#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_ENSG_ID	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_Ens_Gene	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GMAF	i_HGNC	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_Normal_Alt_Count	i_Normal_Ref_Count	i_Normal_VAF	i_ORegAnno_bin	i_PurityEst	i_RNA_Tum_Ref_count	i_RNA_Tum_VAF	i_RNA_Tum_Var_count	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Tier	i_Tumor_Alt_Count	i_Tumor_Ref_Count	i_Tumor_VAF	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_WGS_Norm_Ref_count	i_WGS_Norm_VAF	i_WGS_Norm_Var_count	i_WGS_Tum_Ref_count	i_WGS_Tum_VAF	i_WGS_Tum_Var_count	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_deletion_substructures	i_domain	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	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_rs_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
CAAP1	79886	genome.wustl.edu	37	9	26886119	26886120	+	Frame_Shift_Ins	INS	-	-	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr9:26886119_26886120insT	ENST00000333916.5	-	3	659_660	c.571_572insA	c.(571-573)attfs	p.I191fs	CAAP1_ENST00000495958.1_Intron|CAAP1_ENST00000520187.1_Intron|CAAP1_ENST00000535437.1_Frame_Shift_Ins_p.I46fs	NM_001167575.1|NM_024828.3	NP_001161047.1|NP_079104.3	Q9H8G2	CAAP1_HUMAN	caspase activity and apoptosis inhibitor 1	191					apoptotic process (GO:0006915)												AATCTTCAAAATTTTTTTTTCA	0.292																																																	0								ENSG00000120159																																			CAAP1	SO:0001589	frameshift_variant	0				HGNC	BC014658	CCDS6516.1	9p21.2	2012-04-20	2012-04-20	2012-04-20	ENSG00000120159	ENSG00000120159			25834	protein-coding gene	gene with protein product	"""conserved anti-apoptotic protein"""		"""chromosome 9 open reading frame 82"""	C9orf82		21980415	Standard	NM_024828		Approved	FLJ13657, CAAP	uc003zqc.3	Q9H8G2	OTTHUMG00000019706	ENST00000333916.5:c.572dupA	9.37:g.26886128_26886128dupT	ENSP00000369431:p.Ile191fs	Somatic	0	26	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	27	12.90	B4DWT4|D3DRK4|Q5VY32|Q6IPE6|Q96C59	Frame_Shift_Ins	INS	NA	NA	NA	NA	NA	NA	NULL	p.I191fs	ENST00000333916.5	37	c.572_571	CCDS6516.1	9																																																																																			-	NULL		0.292	CAAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CAAP1	protein_coding	OTTHUMT00000051954.1	-	NM_024828			26886120	-1	no_errors	ENST00000333916	ensembl	human	known	74_37	frame_shift_ins	INS	1.000:1.000	T
KRTAP4-5	85289	genome.wustl.edu	37	17	39305800	39305814	+	In_Frame_Del	DEL	TGGATTCACAGCAAT	TGGATTCACAGCAAT	-	rs141998775|rs377168597		TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	TGGATTCACAGCAAT	TGGATTCACAGCAAT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr17:39305800_39305814delTGGATTCACAGCAAT	ENST00000343246.4	-	1	240_254	c.206_220delATTGCTGTGAATCCA	c.(205-222)tattgctgtgaatccagc>tgc	p.69_74YCCESS>C		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	69	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			cggcagcagctggattcacagcaataggggcggca	0.665																																																	0								ENSG00000198271																																			KRTAP4-5	SO:0001651	inframe_deletion	0				HGNC	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"""Keratin associated proteins"""	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.206_220delATTGCTGTGAATCCA	17.37:g.39305800_39305814delTGGATTCACAGCAAT	ENSP00000340546:p.Tyr69_Ser74delinsCys	Somatic	NA	NA	NA		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA		In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	NULL	p.YCCESS69in_frame_delC	ENST00000343246.4	37	c.220_206	CCDS32650.1	17																																																																																			-	NULL		0.665	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KRTAP4-5	protein_coding	OTTHUMT00000257783.1	TGGATTCACAGCAAT				39305814	-1	no_errors	ENST00000343246	ensembl	human	known	74_37	in_frame_del	DEL	0.689:0.524:0.472:0.042:0.004:0.003:0.006:0.126:0.849:0.943:0.982:0.981:0.896:0.000:0.000	-
OR10W1	81341	genome.wustl.edu	37	11	58034972	58034972	+	Missense_Mutation	SNP	G	G	T	rs144496337	byFrequency	TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr11:58034972G>T	ENST00000395079.2	-	1	760	c.359C>A	c.(358-360)cCg>cAg	p.P120Q		NM_207374.3	NP_997257.2	Q8NGF6	O10W1_HUMAN	olfactory receptor, family 10, subfamily W, member 1	120						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(2)|large_intestine(2)|lung(19)|ovary(2)|skin(1)	26		Breast(21;0.0589)				GTACTGCAACGGGTGGCAAAT	0.537																																																	0								ENSG00000172772						113.0	78.0	90.0					11																	58034972		2201	4295	6496	OR10W1	SO:0001583	missense	0			-	HGNC	AB065850	CCDS7968.1	11q12.1	2012-08-09	2004-03-04	2004-03-05		ENSG00000172772		"""GPCR / Class A : Olfactory receptors"""	15139	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily W, member 1 pseudogene"""	OR10W1P			Standard	NM_207374		Approved		uc001nmq.1	Q8NGF6		ENST00000395079.2:c.359C>A	11.37:g.58034972G>T	ENSP00000378516:p.Pro120Gln	Somatic	0	37	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	16	15.79	A2RUD2|A8MTE1|Q6UXQ2	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	p.P120Q	ENST00000395079.2	37	c.359	CCDS7968.1	11	.	.	.	.	.	.	.	.	.	.	G	15.77	2.932940	0.52866	.	.	ENSG00000172772	ENST00000395079	T	0.01902	4.57	5.81	4.9	0.64082	GPCR, rhodopsin-like superfamily (1);	0.132735	0.34959	N	0.003551	T	0.22437	0.0541	H	0.97940	4.11	0.43879	D	0.996494	D	0.89917	1.0	D	0.68192	0.956	T	0.44452	-0.9327	10	0.87932	D	0	.	14.5519	0.68073	0.0709:0.0:0.9291:0.0	.	120	Q8NGF6	O10W1_HUMAN	Q	120	ENSP00000378516:P120Q	ENSP00000378516:P120Q	P	-	2	0	OR10W1	57791548	1.000000	0.71417	0.307000	0.25127	0.024000	0.10985	7.934000	0.87649	1.458000	0.47871	0.655000	0.94253	CCG	-	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt		0.537	OR10W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR10W1	protein_coding	OTTHUMT00000394704.1	G	NM_207374	-		58034972	-1	no_errors	ENST00000395079	ensembl	human	known	74_37	missense	SNP	0.998	T
DOCK2	1794	genome.wustl.edu	37	5	169482352	169482352	+	Silent	SNP	C	C	A			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr5:169482352C>A	ENST00000256935.8	+	42	4337	c.4257C>A	c.(4255-4257)ccC>ccA	p.P1419P	DOCK2_ENST00000540750.1_Silent_p.P480P|DOCK2_ENST00000520908.1_Silent_p.P911P|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1419	DHR-2.|Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ATGAACATCCCAGGTTCAAGA	0.473																																																	0								ENSG00000134516						90.0	85.0	87.0					5																	169482352		2203	4300	6503	DOCK2	SO:0001819	synonymous_variant	0			-	HGNC	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.4257C>A	5.37:g.169482352C>A		Somatic	0	37	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	23	11.54	Q2M3I0|Q96AK7	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_DOCK_C,pfam_SH3_2,superfamily_SH3_domain,superfamily_Cyt_c-like_dom,superfamily_ARM-type_fold,superfamily_Ferritin-like_SF,smart_SH3_domain,pfscan_SH3_domain	p.P1419	ENST00000256935.8	37	c.4257	CCDS4371.1	5																																																																																			-	NULL		0.473	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DOCK2	protein_coding	OTTHUMT00000252828.2	C	NM_004946	-		169482352	+1	no_errors	ENST00000256935	ensembl	human	known	74_37	silent	SNP	0.147	A
WHAMMP2	440253	genome.wustl.edu	37	15	29000160	29000162	+	RNA	DEL	ATT	ATT	-	rs3830500		TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	ATT	ATT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr15:29000160_29000162delATT	ENST00000512149.2	+	0	585_587					NR_026589.1				WAS protein homolog associated with actin, golgi membranes and microtubules pseudogene 2																		AAAAAATAACATTATTTCTGGTA	0.305																																																	0								ENSG00000248334																																			WHAMMP2			0				HGNC	BC035099		15q13.1	2014-03-20	2011-06-24	2011-06-24	ENSG00000248334	ENSG00000248334			32360	pseudogene	pseudogene			"""WAS protein homology region 2 domain containing 1-like 2 (pseudogene)"", ""WAS protein homolog associated with actin, golgi membranes and microtubules-like 2 (pseudogene)"""	WHDC1L2, WHAMML2			Standard	NR_026589		Approved		uc010uap.2		OTTHUMG00000176340		15.37:g.29000163_29000165delATT		Somatic	0	8	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	4	50.00		RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000512149.2	37	NULL		15																																																																																			-	-		0.305	WHAMMP2-003	PUTATIVE	basic	processed_transcript	WHAMMP2	pseudogene	OTTHUMT00000431783.1	ATT	NR_026589			29000162	+1	no_errors	ENST00000512149	ensembl	human	putative	74_37	rna	DEL	0.032:0.037:0.049	-
