04414	.	.	ENSG00000138684	ENST00000264497	.	.	.	5.12	-1.82	0.07857	.	1.007950	0.07961	N	0.982368	T	0.12347	0.0300	N	0.03608	-0.345	0.23879	N	0.99658	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31223	-0.9951	9	0.06365	T	0.9	-3.3485	5.7131	0.17945	0.0:0.271:0.1645:0.5646	.	62;62	Q9HBE4-2;Q9HBE4	.;IL21_HUMAN	K	69	.	ENSP00000264497:T69K	T	-	2	0	IL21	123756441	0.123000	0.22298	0.924000	0.36721	0.934000	0.57294	-0.939000	0.03933	-0.241000	0.09681	-0.344000	0.07964	ACA	IL21	-	pfam_Interleukin_15-like	ENSG00000138684		0.328	IL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IL21	HGNC	protein_coding	OTTHUMT00000256713.1	201	0.00	0	G	NM_021803	Missense_Mutation	123536991	123536991	-1	no_errors	ENST00000264497	ensembl	human	known	69_37n	missense	132	32.65	64	SNP	0.772	T
LRBA	987	genome.wustl.edu	37	4	151392804	151392804	+	Silent	SNP	C	C	T			TCGA-B6-A0RI-01A-11W-A071-09	TCGA-B6-A0RI-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	50d83050-b98c-4a1a-a673-91dbc67c37c6	71508273-8303-4261-bcf2-b5ace767bfe2	g.chr4:151392804C>T	ENST00000357115.3	-	44	6915	c.6672G>A	c.(6670-6672)gaG>gaA	p.E2224E	LRBA_ENST00000507224.1_Silent_p.E2213E|LRBA_ENST00000535741.1_Silent_p.E2213E|LRBA_ENST00000510413.1_Silent_p.E2213E|LRBA_ENST00000503716.1_5'UTR	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	2224	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.					cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					ACATCAAGTACTCAAAATTAG	0.318																																						dbGAP											0													121.0	120.0	120.0					4																	151392804		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"""WD repeat domain containing"""	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.6672G>A	4.37:g.151392804C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	pfam_BEACH_dom,pfam_DUF1088,pfam_WD40_repeat,superfamily_BEACH_dom,superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_BEACH_dom	p.S866N	ENST00000357115.3	37	c.2597	CCDS3773.1	4	.	.	.	.	.	.	.	.	.	.	C	8.139	0.784908	0.16189	.	.	ENSG00000198589	ENST00000509835	.	.	.	5.28	1.66	0.24008	.	.	.	.	.	T	0.57051	0.2027	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47812	-0.9088	4	.	.	.	.	8.4244	0.32720	0.0:0.5202:0.0:0.4798	.	.	.	.	N	866	.	.	S	-	2	0	LRBA	151612254	0.995000	0.38212	0.998000	0.56505	0.965000	0.64279	0.363000	0.20301	0.055000	0.16094	-0.145000	0.13849	AGT	LRBA	-	pfam_BEACH_dom,superfamily_BEACH_dom,pfscan_BEACH_dom	ENSG00000198589		0.318	LRBA-002	KNOWN	basic|CCDS	protein_coding	LRBA	HGNC	protein_coding	OTTHUMT00000364939.1	190	0.00	0	C			151392804	151392804	-1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000509835	ensembl	human	novel	69_37n	missense	177	30.04	76	SNP	0.992	T