OR13C5	138799	genome.wustl.edu	37	9	107361256	107361256	+	Missense_Mutation	SNP	C	C	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr9:107361256C>T	ENST00000374779.2	-	1	532	c.439G>A	c.(439-441)Ggg>Agg	p.G147R		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	147						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						ATCCAGGACCCAGCTGCCATG	0.473																																																	0								ENSG00000255800						116.0	112.0	113.0					9																	107361256		2203	4300	6503	OR13C5	SO:0001583	missense	0			-	HGNC		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.439G>A	9.37:g.107361256C>T	ENSP00000363911:p.Gly147Arg	Somatic	0	65	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	13	36	26.53	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	p.G147R	ENST00000374779.2	37	c.439	CCDS35091.1	9	.	.	.	.	.	.	.	.	.	.	C	10.41	1.341942	0.24339	.	.	ENSG00000255800	ENST00000374779	T	0.39592	1.07	4.17	3.18	0.36537	GPCR, rhodopsin-like superfamily (1);	0.219101	0.23100	U	0.051925	T	0.48696	0.1514	M	0.89601	3.045	0.09310	N	1	B	0.15719	0.014	B	0.24394	0.053	T	0.42582	-0.9443	10	0.25106	T	0.35	.	10.8541	0.46789	0.2005:0.7994:0.0:0.0	.	147	Q8NGS8	O13C5_HUMAN	R	147	ENSP00000363911:G147R	ENSP00000363911:G147R	G	-	1	0	OR13C5	106401077	0.000000	0.05858	0.629000	0.29254	0.370000	0.29829	0.876000	0.28092	2.169000	0.68431	0.531000	0.56144	GGG	-	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM		0.473	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR13C5	protein_coding	OTTHUMT00000053479.2	C	NM_001004482	-		107361256	-1	no_errors	ENST00000374779	ensembl	human	known	74_37	missense	SNP	0.012	T
MAP7D1	55700	genome.wustl.edu	37	1	36644133	36644133	+	Missense_Mutation	SNP	C	C	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr1:36644133C>T	ENST00000373151.2	+	10	2038	c.1822C>T	c.(1822-1824)Cgc>Tgc	p.R608C	MAP7D1_ENST00000373150.4_Missense_Mutation_p.R576C|MAP7D1_ENST00000373148.4_Missense_Mutation_p.R145C|MAP7D1_ENST00000316156.4_Missense_Mutation_p.R571C	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	608					microtubule cytoskeleton organization (GO:0000226)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)				breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	19		Myeloproliferative disorder(586;0.0393)				TGAGAAGCGGCGCCAGGCCCG	0.697																																																	0								ENSG00000116871						12.0	17.0	16.0					1																	36644133		2194	4285	6479	MAP7D1	SO:0001583	missense	0			-	HGNC	AK096341	CCDS30673.1, CCDS65492.1, CCDS65493.1	1p34.3	2008-02-05	2007-02-08	2007-02-08	ENSG00000116871	ENSG00000116871			25514	protein-coding gene	gene with protein product			"""proline arginine rich coiled coil 1"", ""arginine/proline rich coiled-coil 1"""	PARCC1, RPRC1		10574461	Standard	XM_005271024		Approved	FLJ10350, FLJ39022	uc001bzz.3	Q3KQU3	OTTHUMG00000007714	ENST00000373151.2:c.1822C>T	1.37:g.36644133C>T	ENSP00000362244:p.Arg608Cys	Somatic	0	50	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	26	12	68.42	D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_MAP7	p.R608C	ENST00000373151.2	37	c.1822	CCDS30673.1	1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.2|20.2	3.957020|3.957020	0.73902|0.73902	.|.	.|.	ENSG00000116871|ENSG00000116871	ENST00000530975|ENST00000316156;ENST00000373150;ENST00000373151;ENST00000373148	.|T;T;T;T	.|0.38401	.|1.14;1.14;1.14;1.14	4.81|4.81	4.81|4.81	0.61882|0.61882	.|.	.|0.379499	.|0.19576	.|N	.|0.110966	T|T	0.67040|0.67040	0.2851|0.2851	M|M	0.88775|0.88775	2.98|2.98	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.91635	.|0.999;0.999;0.999;0.998;0.999	T|T	0.73933|0.73933	-0.3826|-0.3826	5|10	.|0.87932	.|D	.|0	-5.1069|-5.1069	16.6044|16.6044	0.84824|0.84824	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|145;608;571;576;608	.|Q3KQU3-3;D3DPS3;Q3KQU3-2;Q3KQU3-4;Q3KQU3	.|.;.;.;.;MA7D1_HUMAN	V|C	181|571;576;608;145	.|ENSP00000320228:R571C;ENSP00000362243:R576C;ENSP00000362244:R608C;ENSP00000362241:R145C	.|ENSP00000320228:R571C	A|R	+|+	2|1	0|0	MAP7D1|MAP7D1	36416720|36416720	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	2.822000|2.822000	0.48073|0.48073	2.490000|2.490000	0.84030|0.84030	0.563000|0.563000	0.77884|0.77884	GCG|CGC	-	pfam_MAP7		0.697	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	MAP7D1	protein_coding	OTTHUMT00000382095.1	C	NM_018067	-		36644133	+1	no_errors	ENST00000373151	ensembl	human	known	74_37	missense	SNP	1.000	T
SERPINI1	5274	genome.wustl.edu	37	3	167508312	167508312	+	Missense_Mutation	SNP	G	G	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr3:167508312G>T	ENST00000295777.5	+	3	834	c.403G>T	c.(403-405)Gca>Tca	p.A135S	SERPINI1_ENST00000446050.2_Missense_Mutation_p.A135S	NM_005025.4	NP_005016.1	Q99574	NEUS_HUMAN	serpin peptidase inhibitor, clade I (neuroserpin), member 1	135					cell death (GO:0008219)|central nervous system development (GO:0007417)|negative regulation of endopeptidase activity (GO:0010951)|peripheral nervous system development (GO:0007422)|regulation of cell adhesion (GO:0030155)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(7)|skin(2)	20						TTTTAATGCAGCAGTAAATCA	0.363																																																	0								ENSG00000163536						115.0	116.0	116.0					3																	167508312		2203	4300	6503	SERPINI1	SO:0001583	missense	0			-	HGNC	Z81326	CCDS3203.1	3q26.1	2014-02-18	2005-08-18		ENSG00000163536	ENSG00000163536		"""Serine (or cysteine) peptidase inhibitors"""	8943	protein-coding gene	gene with protein product		602445	"""serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 1"""	PI12		24172014	Standard	NM_005025		Approved	neuroserpin	uc003ffa.4	Q99574	OTTHUMG00000158450	ENST00000295777.5:c.403G>T	3.37:g.167508312G>T	ENSP00000295777:p.Ala135Ser	Somatic	0	31	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	15	16.67	A8K217|D3DNP1|Q6AHZ4	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Serpin_dom,superfamily_Serpin_dom,smart_Serpin_dom	p.A135S	ENST00000295777.5	37	c.403	CCDS3203.1	3	.	.	.	.	.	.	.	.	.	.	G	14.20	2.464383	0.43736	.	.	ENSG00000163536	ENST00000472941;ENST00000446050;ENST00000295777;ENST00000472747	D;D;D;D	0.84070	-1.8;-1.8;-1.8;-1.8	5.51	5.51	0.81932	Serpin domain (3);	0.144593	0.64402	D	0.000010	T	0.70011	0.3175	N	0.04787	-0.16	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.63594	-0.6602	10	0.33141	T	0.24	.	19.4144	0.94689	0.0:0.0:1.0:0.0	.	135	Q99574	NEUS_HUMAN	S	135	ENSP00000420133:A135S;ENSP00000397373:A135S;ENSP00000295777:A135S;ENSP00000420561:A135S	ENSP00000295777:A135S	A	+	1	0	SERPINI1	168991006	1.000000	0.71417	1.000000	0.80357	0.579000	0.36224	5.223000	0.65283	2.586000	0.87340	0.557000	0.71058	GCA	-	pfam_Serpin_dom,superfamily_Serpin_dom,smart_Serpin_dom		0.363	SERPINI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SERPINI1	protein_coding	OTTHUMT00000351056.1	G		-		167508312	+1	no_errors	ENST00000295777	ensembl	human	known	74_37	missense	SNP	1.000	T
TMEM191C	645426	genome.wustl.edu	37	22	21822373	21822385	+	lincRNA	DEL	AGGATCCGGGGGT	AGGATCCGGGGGT	-	rs3016118		TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	AGGATCCGGGGGT	AGGATCCGGGGGT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr22:21822373_21822385delAGGATCCGGGGGT	ENST00000449424.1	+	0	415_427							A6NGB0	T191C_HUMAN	transmembrane protein 191C							integral component of membrane (GO:0016021)											ggaagggggcaggatccgggggtggggtgaggt	0.704																																																	0								ENSG00000206140																																			TMEM191C			0				HGNC			22q11.21	2013-04-03			ENSG00000206140	ENSG00000206140			33601	other	unknown							Standard	NM_001207052		Approved		uc021wmg.1	A6NGB0	OTTHUMG00000150780		22.37:g.21822373_21822385delAGGATCCGGGGGT		Somatic	NA	NA	NA		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA		RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000449424.1	37	NULL		22																																																																																			-	-		0.704	TMEM191C-004	KNOWN	basic|exp_conf	lincRNA	TMEM191C	lincRNA	OTTHUMT00000320053.1	AGGATCCGGGGGT	NM_001207052			21822385	+1	no_errors	ENST00000449424	ensembl	human	known	74_37	rna	DEL	0.003:0.005:0.001:0.001:0.002:0.003:0.000:0.000:0.000:0.057:0.077:0.000:0.000	-
IL13RA2	3598	genome.wustl.edu	37	X	114248419	114248419	+	Missense_Mutation	SNP	C	C	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chrX:114248419C>T	ENST00000371936.1	-	6	683	c.434G>A	c.(433-435)tGc>tAc	p.C145Y	IL13RA2_ENST00000468224.1_5'Flank|IL13RA2_ENST00000243213.1_Missense_Mutation_p.C145Y			Q14627	I13R2_HUMAN	interleukin 13 receptor, alpha 2	145	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	23						GTAATATACGCAATCCATATC	0.333																																																	0								ENSG00000123496						81.0	74.0	76.0					X																	114248419		2203	4299	6502	IL13RA2	SO:0001583	missense	0			-	HGNC	X95302	CCDS14565.1	Xq23	2014-01-21			ENSG00000123496	ENSG00000123496		"""Interleukins and interleukin receptors"", ""CD molecules"""	5975	protein-coding gene	gene with protein product	"""cancer/testis antigen 19"""	300130				8663118, 9083087	Standard	NM_000640		Approved	IL-13R, IL13BP, CD213a2, CT19	uc004epx.3	Q14627	OTTHUMG00000022229	ENST00000371936.1:c.434G>A	X.37:g.114248419C>T	ENSP00000361004:p.Cys145Tyr	Somatic	0	80	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	23	18	56.10	A8K7E2|O00667	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_IL-6_rcpt_alpha-bd,superfamily_Fibronectin_type3	p.C145Y	ENST00000371936.1	37	c.434	CCDS14565.1	X	.	.	.	.	.	.	.	.	.	.	C	14.96	2.691310	0.48097	.	.	ENSG00000123496	ENST00000371936;ENST00000243213	D;D	0.98178	-4.77;-4.77	4.68	4.68	0.58851	Interleukin-6 receptor alpha chain, binding (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.044737	0.85682	D	0.000000	D	0.98963	0.9647	M	0.89968	3.075	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99349	1.0914	10	0.87932	D	0	-20.5806	11.8882	0.52615	0.0:1.0:0.0:0.0	.	145;145	D0EFR8;Q14627	.;I13R2_HUMAN	Y	145	ENSP00000361004:C145Y;ENSP00000243213:C145Y	ENSP00000243213:C145Y	C	-	2	0	IL13RA2	114154675	0.973000	0.33851	0.928000	0.36995	0.551000	0.35334	4.076000	0.57591	2.290000	0.77057	0.600000	0.82982	TGC	-	pfam_IL-6_rcpt_alpha-bd,superfamily_Fibronectin_type3		0.333	IL13RA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IL13RA2	protein_coding	OTTHUMT00000057966.1	C	NM_000640	-		114248419	-1	no_errors	ENST00000243213	ensembl	human	known	74_37	missense	SNP	0.884	T
CACNA1B	774	genome.wustl.edu	37	9	140850187	140850187	+	Missense_Mutation	SNP	C	C	A			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr9:140850187C>A	ENST00000371372.1	+	8	1253	c.1108C>A	c.(1108-1110)Cgc>Agc	p.R370S	CACNA1B_ENST00000371355.4_Missense_Mutation_p.R370S|CACNA1B_ENST00000371357.1_Missense_Mutation_p.R370S|CACNA1B_ENST00000277549.5_5'UTR|CACNA1B_ENST00000277551.2_Missense_Mutation_p.R370S|CACNA1B_ENST00000371363.1_Missense_Mutation_p.R370S	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	370					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	GGAGAACCGCCGCGCCTTCCT	0.642																																																	0								ENSG00000148408						21.0	26.0	25.0					9																	140850187		2002	4168	6170	CACNA1B	SO:0001583	missense	0			-	HGNC	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.1108C>A	9.37:g.140850187C>A	ENSP00000360423:p.Arg370Ser	Somatic	0	76	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	32	11.11	B1AQK5	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Ion_trans_dom,pfam_VDCC_a1su_IQ,pfam_PKD1_2_channel,pfscan_EF_hand_dom,prints_VDCCAlpha1,prints_VDCC_N_a1su,prints_PKD_2	p.R370S	ENST00000371372.1	37	c.1108	CCDS59522.1	9	.	.	.	.	.	.	.	.	.	.	C	17.07	3.293995	0.60086	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D	0.92965	-3.14;-3.14;-3.14;-3.14;-3.14	5.65	3.61	0.41365	.	0.123853	0.56097	D	0.000026	D	0.89608	0.6764	L	0.46157	1.445	0.80722	D	1	D	0.54601	0.967	P	0.45138	0.471	D	0.88577	0.3134	10	0.40728	T	0.16	.	14.1087	0.65109	0.3181:0.6819:0.0:0.0	.	370	B1AQK6	.	S	370	ENSP00000360423:R370S;ENSP00000277551:R370S;ENSP00000360414:R370S;ENSP00000360408:R370S;ENSP00000360406:R370S	ENSP00000277551:R370S	R	+	1	0	CACNA1B	139970008	0.995000	0.38212	0.989000	0.46669	0.971000	0.66376	2.807000	0.47955	1.228000	0.43614	0.485000	0.47835	CGC	-	prints_VDCCAlpha1		0.642	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	CACNA1B	protein_coding	OTTHUMT00000055380.1	C	NM_000718	-		140850187	+1	no_errors	ENST00000371355	ensembl	human	known	74_37	missense	SNP	1.000	A
TET3	200424	genome.wustl.edu	37	2	74274511	74274511	+	Missense_Mutation	SNP	G	G	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr2:74274511G>T	ENST00000409262.3	+	1	1062	c.1062G>T	c.(1060-1062)aaG>aaT	p.K354N		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	354					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)			NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CCAAGCCCAAGGTCAAGGTGG	0.642																																																	0								ENSG00000187605						34.0	39.0	37.0					2																	74274511		2022	4171	6193	TET3	SO:0001583	missense	0			-	HGNC		CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"""tet oncogene family member 3"""			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.1062G>T	2.37:g.74274511G>T	ENSP00000386869:p.Lys354Asn	Somatic	0	35	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	40	9.09	A6NEI3|Q86Z24|Q8TBM9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.K354N	ENST00000409262.3	37	c.1062	CCDS46339.1	2	.	.	.	.	.	.	.	.	.	.	G	4.990	0.183791	0.09495	.	.	ENSG00000187605	ENST00000305799;ENST00000409262;ENST00000233310	T;T	0.27890	1.64;2.54	5.18	3.34	0.38264	.	.	.	.	.	T	0.13586	0.0329	N	0.08118	0	0.26556	N	0.973818	B	0.24618	0.107	B	0.18263	0.021	T	0.21621	-1.0240	9	0.20046	T	0.44	.	6.4226	0.21752	0.166:0.0:0.6839:0.15	.	354	O43151	TET3_HUMAN	N	396;354;354	ENSP00000307803:K396N;ENSP00000386869:K354N	ENSP00000233310:K354N	K	+	3	2	TET3	74128019	0.986000	0.35501	0.998000	0.56505	0.895000	0.52256	0.979000	0.29500	1.303000	0.44873	0.655000	0.94253	AAG	-	NULL		0.642	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	TET3	protein_coding	OTTHUMT00000328141.4	G		-		74274511	+1	no_errors	ENST00000409262	ensembl	human	known	74_37	missense	SNP	0.995	T
SERPINB9	5272	genome.wustl.edu	37	6	2890727	2890727	+	Silent	SNP	A	A	G			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr6:2890727A>G	ENST00000380698.4	-	7	890	c.801T>C	c.(799-801)gtT>gtC	p.V267V		NM_004155.5	NP_004146.1	P50453	SPB9_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 9	267					cellular response to estrogen stimulus (GO:0071391)|immune response (GO:0006955)|mast cell mediated immunity (GO:0002448)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(4)|large_intestine(3)|lung(5)|pancreas(1)|prostate(1)	15	Ovarian(93;0.0412)	all_hematologic(90;0.108)				TTGGAAGGAGAACTTCAACCT	0.423																																																	0								ENSG00000170542						93.0	94.0	94.0					6																	2890727		2203	4300	6503	SERPINB9	SO:0001819	synonymous_variant	0			-	HGNC	L40378	CCDS4478.1	6p25.2	2014-02-18	2005-08-18		ENSG00000170542	ENSG00000170542		"""Serine (or cysteine) peptidase inhibitors"""	8955	protein-coding gene	gene with protein product		601799	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 9"""	PI9		8530382, 9858835, 24172014	Standard	NM_004155		Approved	CAP3	uc003mug.4	P50453	OTTHUMG00000014131	ENST00000380698.4:c.801T>C	6.37:g.2890727A>G		Somatic	0	21	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	15	7	68.18	B2RBW3|Q5TD03	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Serpin_dom,superfamily_Serpin_dom,smart_Serpin_dom,prints_Serpin_B9/Maspin	p.V267	ENST00000380698.4	37	c.801	CCDS4478.1	6																																																																																			-	pfam_Serpin_dom,superfamily_Serpin_dom,smart_Serpin_dom,prints_Serpin_B9/Maspin		0.423	SERPINB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SERPINB9	protein_coding	OTTHUMT00000039656.1	A		-		2890727	-1	no_errors	ENST00000380698	ensembl	human	known	74_37	silent	SNP	0.001	G
U1	0	genome.wustl.edu	37	1	17198711	17198711	+	lincRNA	SNP	G	G	A			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr1:17198711G>A	ENST00000362684.1	+	0	0																											GGGTGCCCCCGTCTCACCCTG	0.652																																																	0								ENSG00000228549																																			U1			0			-	RFAM																													1.37:g.17198711G>A		Somatic	0	37	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	9	42	17.65		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000362684.1	37	NULL		1																																																																																			-	-		0.652	U1.1-201	KNOWN	basic	snRNA	LOC101927806	lincRNA		G		-		17198711	+1	no_errors	ENST00000438002	ensembl	human	known	74_37	rna	SNP	0.007	A
TRIM44	54765	genome.wustl.edu	37	11	35828045	35828045	+	3'UTR	SNP	C	C	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr11:35828045C>T	ENST00000299413.5	+	0	1452				TRIM44_ENST00000532066.1_3'UTR	NM_017583.4	NP_060053.2	Q96DX7	TRI44_HUMAN	tripartite motif containing 44							intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18	all_lung(20;0.0317)|Lung NSC(22;0.0661)|all_epithelial(35;0.115)	all_hematologic(20;0.107)				AAACGTACTTCCACCAGATGT	0.498																																																	0								ENSG00000166326																																			TRIM44	SO:0001624	3_prime_UTR_variant	0			-	HGNC	BC024031	CCDS31461.1	11p13	2011-04-20	2011-01-25		ENSG00000166326	ENSG00000166326		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19016	protein-coding gene	gene with protein product		612298	"""tripartite motif-containing 44"""				Standard	NM_017583		Approved	DIPB, MC7	uc001mwi.2	Q96DX7	OTTHUMG00000166312	ENST00000299413.5:c.*110C>T	11.37:g.35828045C>T		Somatic	0	73	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	18	42	30.00	D3DR14|Q96QY2|Q9UGK0	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000299413.5	37	NULL	CCDS31461.1	11																																																																																			-	-		0.498	TRIM44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TRIM44	protein_coding	OTTHUMT00000389081.1	C	NM_017583	-		35828045	+1	no_errors	ENST00000532066	ensembl	human	known	74_37	rna	SNP	0.000	T