OR56B4	196335	genome.wustl.edu	37	11	6129525	6129526	+	In_Frame_Ins	INS	-	-	ACT			TCGA-B6-A0RI-01A-11W-A071-09	TCGA-B6-A0RI-10A-01W-A071-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	50d83050-b98c-4a1a-a673-91dbc67c37c6	71508273-8303-4261-bcf2-b5ace767bfe2	g.chr11:6129525_6129526insACT	ENST00000316529.3	+	1	612_613	c.517_518insACT	c.(517-519)cac>cACTac	p.174_175insY	RP11-290F24.3_ENST00000529961.1_RNA	NM_001005181.1	NP_001005181.1	Q8NH76	O56B4_HUMAN	olfactory receptor, family 56, subfamily B, member 4	174						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(1)|lung(10)|skin(6)|urinary_tract(2)	21		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.31e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGCCCAGAGACACTACTGTTCC	0.48																																						dbGAP											0																																										-	-	-	SO:0001652	inframe_insertion	0			AB065513	CCDS31406.1	11p15.4	2012-08-09			ENSG00000180919	ENSG00000180919		"""GPCR / Class A : Olfactory receptors"""	15248	protein-coding gene	gene with protein product							Standard	NM_001005181		Approved		uc010qzx.2	Q8NH76	OTTHUMG00000165531	ENST00000316529.3:c.521_523dupACT	11.37:g.6129529_6129531dupACT	ENSP00000321196:p.Tyr174_Tyr174dup	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6IFD7	In_Frame_Ins	INS	pfam_7TM_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,prints_Olfact_rcpt,pfscan_GPCR_Rhodpsn_supfam	p.175in_frame_insY	ENST00000316529.3	37	c.517_518	CCDS31406.1	11																																																																																			OR56B4	-	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam	ENSG00000180919		0.480	OR56B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR56B4	HGNC	protein_coding	OTTHUMT00000384668.1	341	0.00	0	-	NM_001005181		6129525	6129526	+1	no_errors	ENST00000316529	ensembl	human	known	69_37n	in_frame_ins	289	25.32	98	INS	0.000:0.000	ACT
PKN2	5586	genome.wustl.edu	37	1	89299057	89299057	+	Nonsense_Mutation	SNP	C	C	T			TCGA-B6-A0RI-01A-11W-A071-09	TCGA-B6-A0RI-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	50d83050-b98c-4a1a-a673-91dbc67c37c6	71508273-8303-4261-bcf2-b5ace767bfe2	g.chr1:89299057C>T	ENST00000370521.3	+	22	3240	c.2881C>T	c.(2881-2883)Cga>Tga	p.R961*	PKN2_ENST00000370505.3_Nonsense_Mutation_p.R804*|PKN2_ENST00000370513.5_Nonsense_Mutation_p.R913*|PKN2_ENST00000495119.1_3'UTR|PKN2_ENST00000544045.1_Nonsense_Mutation_p.R635*	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	961	AGC-kinase C-terminal.|Necessary for the catalytic activity.				apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.R961*(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		GACTCCACCTCGAGAACCAAG	0.403																																						dbGAP											1	Substitution - Nonsense(1)	large_intestine(1)											99.0	96.0	97.0					1																	89299057		1943	4118	6061	-	-	-	SO:0001587	stop_gained	0			U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"""cardiolipin-activated protein kinase Pak2"""	602549	"""protein kinase C-like 2"""	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.2881C>T	1.37:g.89299057C>T	ENSP00000359552:p.Arg961*	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Nonsense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_HR1_rho-bd,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Pkinase_C,superfamily_Kinase-like_dom,superfamily_HR1_rho-bd,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_HR1_rho-bd,smart_C2_Ca-dep,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_AGC-kinase_C,pfscan_Prot_kinase_cat_dom	p.R961*	ENST00000370521.3	37	c.2881	CCDS714.1	1	.	.	.	.	.	.	.	.	.	.	C	38	7.219799	0.98143	.	.	