DCAF7	10238	genome.wustl.edu	37	17	61666515	61666515	+	Missense_Mutation	SNP	T	T	C			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr17:61666515T>C	ENST00000310827.4	+	8	1227	c.1010T>C	c.(1009-1011)cTg>cCg	p.L337P	DCAF7_ENST00000577702.1_3'UTR|DCAF7_ENST00000415273.2_Missense_Mutation_p.L137P|DCAF7_ENST00000431926.1_Intron	NM_005828.3	NP_005819.3	P61962	DCAF7_HUMAN	DDB1 and CUL4 associated factor 7	337					multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|protein complex (GO:0043234)				endometrium(6)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)	18						AACAACTGCCTGGAGATACTC	0.542																																																	0								ENSG00000136485						105.0	102.0	103.0					17																	61666515		2043	4185	6228	DCAF7	SO:0001583	missense	0			-	HGNC	U94747	CCDS74127.1	17q23.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000136485		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	30915	protein-coding gene	gene with protein product	"""seven-WD-repeat protein of the AN11 family-1"", ""human anthocyanin"""	605973	"""WD repeat domain 68"""	WDR68		9192870, 20940704	Standard	NM_005828		Approved	HAN11, SWAN-1	uc002jbc.4	P61962		ENST00000310827.4:c.1010T>C	17.37:g.61666515T>C	ENSP00000308344:p.Leu337Pro	Somatic	0	40	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	43	8.51	B4E039|D3DU14|O15491|Q9DAE4	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.L337P	ENST00000310827.4	37	c.1010		17	.	.	.	.	.	.	.	.	.	.	T	23.9	4.468013	0.84533	.	.	ENSG00000136485	ENST00000310827;ENST00000415273	T;T	0.22134	2.43;1.97	5.31	5.31	0.75309	.	0.071335	0.64402	D	0.000018	T	0.41696	0.1170	.	.	.	0.80722	D	1	D;P	0.62365	0.991;0.921	P;P	0.57960	0.83;0.792	T	0.38001	-0.9681	9	0.87932	D	0	-17.1767	15.422	0.75018	0.0:0.0:0.0:1.0	.	137;337	B4E039;P61962	.;DCAF7_HUMAN	P	337;137	ENSP00000308344:L337P;ENSP00000403920:L137P	ENSP00000308344:L337P	L	+	2	0	DCAF7	59020247	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.868000	0.87116	2.226000	0.72624	0.460000	0.39030	CTG	-	NULL		0.542	DCAF7-201	KNOWN	basic|appris_principal	protein_coding	DCAF7	protein_coding		T	NM_005828	-		61666515	+1	no_errors	ENST00000310827	ensembl	human	known	74_37	missense	SNP	1.000	C
SCD	6319	genome.wustl.edu	37	10	102107836	102107838	+	In_Frame_Del	DEL	ACC	ACC	-			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	ACC	ACC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr10:102107836_102107838delACC	ENST00000370355.2	+	2	424_426	c.43_45delACC	c.(43-45)accdel	p.T19del	RP11-34D15.2_ENST00000429420.1_RNA	NM_005063.4	NP_005054.3	O00767	ACOD_HUMAN	stearoyl-CoA desaturase (delta-9-desaturase)	19					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|large_intestine(3)|lung(5)	9		Colorectal(252;0.0323)		Epithelial(162;1.97e-10)|all cancers(201;1.73e-08)		TAGCTCCTATACCACCACCACCA	0.581																																					Colon(67;260 1459 9574 11663)												0								ENSG00000099194																																			SCD	SO:0001651	inframe_deletion	0				HGNC	AF097514	CCDS7493.1	10q23-q24	2013-01-25			ENSG00000099194	ENSG00000099194	1.14.19.1	"""Fatty acid desaturases"""	10571	protein-coding gene	gene with protein product	"""acyl-CoA desaturase"", ""fatty acid desaturase"", ""delta-9-desaturase"""	604031	"""stearoyl-CoA desaturase opposite strand"""	SCDOS		7909540, 10229681	Standard	NM_005063		Approved	FADS5	uc001kqy.3	O00767	OTTHUMG00000018906	ENST00000370355.2:c.43_45delACC	10.37:g.102107845_102107847delACC	ENSP00000359380:p.Thr19del	Somatic	0	31	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	2	10	16.67	B2R5U0|D3DR68|Q16150|Q53GR9|Q5W037|Q5W038|Q6GSS4|Q96KF6|Q9BS07|Q9Y695	In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Fatty_acid_desaturase-1,prints_Fatty_acid_desaturase-1_core	p.T18in_frame_del	ENST00000370355.2	37	c.43_45	CCDS7493.1	10																																																																																			-	NULL		0.581	SCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SCD	protein_coding	OTTHUMT00000049857.2	ACC	NM_005063			102107838	+1	no_errors	ENST00000370355	ensembl	human	known	74_37	in_frame_del	DEL	0.998:0.990:0.094	-
PTPN4	5775	genome.wustl.edu	37	2	120690023	120690023	+	Missense_Mutation	SNP	G	G	T	rs532212706	byFrequency	TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr2:120690023G>T	ENST00000263708.2	+	14	1865	c.1094G>T	c.(1093-1095)cGg>cTg	p.R365L	PTPN4_ENST00000544261.1_5'UTR	NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	365					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30					Alendronate(DB00630)	CCCTTGGCACGGAAATTAATG	0.353																																																	0								ENSG00000088179						59.0	55.0	56.0					2																	120690023		2203	4300	6503	PTPN4	SO:0001583	missense	0			-	HGNC		CCDS2129.1	2q14.2	2011-06-09			ENSG00000088179	ENSG00000088179		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9656	protein-coding gene	gene with protein product		176878				1648233	Standard	NM_002830		Approved	PTPMEG	uc002tmf.2	P29074	OTTHUMG00000131436	ENST00000263708.2:c.1094G>T	2.37:g.120690023G>T	ENSP00000263708:p.Arg365Leu	Somatic	0	26	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	14	16.67	B2RBV8|Q9UDA7	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Tyr_Pase_rcpt/non-rcpt,pfam_FERM_PH-like_C,pfam_FERM_central,pfam_FERM_N,pfam_PDZ,pfam_FERM-adjacent,superfamily_FERM_central,superfamily_PDZ,smart_Band_41_domain,smart_PDZ,smart_Tyr_Pase_rcpt/non-rcpt,smart_Tyr_Pase_cat,pirsf_Tyr_Pase_non-rcpt_typ-3/4,pfscan_FERM_domain,pfscan_PDZ,pfscan_Tyr/Dual-sp_Pase,pfscan_Tyr_Pase_rcpt/non-rcpt,prints_Tyr_Pase_rcpt/non-rcpt,prints_Band_41_fam,prints_Ez/rad/moesin_like	p.R365L	ENST00000263708.2	37	c.1094	CCDS2129.1	2	.	.	.	.	.	.	.	.	.	.	G	24.6	4.546490	0.86022	.	.	ENSG00000088179	ENST00000263708	T	0.73575	-0.76	5.1	4.22	0.49857	.	0.000000	0.85682	D	0.000000	D	0.86167	0.5868	M	0.79693	2.465	0.80722	D	1	D	0.69078	0.997	D	0.81914	0.995	D	0.87512	0.2440	10	0.51188	T	0.08	.	16.0218	0.80503	0.0:0.1345:0.8655:0.0	.	365	P29074	PTN4_HUMAN	L	365	ENSP00000263708:R365L	ENSP00000263708:R365L	R	+	2	0	PTPN4	120406493	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.675000	0.61619	1.267000	0.44247	0.563000	0.77884	CGG	-	pirsf_Tyr_Pase_non-rcpt_typ-3/4		0.353	PTPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PTPN4	protein_coding	OTTHUMT00000254233.2	G		-		120690023	+1	no_errors	ENST00000263708	ensembl	human	known	74_37	missense	SNP	1.000	T
FBXL12	54850	genome.wustl.edu	37	19	9931205	9931205	+	5'Flank	SNP	T	T	A	rs71188840|rs528156854		TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr19:9931205T>A	ENST00000247977.4	-	0	0				FBXL12_ENST00000592067.1_5'Flank|FBXL12_ENST00000586469.1_5'Flank|FBXL12_ENST00000586651.1_5'Flank|AC008752.1_ENST00000401283.1_RNA|FBXL12_ENST00000588922.1_5'Flank|FBXL12_ENST00000586073.1_5'Flank|SNORA70_ENST00000363367.1_RNA|FBXL12_ENST00000585379.1_Intron|FBXL12_ENST00000589626.1_5'Flank	NM_017703.1	NP_060173.1	Q9NXK8	FXL12_HUMAN	F-box and leucine-rich repeat protein 12						protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)				endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(2)	10						AAAAAAAAAAtgtgtgtgtgt	0.448																																																	0								ENSG00000216102																																			AC008752.1	SO:0001631	upstream_gene_variant	0			-	Clone_based_ensembl_gene	AK000195	CCDS12218.1	19p13.2	2011-06-09				ENSG00000127452		"""F-boxes / Leucine-rich repeats"""	13611	protein-coding gene	gene with protein product		609079				10531037	Standard	XM_005259964		Approved	FLJ20188, Fbl12	uc002mme.3	Q9NXK8			19.37:g.9931205T>A	Exception_encountered	Somatic	0	23	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	18	54	24.00	B3KSJ8|Q9H5K4	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000247977.4	37	NULL	CCDS12218.1	19																																																																																			-	-		0.448	FBXL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000216102	protein_coding	OTTHUMT00000450265.1	T	NM_017703	-		9931205	+1	no_errors	ENST00000401283	ensembl	human	novel	74_37	rna	SNP	0.000	A
NDUFB6	4712	genome.wustl.edu	37	9	32570976	32570976	+	Nonsense_Mutation	SNP	G	G	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr9:32570976G>T	ENST00000379847.3	-	2	356	c.255C>A	c.(253-255)taC>taA	p.Y85*	NDUFB6_ENST00000350021.2_Nonsense_Mutation_p.Y85*	NM_002493.4	NP_002484.1	O95139	NDUB6_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6, 17kDa	85					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|urinary_tract(1)	8			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00199)		GATACTTCATGTAATAATGAA	0.333																																																	0								ENSG00000165264						48.0	48.0	48.0					9																	32570976		2203	4293	6496	NDUFB6	SO:0001587	stop_gained	0			-	HGNC	AF035840	CCDS6528.1, CCDS6529.1, CCDS75826.1	9p13.2	2011-07-04	2002-08-29		ENSG00000165264	ENSG00000165264		"""Mitochondrial respiratory chain complex / Complex I"""	7701	protein-coding gene	gene with protein product	"""NADH-ubiquinone oxidoreductase beta subunit, 6"", ""NADH-ubiquinone oxidoreductase B17 subunit"", ""complex I, mitochondrial respiratory chain, B17 subunit"""	603322	"""NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6 (17kD, B17)"""			9763677, 9760212	Standard	NM_002493		Approved	B17, CI	uc003zre.2	O95139	OTTHUMG00000019741	ENST00000379847.3:c.255C>A	9.37:g.32570976G>T	ENSP00000369176:p.Tyr85*	Somatic	0	30	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	17	15.00	A8K0Y7|Q5VYT2|Q6IB84	Nonsense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_NADH_DH_b-subcmplx_su6	p.Y85*	ENST00000379847.3	37	c.255	CCDS6528.1	9	.	.	.	.	.	.	.	.	.	.	G	11.96	1.794302	0.31777	.	.	ENSG00000165264	ENST00000379847;ENST00000350021	.	.	.	5.41	-0.908	0.10517	.	0.123416	0.64402	D	0.000015	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.7569	10.7597	0.46258	0.5692:0.0:0.4308:0.0	.	.	.	.	X	85	.	ENSP00000297983:Y85X	Y	-	3	2	NDUFB6	32560976	0.737000	0.28175	0.033000	0.17914	0.040000	0.13550	1.410000	0.34691	-0.303000	0.08856	-0.302000	0.09304	TAC	-	pfam_NADH_DH_b-subcmplx_su6		0.333	NDUFB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NDUFB6	protein_coding	OTTHUMT00000052001.1	G	NM_002493	-		32570976	-1	no_errors	ENST00000379847	ensembl	human	known	74_37	nonsense	SNP	0.185	T
PCDH15	65217	genome.wustl.edu	37	10	56129015	56129015	+	Silent	SNP	G	G	A			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr10:56129015G>A	ENST00000320301.6	-	5	733	c.339C>T	c.(337-339)tcC>tcT	p.S113S	PCDH15_ENST00000373965.2_Silent_p.S113S|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000437009.1_Silent_p.S113S|PCDH15_ENST00000395442.1_Silent_p.S113S|PCDH15_ENST00000395440.1_Silent_p.S113S|PCDH15_ENST00000395433.1_Silent_p.S91S|PCDH15_ENST00000395432.2_Silent_p.S113S|PCDH15_ENST00000373955.1_Silent_p.S113S|PCDH15_ENST00000361849.3_Silent_p.S113S|PCDH15_ENST00000395430.1_Silent_p.S113S|PCDH15_ENST00000395438.1_Silent_p.S113S|PCDH15_ENST00000395445.1_Silent_p.S113S|PCDH15_ENST00000373957.3_Silent_p.S91S|PCDH15_ENST00000395446.1_Silent_p.S113S|PCDH15_ENST00000414778.1_Silent_p.S118S	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	113	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GCACCACAATGGAGTGTATGT	0.403										HNSCC(58;0.16)																																							0								ENSG00000150275						112.0	92.0	99.0					10																	56129015		2203	4299	6502	PCDH15	SO:0001819	synonymous_variant	0			-	HGNC	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.339C>T	10.37:g.56129015G>A		Somatic	0	59	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	16	23	41.03	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.S113	ENST00000320301.6	37	c.339	CCDS7248.1	10																																																																																			-	smart_Cadherin		0.403	PCDH15-001	KNOWN	basic|CCDS	protein_coding	PCDH15	protein_coding	OTTHUMT00000048121.2	G	NM_033056	-		56129015	-1	no_errors	ENST00000320301	ensembl	human	known	74_37	silent	SNP	1.000	A
CDK4	1019	genome.wustl.edu	37	12	58145458	58145458	+	Missense_Mutation	SNP	C	C	G			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr12:58145458C>G	ENST00000257904.6	-	2	408	c.43G>C	c.(43-45)Ggt>Cgt	p.G15R	CDK4_ENST00000540325.1_5'UTR|CDK4_ENST00000551888.1_5'UTR|CDK4_ENST00000312990.6_Missense_Mutation_p.G15R|CDK4_ENST00000549606.1_Intron	NM_000075.3	NP_000066.1	P11802	CDK4_HUMAN	cyclin-dependent kinase 4	15	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell division (GO:0051301)|circadian rhythm (GO:0007623)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell cycle arrest (GO:0071157)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell size (GO:0045793)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of translation (GO:0045727)|protein phosphorylation (GO:0006468)|regulation of gene expression (GO:0010468)|response to drug (GO:0042493)|response to hyperoxia (GO:0055093)|response to lead ion (GO:0010288)|response to testosterone (GO:0033574)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)	chromatin (GO:0000785)|cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	21	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)			CCATAGGCACCGACACCAATT	0.542			Mis			melanoma			Hereditary Melanoma																														yes	Dom		Familial malignant melanoma	12	12q14	1019	cyclin-dependent kinase 4		E	0								ENSG00000135446						63.0	64.0	64.0					12																	58145458		2203	4300	6503	CDK4	SO:0001583	missense	0	Familial Cancer Database	Familial Atypical Multiple Mole Melanoma sydrome, FAMMM, Familial Dysplastic Nevus syndrome	-	HGNC	M14505	CCDS8953.1	12q13	2014-09-17				ENSG00000135446		"""Cyclin-dependent kinases"""	1773	protein-coding gene	gene with protein product		123829				8275715	Standard	NM_000075		Approved	PSK-J3	uc001spv.3	P11802		ENST00000257904.6:c.43G>C	12.37:g.58145458C>G	ENSP00000257904:p.Gly15Arg	Somatic	0	27	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	9	35.71	B2R9A0|B4DNF9|O00576|Q6FG61	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Aminoglycoside_PTrfase,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom	p.G15R	ENST00000257904.6	37	c.43	CCDS8953.1	12	.	.	.	.	.	.	.	.	.	.	C	24.8	4.573793	0.86542	.	.	ENSG00000135446	ENST00000257904;ENST00000312990;ENST00000552254;ENST00000552388;ENST00000552862	D;D;D;D;D	0.96365	-3.99;-2.8;-3.99;-3.99;-3.99	5.17	4.28	0.50868	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	0.85682	D	0.000000	D	0.98931	0.9637	H	0.99074	4.42	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98810	1.0743	10	0.87932	D	0	.	13.0921	0.59171	0.0:0.9209:0.0:0.0791	.	15	P11802	CDK4_HUMAN	R	15	ENSP00000257904:G15R;ENSP00000316889:G15R;ENSP00000449179:G15R;ENSP00000448963:G15R;ENSP00000446763:G15R	ENSP00000257904:G15R	G	-	1	0	CDK4	56431725	1.000000	0.71417	0.955000	0.39395	0.978000	0.69477	7.325000	0.79124	1.557000	0.49525	-0.140000	0.14226	GGT	-	pfam_Prot_kinase_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_dom		0.542	CDK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDK4	protein_coding	OTTHUMT00000408790.2	C	NM_000075	-		58145458	-1	no_errors	ENST00000257904	ensembl	human	known	74_37	missense	SNP	0.999	G
FRG2B	441581	genome.wustl.edu	37	10	135438753	135438753	+	Silent	SNP	G	G	A	rs375000694		TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr10:135438753G>A	ENST00000425520.1	-	4	739	c.687C>T	c.(685-687)acC>acT	p.T229T	FRG2B_ENST00000443774.1_Silent_p.T230T	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	229						nucleus (GO:0005634)				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		AAGCTGCCTGGGTGGCCATGG	0.597																																																	0								ENSG00000225899						3.0	4.0	4.0					10																	135438753		1467	3364	4831	FRG2B	SO:0001819	synonymous_variant	0			-	HGNC	AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899			33518	protein-coding gene	gene with protein product						15520407	Standard	NM_001080998		Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.687C>T	10.37:g.135438753G>A		Somatic	0	20	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	6	18	25.00	Q5VSQ1	Silent	SNP	NA	NA	NA	NA	NA	NA	NULL	p.T229	ENST00000425520.1	37	c.687	CCDS44502.1	10																																																																																			-	NULL		0.597	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	FRG2B	protein_coding	OTTHUMT00000467780.1	G	NM_001080998	-		135438753	-1	no_errors	ENST00000425520	ensembl	human	known	74_37	silent	SNP	0.707	A
DAPK1	1612	genome.wustl.edu	37	9	90113961	90113961	+	5'UTR	SNP	C	C	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr9:90113961C>T	ENST00000408954.3	+	0	304				DAPK1_ENST00000472284.1_5'UTR|DAPK1_ENST00000469640.2_5'UTR|DAPK1_ENST00000358077.5_5'UTR|DAPK1_ENST00000491893.1_5'UTR	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1						apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						AGCTGAAGTGCCCTGGGCTTT	0.537									Chronic Lymphocytic Leukemia, Familial Clustering of																																								0								ENSG00000196730						93.0	101.0	98.0					9																	90113961		2098	4221	6319	DAPK1	SO:0001623	5_prime_UTR_variant	0	Familial Cancer Database	Familial CLL	-	HGNC	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.-32C>T	9.37:g.90113961C>T		Somatic	0	43	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	44	8.33	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000408954.3	37	NULL	CCDS43842.1	9																																																																																			-	-		0.537	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	DAPK1	protein_coding	OTTHUMT00000356843.1	C	NM_004938	-		90113961	+1	no_errors	ENST00000472344	ensembl	human	known	74_37	rna	SNP	0.957	T
FAM230B	642633	genome.wustl.edu	37	22	21537809	21537809	+	RNA	SNP	A	A	G			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr22:21537809A>G	ENST00000451257.1	+	0	795									family with sequence similarity 230, member B (non-protein coding)																		GGCATCGCCAACGAGGACACC	0.741																																																	0								ENSG00000215498																																			FAM230B			0			-	HGNC	BC039313, AK128837		22q11.21	2014-01-24	2014-01-06		ENSG00000215498	ENSG00000215498			32943	non-coding RNA	RNA, long non-coding			"""family with sequence similarity 230, member B"""				Standard	NR_108107		Approved	FLJ46366			OTTHUMG00000150782		22.37:g.21537809A>G		Somatic	0	23	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	11	40	21.57		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000451257.1	37	NULL		22																																																																																			-	-		0.741	FAM230B-002	KNOWN	basic	lincRNA	FAM230B	processed_transcript	OTTHUMT00000320063.1	A	NR_108107	-		21537809	+1	no_errors	ENST00000451257	ensembl	human	known	74_37	rna	SNP	0.000	G