ENSG00000065243	ENST00000370521;ENST00000370505;ENST00000370513;ENST00000544045	.	.	.	5.84	5.84	0.93424	.	0.000000	0.37577	U	0.002027	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.3881	0.83523	0.1322:0.8678:0.0:0.0	.	.	.	.	X	961;804;913;635	.	ENSP00000359536:R804X	R	+	1	2	PKN2	89071645	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.560000	0.60802	2.758000	0.94735	0.591000	0.81541	CGA	PKN2	-	pfam_Pkinase_C,superfamily_Kinase-like_dom,smart_AGC-kinase_C	ENSG00000065243		0.403	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PKN2	HGNC	protein_coding	OTTHUMT00000027828.3	154	0.00	0	C	NM_006256		89299057	89299057	+1	no_errors	ENST00000370521	ensembl	human	known	69_37n	nonsense	104	27.78	40	SNP	1.000	T
PRKAR1B	5575	genome.wustl.edu	37	7	720280	720281	+	Frame_Shift_Ins	INS	-	-	G	rs545804273		TCGA-B6-A0RI-01A-11W-A071-09	TCGA-B6-A0RI-10A-01W-A071-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	50d83050-b98c-4a1a-a673-91dbc67c37c6	71508273-8303-4261-bcf2-b5ace767bfe2	g.chr7:720280_720281insG	ENST00000406797.1	-	3	434_435	c.260_261insC	c.(259-261)ccgfs	p.P87fs	PRKAR1B_ENST00000403562.1_Frame_Shift_Ins_p.P87fs|PRKAR1B_ENST00000537384.1_Frame_Shift_Ins_p.P87fs|PRKAR1B_ENST00000544935.1_Frame_Shift_Ins_p.P87fs|PRKAR1B_ENST00000360274.4_Frame_Shift_Ins_p.P87fs	NM_001164761.1	NP_001158233.1	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, beta	87	Dimerization and phosphorylation.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)			endometrium(4)|large_intestine(1)|liver(1)|lung(10)|prostate(1)	17		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		CCACAGGGTTCGGGGGGGTGGG	0.619																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			M65066	CCDS34579.1	7p22.3	2013-09-19			ENSG00000188191	ENSG00000188191	2.7.11.1		9390	protein-coding gene	gene with protein product		176911				1358799, 3479018	Standard	NM_002735		Approved		uc003siw.2	P31321	OTTHUMG00000151411	ENST00000406797.1:c.261dupC	7.37:g.720287_720287dupG	ENSP00000385749:p.Pro87fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8N422	Frame_Shift_Ins	INS	pfam_cNMP-bd_dom,pfam_cAMP_dep_PK_reg_su_I/II_a/b,superfamily_cNMP-bd-like,superfamily_cAMP_dep_PK_reg_su_I/II_a/b,smart_cAMP_dep_PK_reg_su_I/II_a/b,smart_cNMP-bd_dom,pirsf_cAMP_dep_PK_reg_su,pfscan_cNMP-bd_dom,prints_cAMP/cGMP_kin	p.N88fs	ENST00000406797.1	37	c.261_260	CCDS34579.1	7																																																																																			PRKAR1B	-	pirsf_cAMP_dep_PK_reg_su	ENSG00000188191		0.619	PRKAR1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	PRKAR1B	HGNC	protein_coding	OTTHUMT00000322525.1	32	0.00	0	-			720280	720281	-1	no_errors	ENST00000360274	ensembl	human	known	69_37n	frame_shift_ins	32	15.79	6	INS	0.026:0.998	G