MIR3689A	100500846	genome.wustl.edu	37	9	137742013	137742013	+	RNA	SNP	C	C	G	rs369116995		TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr9:137742013C>G	ENST00000578854.1	-	0	0				MIR3689D1_ENST00000579706.1_RNA|AL603650.1_ENST00000583957.1_RNA|AL603650.4_ENST00000583817.1_RNA|MIR3689C_ENST00000581239.1_RNA|MIR3689B_ENST00000581772.1_RNA|AL603650.2_ENST00000581079.1_RNA|MIR3689E_ENST00000582479.1_RNA|MIR3689F_ENST00000579617.1_RNA|MIR3689D2_ENST00000580187.1_RNA|AL603650.3_ENST00000582742.1_RNA	NR_037460.1				microRNA 3689a																		CTCCCAGGAACCACAATATCA	0.617																																																	0								ENSG00000264163																																			MIR3689B			0			-	HGNC			9	2011-09-12				ENSG00000265872		"""ncRNAs / Micro RNAs"""	38904	non-coding RNA	RNA, micro							Standard	NR_037460		Approved	hsa-mir-3689a	uc022bpb.1				9.37:g.137742013C>G		Somatic	0	41	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	25	21.88		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000578854.1	37	NULL		9																																																																																			-	-		0.617	MIR3689A-201	KNOWN	basic	miRNA	MIR3689B	miRNA		C	NR_037460	rs71483239		137742013	-1	no_errors	ENST00000581772	ensembl	human	known	74_37	rna	SNP	0.000	G
RIMS2	9699	genome.wustl.edu	37	8	104863873	104863878	+	Intron	DEL	ACACAC	ACACAC	-	rs56306101|rs10529078|rs369439768|rs59712615	byFrequency	TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	ACACAC	ACACAC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr8:104863873_104863878delACACAC	ENST00000507740.1	+	1	358				RIMS2_ENST00000262231.10_Intron|RIMS2_ENST00000406091.3_Intron|AP001572.1_ENST00000401294.1_RNA|RIMS2_ENST00000522174.1_Intron	NM_014677.4	NP_055492.3	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2						calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			AATGCTATGTacacacacacacacac	0.359										HNSCC(12;0.0054)																																							0								ENSG00000216113																																			AP001572.1	SO:0001627	intron_variant	0				Clone_based_ensembl_gene	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"""RAB3 interacting protein 3"""	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000507740.1:c.122+32016ACACAC>-	8.37:g.104863879_104863884delACACAC		Somatic	NA	NA	NA		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000507740.1	37	NULL	CCDS43761.1	8																																																																																			-	-		0.359	RIMS2-005	NOVEL	basic|CCDS	protein_coding	ENSG00000216113	protein_coding	OTTHUMT00000367215.1	ACACAC	NM_001100117			104863878	+1	no_errors	ENST00000401294	ensembl	human	novel	74_37	rna	DEL	0.000:0.000:0.000:0.000:0.000:0.000	-
COG4	25839	genome.wustl.edu	37	16	70546170	70546170	+	Missense_Mutation	SNP	C	C	A			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr16:70546170C>A	ENST00000323786.5	-	5	731	c.710G>T	c.(709-711)aGa>aTa	p.R237I	COG4_ENST00000393612.4_Missense_Mutation_p.R233I|COG4_ENST00000564653.1_3'UTR	NM_001195139.1|NM_015386.2	NP_001182068.1|NP_056201.2	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	233					Golgi organization (GO:0007030)|Golgi vesicle prefusion complex stabilization (GO:0048213)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|pancreas(1)|prostate(2)	33		Ovarian(137;0.0694)				CGAGAACTTTCTTAATCCCTC	0.527																																																	0								ENSG00000103051						92.0	81.0	84.0					16																	70546170		2198	4300	6498	COG4	SO:0001583	missense	0			-	HGNC	AL050101	CCDS10892.2, CCDS73909.1	16q22.1	2013-09-20			ENSG00000103051	ENSG00000103051		"""Components of oligomeric golgi complex"""	18620	protein-coding gene	gene with protein product		606976				11980916	Standard	NM_015386		Approved	COD1, DKFZP586E1519	uc002ezc.3	Q9H9E3	OTTHUMG00000128515	ENST00000323786.5:c.710G>T	16.37:g.70546170C>A	ENSP00000315775:p.Arg237Ile	Somatic	0	24	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	18	14.29	B4DMN8|C9JS23|Q96D40|Q9BRF0|Q9BVZ2|Q9H5Y4|Q9Y3W3	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_COG_su4,smart_COG_su4	p.R237I	ENST00000323786.5	37	c.710	CCDS10892.2	16	.	.	.	.	.	.	.	.	.	.	C	18.85	3.711039	0.68730	.	.	ENSG00000103051	ENST00000323786;ENST00000338984;ENST00000393612	T;T	0.44482	0.92;0.92	5.53	5.53	0.82687	Conserved oligomeric Golgi complex, subunit 4 (2);	0.126316	0.64402	D	0.000001	T	0.36413	0.0966	N	0.24115	0.695	0.47183	D	0.99934	B;B	0.14438	0.01;0.01	B;B	0.26310	0.068;0.068	T	0.10636	-1.0621	10	0.45353	T	0.12	-9.058	19.466	0.94939	0.0:1.0:0.0:0.0	.	232;233	Q6PIW8;Q9H9E3	.;COG4_HUMAN	I	237;233;233	ENSP00000315775:R237I;ENSP00000377236:R233I	ENSP00000315775:R237I	R	-	2	0	COG4	69103671	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.695000	0.61767	2.607000	0.88179	0.655000	0.94253	AGA	-	pfam_COG_su4,smart_COG_su4		0.527	COG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COG4	protein_coding	OTTHUMT00000250326.3	C		-		70546170	-1	no_errors	ENST00000323786	ensembl	human	known	74_37	missense	SNP	1.000	A
CPSF4L	642843	genome.wustl.edu	37	17	71246420	71246420	+	Intron	SNP	G	G	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr17:71246420G>T	ENST00000344935.4	-	6	559				CPSF4L_ENST00000397671.1_Missense_Mutation_p.Q152K	NM_001129885.1	NP_001123357.1	A6NMK7	CPS4L_HUMAN	cleavage and polyadenylation specific factor 4-like								metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|prostate(1)	2						TGTACTTACTGGCATAATGGC	0.378																																																	0								ENSG00000187959																																			CPSF4L	SO:0001627	intron_variant	0			-	HGNC		CCDS45768.1	17q25.1	2010-07-06			ENSG00000187959	ENSG00000187959			33632	protein-coding gene	gene with protein product							Standard	NM_001129885		Approved		uc010dfk.1	A6NMK7	OTTHUMG00000132640	ENST00000344935.4:c.498-1745C>A	17.37:g.71246420G>T		Somatic	0	45	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	34	10.53	A8MU95|B2RXI9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Znf_CCCH,smart_Znf_CCCH	p.Q152K	ENST00000344935.4	37	c.454	CCDS45768.1	17	.	.	.	.	.	.	.	.	.	.	G	5.527	0.282091	0.10458	.	.	ENSG00000187959	ENST00000397671	T	0.30714	1.52	3.71	-5.11	0.02901	.	114.965000	0.01424	U	0.014498	T	0.26774	0.0655	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.39210	-0.9625	7	0.87932	D	0	.	5.6846	0.17794	0.5846:0.0:0.2666:0.1488	.	.	.	.	K	152	ENSP00000380788:Q152K	ENSP00000380788:Q152K	Q	-	1	0	CPSF4L	68758015	0.961000	0.32948	0.000000	0.03702	0.058000	0.15608	0.880000	0.28159	-0.927000	0.03766	-1.036000	0.02392	CAG	-	NULL		0.378	CPSF4L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	CPSF4L	protein_coding	OTTHUMT00000441896.1	G	NM_001129885	-		71246420	-1	no_errors	ENST00000397671	ensembl	human	known	74_37	missense	SNP	0.000	T
RBMX2	51634	genome.wustl.edu	37	X	129543263	129543263	+	Missense_Mutation	SNP	G	G	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chrX:129543263G>T	ENST00000305536.6	+	4	270	c.206G>T	c.(205-207)cGg>cTg	p.R69L	RBMX2_ENST00000469953.1_3'UTR	NM_016024.2	NP_057108.2	Q9Y388	RBMX2_HUMAN	RNA binding motif protein, X-linked 2	69	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(2)|large_intestine(1)|liver(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	19						AATCTCGTGCGGGACAAGAAA	0.378																																																	0								ENSG00000134597						73.0	67.0	69.0					X																	129543263		1806	4069	5875	RBMX2	SO:0001583	missense	0			-	HGNC	AF078865	CCDS43993.1	Xq26.1	2013-02-12			ENSG00000134597	ENSG00000134597		"""RNA binding motif (RRM) containing"""	24282	protein-coding gene	gene with protein product						10810093	Standard	NM_016024		Approved	CGI-79	uc004evt.3	Q9Y388	OTTHUMG00000022395	ENST00000305536.6:c.206G>T	X.37:g.129543263G>T	ENSP00000339090:p.Arg69Leu	Somatic	0	29	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	15	16.67	A8K9Z0|Q5JY82|Q9Y3I8	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom	p.R69L	ENST00000305536.6	37	c.206	CCDS43993.1	X	.	.	.	.	.	.	.	.	.	.	G	26.7	4.761871	0.89932	.	.	ENSG00000134597	ENST00000305536;ENST00000538614	T	0.75704	-0.96	5.34	5.34	0.76211	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.109197	0.64402	D	0.000005	T	0.75421	0.3847	N	0.13235	0.315	0.80722	D	1	D	0.62365	0.991	D	0.66716	0.946	T	0.80264	-0.1455	10	0.87932	D	0	.	15.561	0.76244	0.0:0.0:1.0:0.0	.	69	Q9Y388	RBMX2_HUMAN	L	69	ENSP00000339090:R69L	ENSP00000339090:R69L	R	+	2	0	RBMX2	129370944	1.000000	0.71417	0.944000	0.38274	0.887000	0.51463	5.829000	0.69316	2.358000	0.79984	0.506000	0.49869	CGG	-	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom		0.378	RBMX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RBMX2	protein_coding	OTTHUMT00000058265.1	G	NM_016024	-		129543263	+1	no_errors	ENST00000305536	ensembl	human	known	74_37	missense	SNP	0.996	T
WASH6P	653440	genome.wustl.edu	37	X	155252987	155252988	+	RNA	INS	-	-	CAGCACCAC			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chrX:155252987_155252988insCAGCACCAC	ENST00000461007.1	+	0	1903_1904				AJ271736.10_ENST00000285718.7_RNA			Q9NQA3	WASH6_HUMAN	WAS protein family homolog 6 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)										TGGGGTactaacaccaccccca	0.658														2815	0.562101	0.5726	0.585	5008	,	,		4013	0.4742		0.6402	False		,,,				2504	0.5419																0								ENSG00000270726																																			AJ271736.10			0				Clone_based_vega_gene	AI042587		Xq28 and Yq12	2014-08-28	2008-01-16	2008-01-16	ENSG00000182484	ENSG00000182484		"""Pseudoautosomal regions / PAR2"", ""WAS protein homologs"""	31685	pseudogene	pseudogene			"""family with sequence similarity 39, member A"", ""chromosomes X and Y open reading frame 1"""	FAM39A, CXYorf1		10655549, 12566406, 18159949	Standard	NG_008380		Approved			Q9NQA3	OTTHUMG00000022677		X.37:g.155252987_155252988insCAGCACCAC		Somatic	NA	NA	NA		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	A6NGF1|Q8N305	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000461007.1	37	NULL		X																																																																																			-	-		0.658	WASH6P-016	KNOWN	basic	processed_transcript	ENSG00000270726	pseudogene	OTTHUMT00000058840.1	-	NG_008380			155252988	+1	no_errors	ENST00000285718	ensembl	human	known	74_37	rna	INS	0.959:1.000	CAGCACCAC
LINC01010	154092	genome.wustl.edu	37	6	134824057	134824057	+	lincRNA	SNP	A	A	G			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr6:134824057A>G	ENST00000431422.1	+	0	407				RP11-557H15.3_ENST00000417483.1_lincRNA	NR_038217.1|NR_038218.1				long intergenic non-protein coding RNA 1010																		GGTAATAGGCAAGCCAAGGCA	0.498																																																	0								ENSG00000236700																																			LINC01010			0			-	HGNC			6q23.2	2013-07-24			ENSG00000236700	ENSG00000236700		"""Long non-coding RNAs"""	48978	non-coding RNA	RNA, long non-coding							Standard	NR_038216		Approved				OTTHUMG00000015616		6.37:g.134824057A>G		Somatic	0	22	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	14	33.33		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000431422.1	37	NULL		6																																																																																			-	-		0.498	LINC01010-001	KNOWN	basic	lincRNA	LINC01010	lincRNA	OTTHUMT00000042322.1	A		-		134824057	+1	no_errors	ENST00000431422	ensembl	human	known	74_37	rna	SNP	0.013	G
BDP1	55814	genome.wustl.edu	37	5	70840897	70840897	+	Missense_Mutation	SNP	G	G	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr5:70840897G>T	ENST00000358731.4	+	32	6858	c.6595G>T	c.(6595-6597)Gtt>Ttt	p.V2199F	BDP1_ENST00000380675.2_Missense_Mutation_p.V335F	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	2199					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		CTCTCAGGAGGTTCACATGTT	0.438																																																	0								ENSG00000145734						113.0	108.0	109.0					5																	70840897		1852	4099	5951	BDP1	SO:0001583	missense	0			-	HGNC	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"""	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.6595G>T	5.37:g.70840897G>T	ENSP00000351575:p.Val2199Phe	Somatic	0	51	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	43	8.51	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	superfamily_Homeodomain-like,smart_SANT/Myb	p.V2199F	ENST00000358731.4	37	c.6595	CCDS43328.1	5	.	.	.	.	.	.	.	.	.	.	G	13.07	2.126193	0.37533	.	.	ENSG00000145734	ENST00000358731;ENST00000451951;ENST00000380675;ENST00000545546	T;T	0.52526	3.54;0.66	4.36	0.1	0.14510	.	0.932737	0.08996	N	0.863745	T	0.56262	0.1973	L	0.54323	1.7	0.09310	N	1	D;D	0.71674	0.964;0.998	P;D	0.65443	0.778;0.935	T	0.43507	-0.9387	10	0.62326	D	0.03	.	4.6587	0.12632	0.2041:0.3471:0.4489:0.0	.	2199;2199	A6H8Y1;A6H8Y1-2	BDP1_HUMAN;.	F	2199;1747;335;335	ENSP00000351575:V2199F;ENSP00000370050:V335F	ENSP00000351575:V2199F	V	+	1	0	BDP1	70876653	0.334000	0.24739	0.001000	0.08648	0.043000	0.13939	0.839000	0.27586	0.176000	0.19873	-0.136000	0.14681	GTT	-	NULL		0.438	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	BDP1	protein_coding	OTTHUMT00000374681.2	G	NM_018429	-		70840897	+1	no_errors	ENST00000358731	ensembl	human	known	74_37	missense	SNP	0.000	T
RGMB	285704	genome.wustl.edu	37	5	98129279	98129279	+	Missense_Mutation	SNP	C	C	A			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr5:98129279C>A	ENST00000513185.1	+	3	1572	c.1136C>A	c.(1135-1137)aCt>aAt	p.T379N	RGMB_ENST00000308234.7_Missense_Mutation_p.T420N			Q6NW40	RGMB_HUMAN	repulsive guidance molecule family member b	379					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell adhesion (GO:0007155)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	anchored component of plasma membrane (GO:0046658)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)	identical protein binding (GO:0042802)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	10		all_cancers(142;2.76e-08)|all_epithelial(76;2.98e-11)|all_lung(232;0.000485)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0587)		CTGCTCACCACTGGTGATGCC	0.562																																																	0								ENSG00000174136						87.0	86.0	86.0					5																	98129279		2096	4230	6326	RGMB	SO:0001583	missense	0			-	HGNC	AK074887	CCDS47251.1	5q21.1	2013-11-06	2013-11-06		ENSG00000174136	ENSG00000174136			26896	protein-coding gene	gene with protein product		612687	"""RGM domain family, member B"""			19324014	Standard	NM_001012761		Approved	FLJ90406, DRAGON	uc003knc.3	Q6NW40	OTTHUMG00000162745	ENST00000513185.1:c.1136C>A	5.37:g.98129279C>A	ENSP00000423256:p.Thr379Asn	Somatic	0	50	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	22	30	42.31	D6R9A0|Q8NC92	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_RGM_C,pfam_RGM_N	p.T420N	ENST00000513185.1	37	c.1259		5	.	.	.	.	.	.	.	.	.	.	C	21.5	4.164881	0.78339	.	.	ENSG00000174136	ENST00000308234;ENST00000513185	D;D	0.90385	-2.66;-2.66	5.62	4.74	0.60224	Repulsive guidance molecule, C-terminal (1);	0.045263	0.85682	N	0.000000	D	0.95452	0.8523	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95983	0.8979	10	0.87932	D	0	-14.8558	15.757	0.78043	0.1377:0.8623:0.0:0.0	.	379	Q6NW40	RGMB_HUMAN	N	420;379	ENSP00000308219:T420N;ENSP00000423256:T379N	ENSP00000308219:T420N	T	+	2	0	RGMB	98157179	1.000000	0.71417	0.916000	0.36221	0.976000	0.68499	7.784000	0.85713	1.328000	0.45358	0.655000	0.94253	ACT	-	pfam_RGM_C		0.562	RGMB-003	KNOWN	basic	protein_coding	RGMB	protein_coding	OTTHUMT00000370308.1	C	NM_173670	-		98129279	+1	no_errors	ENST00000308234	ensembl	human	known	74_37	missense	SNP	1.000	A
WNT2B	7482	genome.wustl.edu	37	1	113057686	113057686	+	Missense_Mutation	SNP	C	C	A			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr1:113057686C>A	ENST00000369684.4	+	2	858	c.373C>A	c.(373-375)Cac>Aac	p.H125N	WNT2B_ENST00000256640.5_Missense_Mutation_p.H33N|WNT2B_ENST00000478360.1_3'UTR|RP4-671G15.2_ENST00000608357.1_RNA|WNT2B_ENST00000369686.5_Missense_Mutation_p.H106N	NM_024494.2	NP_078613.1	Q93097	WNT2B_HUMAN	wingless-type MMTV integration site family, member 2B	125					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)			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)		GGACCGGGACCACACCGTCTT	0.587																																																	0								ENSG00000134245						77.0	56.0	63.0					1																	113057686		2203	4300	6503	WNT2B	SO:0001583	missense	0			-	HGNC	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.373C>A	1.37:g.113057686C>A	ENSP00000358698:p.His125Asn	Somatic	0	32	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	26	13.33	O14903|Q5TEH9|Q5TEI2|Q9HDC1|Q9HDC2	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Wnt,smart_Wnt,prints_Wnt,prints_Wnt2	p.H125N	ENST00000369684.4	37	c.373	CCDS847.1	1	.	.	.	.	.	.	.	.	.	.	C	12.62	1.992043	0.35131	.	.	ENSG00000134245	ENST00000256640;ENST00000369686;ENST00000369684	T;T;T	0.75260	-0.86;-0.92;-0.82	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.56775	0.2008	N	0.26130	0.795	0.80722	D	1	P;P	0.42908	0.664;0.793	P;B	0.45538	0.484;0.352	T	0.57213	-0.7850	10	0.15952	T	0.53	.	18.2577	0.90024	0.0:1.0:0.0:0.0	.	125;106	Q93097;Q93097-2	WNT2B_HUMAN;.	N	33;106;125	ENSP00000256640:H33N;ENSP00000358700:H106N;ENSP00000358698:H125N	ENSP00000256640:H33N	H	+	1	0	WNT2B	112859209	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.959000	0.70339	2.474000	0.83562	0.561000	0.74099	CAC	-	pfam_Wnt,smart_Wnt,prints_Wnt2		0.587	WNT2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	WNT2B	protein_coding	OTTHUMT00000030692.1	C	NM_004185	-		113057686	+1	no_errors	ENST00000369684	ensembl	human	known	74_37	missense	SNP	1.000	A