RHBDF2	79651	genome.wustl.edu	37	17	74473336	74473337	+	Frame_Shift_Ins	INS	-	-	G			TCGA-B6-A0RI-01A-11W-A071-09	TCGA-B6-A0RI-10A-01W-A071-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	50d83050-b98c-4a1a-a673-91dbc67c37c6	71508273-8303-4261-bcf2-b5ace767bfe2	g.chr17:74473336_74473337insG	ENST00000313080.4	-	8	1205_1206	c.932_933insC	c.(931-933)ccafs	p.P311fs	RHBDF2_ENST00000389760.4_Frame_Shift_Ins_p.P282fs|RHBDF2_ENST00000592378.1_5'Flank|RHBDF2_ENST00000591885.1_Frame_Shift_Ins_p.P282fs	NM_024599.5	NP_078875.4	Q6PJF5	RHDF2_HUMAN	rhomboid 5 homolog 2 (Drosophila)	311					negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(4)|skin(1)	27						TGGCAGAGAGTGGGGGGGACTC	0.584																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			BC016034	CCDS32743.1, CCDS32744.1	17q25.3	2014-09-17	2006-02-22	2006-02-22		ENSG00000129667			20788	protein-coding gene	gene with protein product		614404	"""rhomboid, veinlet-like 6 (Drosophila)"", ""tylosis with oesophageal cancer"""	RHBDL6, TOC		12838346, 22265016	Standard	NM_024599		Approved	FLJ22341, RHBDL5, TOCG	uc002jrq.2	Q6PJF5		ENST00000313080.4:c.933dupC	17.37:g.74473343_74473343dupG	ENSP00000322775:p.Pro311fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NEM3|A8K801|Q5U607|Q5YGQ8|Q9H6E9	Frame_Shift_Ins	INS	pfam_Rhomboid_SP,pfam_Peptidase_S54_rhomboid_dom	p.L312fs	ENST00000313080.4	37	c.933_932	CCDS32743.1	17																																																																																			RHBDF2	-	pfam_Rhomboid_SP	ENSG00000129667		0.584	RHBDF2-001	KNOWN	basic|CCDS	protein_coding	RHBDF2	HGNC	protein_coding	OTTHUMT00000450134.1	20	0.00	0	-	NM_024599		74473336	74473337	-1	no_errors	ENST00000313080	ensembl	human	known	69_37n	frame_shift_ins	14	22.22	4	INS	0.581:1.000	G
SLC26A4	5172	genome.wustl.edu	37	7	107342369	107342370	+	Frame_Shift_Ins	INS	-	-	A	rs142104908		TCGA-B6-A0RI-01A-11W-A071-09	TCGA-B6-A0RI-10A-01W-A071-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	50d83050-b98c-4a1a-a673-91dbc67c37c6	71508273-8303-4261-bcf2-b5ace767bfe2	g.chr7:107342369_107342370insA	ENST00000265715.3	+	17	2125_2126	c.1901_1902insA	c.(1900-1905)atagagfs	p.E635fs	SLC26A4_ENST00000543100.1_Frame_Shift_Ins_p.E204fs|SLC26A4_ENST00000544569.1_Frame_Shift_Ins_p.E222fs|SLC26A4_ENST00000541474.1_Frame_Shift_Ins_p.E196fs	NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	635	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				chloride transmembrane transport (GO:1902476)|inorganic anion transport (GO:0015698)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|regulation of protein localization (GO:0032880)|sensory perception of sound (GO:0007605)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chloride transmembrane transporter activity (GO:0015108)|iodide transmembrane transporter activity (GO:0015111)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(8)|lung(16)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						ACCAAGGAAATAGAGATTCAAG	0.416									Pendred syndrome																													dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0	Familial Cancer Database	Goiter-Deafness syndrome	AF030880	CCDS5746.1	7q31	2013-07-18	2013-07-18		ENSG00000091137	ENSG00000091137		"""Solute carriers"""	8818	protein-coding gene	gene with protein product	"""pendrin"""	605646	"""solute carrier family 26, member 4"""	DFNB4		9500541, 11087667	Standard	NM_000441		Approved	PDS	uc003vep.3	O43511	OTTHUMG00000154807	ENST00000265715.3:c.1902dupA	7.37:g.107342370_107342370dupA	ENSP00000265715:p.Glu635fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z266|O43170	Frame_Shift_Ins	INS	pfam_Sulph_transpt,pfam_STAS_dom,superfamily_STAS_dom,pfscan_STAS_dom,tigrfam_SulP_transpt	p.E635fs	ENST00000265715.3	37	c.1901_1902	CCDS5746.1	7																																																																																			SLC26A4	-	pfam_STAS_dom,superfamily_STAS_dom,pfscan_STAS_dom,tigrfam_SulP_transpt	ENSG00000091137		0.416	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC26A4	HGNC	protein_coding	OTTHUMT00000337148.1	125	0.00	0	-	NM_000441		107342369	107342370	+1	no_errors	ENST00000265715	ensembl	human	known	69_37n	frame_shift_ins	102	33.33	51	INS	1.000:0.980	A
SPEN	23013	genome.wustl.edu	37	1	16263797	16263797	+	Missense_Mutation	SNP	C	C	G	rs528449671		TCGA-B6-A0RI-01A-11W-A071-09	TCGA-B6-A0RI-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	50d83050-b98c-4a1a-a673-91dbc67c37c6	71508273-8303-4261-bcf2-b5ace767bfe2	g.chr1:16263797C>G	ENST00000375759.3	+	12	10370	c.10166C>G	c.(10165-10167)tCc>tGc	p.S3389C		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	3389	Pro-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		CCTCAAGTGTCCCAGGAGGCA	0.667																																						dbGAP											0													58.0	67.0	64.0					1																	16263797		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.10166C>G	1.37:g.16263797C>G	ENSP00000364912:p.Ser3389Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	pfam_RRM_dom,pfam_SPOC_C,superfamily_SPOC-like,smart_RRM_dom,pfscan_SPOC_met,pfscan_RRM_dom	p.S3389C	ENST00000375759.3	37	c.10166	CCDS164.1	1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.722406	0.48728	.	.	ENSG00000065526	ENST00000375759	T	0.10005	2.92	5.25	5.25	0.73442	.	.	.	.	.	T	0.30603	0.0770	M	0.65975	2.015	0.37745	D	0.925771	D	0.76494	0.999	D	0.71414	0.973	T	0.05321	-1.0892	9	0.66056	D	0.02	-17.3146	14.7724	0.69691	0.0:0.8558:0.1442:0.0	.	3389	Q96T58	MINT_HUMAN	C	3389	ENSP00000364912:S3389C	ENSP00000364912:S3389C	S	+	2	0	SPEN	16136384	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	4.393000	0.59665	2.591000	0.87537	0.563000	0.77884	TCC	SPEN	-	NULL	ENSG00000065526		0.667	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SPEN	HGNC	protein_coding	OTTHUMT00000025993.1	55	0.00	0	C	NM_015001		16263797	16263797	+1	no_errors	ENST00000375759	ensembl	human	known	69_37n	missense	38	13.64	6	SNP	1.000	G
SPG20	23111	genome.wustl.edu	37	13	36886475	36886475	+	Silent	SNP	T	T	G			TCGA-B6-A0RI-01A-11W-A071-09	TCGA-B6-A0RI-10A-01W-A071-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	50d83050-b98c-4a1a-a673-91dbc67c37c6	71508273-8303-4261-bcf2-b5ace767bfe2	g.chr13:36886475T>G	ENST00000451493.1	-	7	1840	c.1623A>C	c.(1621-1623)gtA>gtC	p.V541V	SPG20_ENST00000494062.2_Silent_p.V541V|SPG20_ENST00000438666.2_Silent_p.V541V|SPG20_ENST00000355182.4_Silent_p.V541V	NM_001142295.1	NP_001135767.1	Q8N0X7	SPG20_HUMAN	spastic paraplegia 20 (Troyer syndrome)	541					abscission (GO:0009838)|adipose tissue development (GO:0060612)|cell death (GO:0008219)|cell division (GO:0051301)|lipid particle organization (GO:0034389)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of collateral sprouting in absence of injury (GO:0048698)|neuromuscular process (GO:0050905)|regulation of mitochondrial membrane potential (GO:0051881)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)|midbody (GO:0030496)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	27		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;2.42e-08)|Epithelial(112;1.58e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00128)|BRCA - Breast invasive adenocarcinoma(63;0.0125)|GBM - Glioblastoma multiforme(144;0.026)		TACTTGCTGCTACAACCATAG	0.378																																						dbGAP											0													136.0	135.0	136.0					13																	36886475		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB011182	CCDS9356.1	13q13.1	2008-07-04	2007-04-23		ENSG00000133104	ENSG00000133104			18514	protein-coding gene	gene with protein product	"""spartin"""	607111				6022528, 12134148	Standard	NM_001142294		Approved	KIAA0610, TAHCCP1	uc001uvm.3	Q8N0X7	OTTHUMG00000016730	ENST00000451493.1:c.1623A>C	13.37:g.36886475T>G		Somatic		WXS	Illumina GAIIx	Phase_IV	O60349|Q86Y67|Q9H1T2|Q9H1T3	Silent	SNP	pfam_Senescence/spartin,pfam_MIT,smart_MIT	p.V541	ENST00000451493.1	37	c.1623	CCDS9356.1	13																																																																																			SPG20	-	pfam_Senescence/spartin	ENSG00000133104		0.378	SPG20-202	KNOWN	basic|appris_principal|CCDS	protein_coding	SPG20	HGNC	protein_coding	OTTHUMT00000044494.2	485	0.00	0	T			36886475	36886475	-1	no_errors	ENST00000355182	ensembl	human	known	69_37n	silent	326	31.87	153	SNP	0.998	G
TBX3	6926	genome.wustl.edu	37	12	115117430	115117431	+	Frame_Shift_Ins	INS	-	-	T			TCGA-B6-A0RI-01A-11W-A071-09	TCGA-B6-A0RI-10A-01W-A071-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	50d83050-b98c-4a1a-a673-91dbc67c37c6	71508273-8303-4261-bcf2-b5ace767bfe2	g.chr12:115117430_115117431insT	ENST00000257566.3	-	4	1132_1133	c.743_744insA	c.(742-744)tacfs	p.Y248fs	TBX3_ENST00000349155.2_Frame_Shift_Ins_p.Y228fs	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	248					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		ACCGGGGCTGGTATTTGTGCAT	0.455																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"""T-boxes"""	11602	protein-coding gene	gene with protein product		601621	"""ulnar mammary syndrome"""	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.744dupA	12.37:g.115117431_115117431dupT	ENSP00000257566:p.Tyr248fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8TB20|Q9UKF8	Frame_Shift_Ins	INS	pfam_TF_T-box,pfam_TBX,superfamily_p53-like_TF_DNA-bd,smart_TF_T-box,pfscan_TF_T-box,prints_TF_T-box	p.Y248fs	ENST00000257566.3	37	c.744_743	CCDS9176.1	12																																																																																			TBX3	-	pfam_TF_T-box,superfamily_p53-like_TF_DNA-bd,smart_TF_T-box,pfscan_TF_T-box	ENSG00000135111		0.455	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TBX3	HGNC	protein_coding	OTTHUMT00000404947.2	293	0.00	0	-	NM_016569, NM_005996		115117430	115117431	-1	no_errors	ENST00000257566	ensembl	human	known	69_37n	frame_shift_ins	106	34.16	55	INS	1.000:1.000	T
UTP20	27340	genome.wustl.edu	37	12	101723202	101723202	+	Missense_Mutation	SNP	C	C	T			TCGA-B6-A0RI-01A-11W-A071-09	TCGA-B6-A0RI-10A-01W-A071-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	50d83050-b98c-4a1a-a673-91dbc67c37c6	71508273-8303-4261-bcf2-b5ace767bfe2	g.chr12:101723202C>T	ENST00000261637.4	+	27	3566	c.3392C>T	c.(3391-3393)tCa>tTa	p.S1131L		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1131					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						GCAACCGTATCACACATCCTT	0.388																																						dbGAP											0													111.0	105.0	107.0					12																	101723202		2203	4300	6503	-	-	-	SO:0001583	missense	0			AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.3392C>T	12.37:g.101723202C>T	ENSP00000261637:p.Ser1131Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q9H3H4	Missense_Mutation	SNP	pfam_DRIM,superfamily_ARM-type_fold	p.S1131L	ENST00000261637.4	37	c.3392	CCDS9081.1	12	.	.	.	.	.	.	.	.	.	.	C	18.19	3.568189	0.65651	.	.	ENSG00000120800	ENST00000261637	T	0.20069	2.1	5.6	5.6	0.85130	Armadillo-type fold (1);	0.059294	0.64402	D	0.000001	T	0.23766	0.0575	L	0.57536	1.79	0.80722	D	1	P	0.44986	0.847	B	0.38803	0.282	T	0.04440	-1.0951	10	0.15952	T	0.53	-5.1347	19.9737	0.97296	0.0:1.0:0.0:0.0	.	1131	O75691	UTP20_HUMAN	L	1131	ENSP00000261637:S1131L	ENSP00000261637:S1131L	S	+	2	0	UTP20	100247333	1.000000	0.71417	0.937000	0.37676	0.091000	0.18340	7.556000	0.82233	2.793000	0.96121	0.591000	0.81541	TCA	UTP20	-	superfamily_ARM-type_fold	ENSG00000120800		0.388	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	UTP20	HGNC	protein_coding	OTTHUMT00000408242.1	138	0.00	0	C	NM_014503		101723202	101723202	+1	no_errors	ENST00000261637	ensembl	human	known	69_37n	missense	72	36.84	42	SNP	1.000	T
WNT2B	7482	genome.wustl.edu	37	1	113057615	113057615	+	Missense_Mutation	SNP	G	G	A	rs140445206	byFrequency	TCGA-B6-A0RI-01A-11W-A071-09	TCGA-B6-A0RI-10A-01W-A071-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	50d83050-b98c-4a1a-a673-91dbc67c37c6	71508273-8303-4261-bcf2-b5ace767bfe2	g.chr1:113057615G>A	ENST00000369684.4	+	2	787	c.302G>A	c.(301-303)cGa>cAa	p.R101Q	WNT2B_ENST00000256640.5_Missense_Mutation_p.R9Q|WNT2B_ENST00000369686.5_Missense_Mutation_p.R82Q|WNT2B_ENST00000478360.1_3'UTR|RP4-671G15.2_ENST00000608357.1_RNA	NM_024494.2	NP_078613.1	Q93097	WNT2B_HUMAN	wingless-type MMTV integration site family, member 2B	101					canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular response to starvation (GO:0009267)|chondrocyte differentiation (GO:0002062)|cornea development in camera-type eye (GO:0061303)|forebrain regionalization (GO:0021871)|hematopoietic stem cell proliferation (GO:0071425)|iris morphogenesis (GO:0061072)|lens development in camera-type eye (GO:0002088)|lung induction (GO:0060492)|male gonad development (GO:0008584)|mesenchymal-epithelial cell signaling (GO:0060638)|neuron differentiation (GO:0030182)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)	p.R101Q(1)		breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(4)|ovary(2)|skin(1)|stomach(1)	18	Lung SC(450;0.246)	all_cancers(81;7.31e-07)|all_epithelial(167;4.59e-06)|all_lung(203;2.56e-05)|Lung NSC(69;4.38e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GAGGGTGCCCGAGAATGGATC	0.602													G|||	9	0.00179712	0.0	0.0	5008	,	,		17872	0.0089		0.0	False		,,,				2504	0.0					dbGAP											1	Substitution - Missense(1)	stomach(1)											92.0	76.0	81.0					1																	113057615		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB045116	CCDS847.1, CCDS846.1	1p13	2008-07-18			ENSG00000134245	ENSG00000134245		"""Wingless-type MMTV integration sites"""	12781	protein-coding gene	gene with protein product	"""XWNT2, Xenopus, homolog of"", ""wingless-type MMTV integration site family, member 13"""	601968		WNT13		8761309, 10944466	Standard	NM_024494		Approved	XWNT2	uc001ecb.3	Q93097	OTTHUMG00000011157	ENST00000369684.4:c.302G>A	1.37:g.113057615G>A	ENSP00000358698:p.Arg101Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	O14903|Q5TEH9|Q5TEI2|Q9HDC1|Q9HDC2	Missense_Mutation	SNP	pfam_Wnt,smart_Wnt,prints_Wnt,prints_Wnt2	p.R101Q	ENST00000369684.4	37	c.302	CCDS847.1	1	7	0.003205128205128205	0	0.0	0	0.0	7	0.012237762237762238	0	0.0	G	9.012	0.982652	0.18889	.	.	ENSG00000134245	ENST00000256640;ENST00000369686;ENST00000369684	T;T;T	0.75154	-0.91;-0.91;-0.91	5.3	4.39	0.52855	.	0.054643	0.64402	D	0.000001	T	0.31199	0.0789	N	0.17872	0.535	0.35064	D	0.761808	B;B	0.30114	0.269;0.227	B;B	0.22753	0.041;0.04	T	0.12400	-1.0549	10	0.09843	T	0.71	.	6.8177	0.23839	0.3022:0.0:0.6977:0.0	.	101;82	Q93097;Q93097-2	WNT2B_HUMAN;.	Q	9;82;101	ENSP00000256640:R9Q;ENSP00000358700:R82Q;ENSP00000358698:R101Q	ENSP00000256640:R9Q	R	+	2	0	WNT2B	112859138	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.434000	0.73408	1.235000	0.43724	0.561000	0.74099	CGA	WNT2B	-	pfam_Wnt,smart_Wnt	ENSG00000134245		0.602	WNT2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	WNT2B	HGNC	protein_coding	OTTHUMT00000030692.1	52	0.00	0	G	NM_004185		113057615	113057615	+1	no_errors	ENST00000369684	ensembl	human	known	69_37n	missense	22	60.00	33	SNP	1.000	A
ZC3H18	124245	genome.wustl.edu	37	16	88690436	88690436	+	Frame_Shift_Del	DEL	A	A	-			TCGA-B6-A0RI-01A-11W-A071-09	TCGA-B6-A0RI-10A-01W-A071-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	50d83050-b98c-4a1a-a673-91dbc67c37c6	71508273-8303-4261-bcf2-b5ace767bfe2	g.chr16:88690436delA	ENST00000301011.5	+	11	2064	c.1864delA	c.(1864-1866)aagfs	p.K622fs	ZC3H18_ENST00000452588.2_Frame_Shift_Del_p.K646fs	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	622	Ser-rich.					nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		CATCAGAACCAAGGGAGAGCC	0.667																																					Ovarian(121;375 2276 20373 38669)	dbGAP											0													85.0	89.0	88.0					16																	88690436		2198	4300	6498	-	-	-	SO:0001589	frameshift_variant	0			BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"""Zinc fingers, CCCH-type domain containing"""	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.1864delA	16.37:g.88690436delA	ENSP00000301011:p.Lys622fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q96DG4|Q96MP7	Frame_Shift_Del	DEL	smart_Znf_CCCH	p.K622fs	ENST00000301011.5	37	c.1864	CCDS10967.1	16																																																																																			ZC3H18	-	NULL	ENSG00000158545		0.667	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	ZC3H18	HGNC	protein_coding	OTTHUMT00000269168.1	55	0.00	0	A	NM_144604		88690436	88690436	+1	no_errors	ENST00000301011	ensembl	human	known	69_37n	frame_shift_del	11	15.38	2	DEL	1.000	-