PIGC	5279	genome.wustl.edu	37	1	172411323	172411323	+	Missense_Mutation	SNP	T	T	A			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr1:172411323T>A	ENST00000367728.1	-	1	1903	c.440A>T	c.(439-441)gAc>gTc	p.D147V	PIGC_ENST00000484368.1_Intron|PIGC_ENST00000258324.1_Missense_Mutation_p.D147V|PIGC_ENST00000344529.4_Missense_Mutation_p.D147V|C1orf105_ENST00000367727.4_Intron			Q92535	PIGC_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class C	147					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)|phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			breast(1)|endometrium(1)|kidney(1)|lung(1)	4						ATAGATGGTGTCAGTGCTGAC	0.478																																																	0								ENSG00000135845						66.0	58.0	61.0					1																	172411323		2203	4300	6503	PIGC	SO:0001583	missense	0			-	HGNC	BC006539	CCDS1302.1	1q23-q25	2013-02-26	2006-06-28		ENSG00000135845	ENSG00000135845	2.4.1.198	"""Phosphatidylinositol glycan anchor biosynthesis"""	8960	protein-coding gene	gene with protein product	"""phosphatidylinositol N-acetylglucosaminyltransferase"""	601730	"""phosphatidylinositol glycan, class C"""			8806613, 9325057	Standard	NM_153747		Approved		uc001gio.3	Q92535	OTTHUMG00000034751	ENST00000367728.1:c.440A>T	1.37:g.172411323T>A	ENSP00000356702:p.Asp147Val	Somatic	0	16	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	8	10	44.44	O14491	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Plno_GlcNAc_GPI2,pirsf_Plno_GlcNAc_GPI2	p.D147V	ENST00000367728.1	37	c.440	CCDS1302.1	1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.190050	0.78789	.	.	ENSG00000135845	ENST00000344529;ENST00000367728;ENST00000258324	T;T;T	0.71341	-0.56;-0.56;-0.56	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	T	0.74711	0.3752	M	0.91140	3.18	0.80722	D	1	P	0.50617	0.937	P	0.46940	0.532	T	0.82416	-0.0468	10	0.87932	D	0	-30.8042	13.6827	0.62496	0.0:0.0:0.0:1.0	.	147	Q92535	PIGC_HUMAN	V	147	ENSP00000356701:D147V;ENSP00000356702:D147V;ENSP00000258324:D147V	ENSP00000258324:D147V	D	-	2	0	PIGC	170677946	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.528000	0.81941	1.917000	0.55516	0.528000	0.53228	GAC	-	pfam_Plno_GlcNAc_GPI2,pirsf_Plno_GlcNAc_GPI2		0.478	PIGC-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	PIGC	protein_coding	OTTHUMT00000084068.1	T	NM_153747	-		172411323	-1	no_errors	ENST00000258324	ensembl	human	known	74_37	missense	SNP	1.000	A
UNC13C	440279	genome.wustl.edu	37	15	54305434	54305435	+	Frame_Shift_Del	DEL	GA	GA	-	rs376146156		TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	GA	GA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr15:54305434_54305435delGA	ENST00000260323.11	+	1	334_335	c.334_335delGA	c.(334-336)gatfs	p.D112fs	UNC13C_ENST00000537900.1_Frame_Shift_Del_p.D112fs|UNC13C_ENST00000545554.1_Frame_Shift_Del_p.D112fs	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	112					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		AACCAACAGTGATAATGAGGAT	0.421																																																	0								ENSG00000137766																																			UNC13C	SO:0001589	frameshift_variant	0				HGNC	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.334_335delGA	15.37:g.54305434_54305435delGA	ENSP00000260323:p.Asp112fs	Somatic	0	25	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	2	20	9.09	Q0P613|Q8ND48|Q96NP3	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Munc13_subgr_dom-2,pfam_Ca-dep_secretion_activator,pfam_C2_dom,pfam_Prot_Kinase_C-like_PE/DAG-bd,superfamily_C2_dom,smart_Prot_Kinase_C-like_PE/DAG-bd,smart_C2_dom,pfscan_C2_dom,pfscan_Prot_Kinase_C-like_PE/DAG-bd,prints_C2_dom	p.D112fs	ENST00000260323.11	37	c.334_335	CCDS45264.1	15																																																																																			-	NULL		0.421	UNC13C-001	KNOWN	basic|CCDS	protein_coding	UNC13C	protein_coding	OTTHUMT00000419028.3	GA	NM_173166			54305435	+1	no_errors	ENST00000260323	ensembl	human	known	74_37	frame_shift_del	DEL	0.453:0.448	-
BUB1B	701	genome.wustl.edu	37	15	40504782	40504782	+	Missense_Mutation	SNP	G	G	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr15:40504782G>T	ENST00000287598.6	+	19	2663	c.2468G>T	c.(2467-2469)tGc>tTc	p.C823F	BUB1B_ENST00000412359.3_Missense_Mutation_p.C837F	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	823	Protein kinase.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|protein localization to chromosome, centromeric region (GO:0071459)|protein localization to kinetochore (GO:0034501)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|condensed chromosome kinetochore (GO:0000777)|condensed chromosome outer kinetochore (GO:0000940)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|perinuclear region of cytoplasm (GO:0048471)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(1)|stomach(2)|urinary_tract(2)	36		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		GATCATTTTTGCAGCTGTTAT	0.333			"""Mis, N, F, S"""			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome																														yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	0								ENSG00000156970						119.0	113.0	115.0					15																	40504782		2203	4300	6503	BUB1B	SO:0001583	missense	0	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	-	HGNC	AF107297	CCDS10053.1	15q15	2014-09-17	2013-01-17		ENSG00000156970	ENSG00000156970			1149	protein-coding gene	gene with protein product		602860	"""budding uninhibited by benzimidazoles 1 (yeast homolog), beta"", ""budding uninhibited by benzimidazoles 1 homolog beta (yeast)"""			9889005	Standard	NM_001211		Approved	BUBR1, MAD3L, Bub1A, SSK1	uc001zkx.4	O60566	OTTHUMG00000129877	ENST00000287598.6:c.2468G>T	15.37:g.40504782G>T	ENSP00000287598:p.Cys823Phe	Somatic	0	62	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	38	9.52	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Mad3_BUB1_I,pfam_Prot_kinase_dom,superfamily_Kinase-like_dom,smart_Mad3_BUB1_I	p.C837F	ENST00000287598.6	37	c.2510	CCDS10053.1	15	.	.	.	.	.	.	.	.	.	.	G	15.18	2.755885	0.49362	.	.	ENSG00000156970	ENST00000287598;ENST00000412359;ENST00000442874	T;T	0.19669	2.13;2.13	5.1	5.1	0.69264	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);	0.169618	0.42682	D	0.000669	T	0.35422	0.0931	L	0.54323	1.7	0.44771	D	0.997771	D	0.62365	0.991	D	0.65773	0.938	T	0.05533	-1.0879	10	0.11182	T	0.66	-7.7283	13.5093	0.61502	0.0:0.0:0.844:0.1559	.	823	O60566	BUB1B_HUMAN	F	823;837;706	ENSP00000287598:C823F;ENSP00000398470:C837F	ENSP00000287598:C823F	C	+	2	0	BUB1B	38292074	1.000000	0.71417	0.998000	0.56505	0.621000	0.37620	3.848000	0.55903	2.368000	0.80403	0.655000	0.94253	TGC	-	pfam_Prot_kinase_dom,superfamily_Kinase-like_dom		0.333	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BUB1B	protein_coding	OTTHUMT00000252122.4	G		-		40504782	+1	no_errors	ENST00000412359	ensembl	human	known	74_37	missense	SNP	1.000	T
OFD1	8481	genome.wustl.edu	37	X	13757181	13757181	+	Intron	SNP	C	C	A			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chrX:13757181C>A	ENST00000340096.6	+	5	739				OFD1_ENST00000490265.1_Intron|OFD1_ENST00000380550.3_Intron|OFD1_ENST00000398395.3_Intron|OFD1_ENST00000380567.1_Intron	NM_003611.2	NP_003602.1	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1						axoneme assembly (GO:0035082)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|gamma-tubulin binding (GO:0043015)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	25						TAGAGAACAGCAACAGTTTTC	0.299																																																	0								ENSG00000046651						20.0	20.0	20.0					X																	13757181		2169	4270	6439	OFD1	SO:0001627	intron_variant	0			-	HGNC	Y15164	CCDS14157.1	Xp22	2014-06-18			ENSG00000046651	ENSG00000046651			2567	protein-coding gene	gene with protein product		300170	"""retinitis pigmentosa 23 (X-linked recessive)"""	CXorf5, RP23		9722947, 9215688, 22619378	Standard	NM_003611		Approved	71-7A, JBTS10	uc004cvp.4	O75665	OTTHUMG00000021159	ENST00000340096.6:c.412+30C>A	X.37:g.13757181C>A		Somatic	0	54	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	44	8.33	B9ZVU5|O75666|Q4VAK4	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000340096.6	37	NULL	CCDS14157.1	X																																																																																			-	-		0.299	OFD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	OFD1	protein_coding	OTTHUMT00000055808.1	C	NM_003611	-		13757181	+1	no_errors	ENST00000466534	ensembl	human	known	74_37	rna	SNP	0.000	A
CFAP54	144535	genome.wustl.edu	37	12	97102550	97102550	+	Silent	SNP	C	C	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr12:97102550C>T	ENST00000524981.4	+	48	6716	c.6693C>T	c.(6691-6693)aaC>aaT	p.N2231N				Q96N23	CL055_HUMAN		0																	TAATTACCAACAAGAGCAAAC	0.348																																																	0								ENSG00000188596						66.0	69.0	68.0					12																	97102550		2203	4299	6502	C12orf55	SO:0001819	synonymous_variant	0			-	HGNC																												ENST00000524981.4:c.6693C>T	12.37:g.97102550C>T		Somatic	0	16	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	14	20	41.18		Silent	SNP	NA	NA	NA	NA	NA	NA	superfamily_Fibronectin_type3	p.N2231	ENST00000524981.4	37	c.6693		12																																																																																			-	NULL		0.348	C12orf55-003	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	C12orf55	protein_coding	OTTHUMT00000395046.4	C		-		97102550	+1	no_errors	ENST00000524981	ensembl	human	putative	74_37	silent	SNP	0.000	T
GMEB1	10691	genome.wustl.edu	37	1	29041385	29041386	+	3'UTR	INS	-	-	A	rs372271712|rs559808019|rs528044464	byFrequency	TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr1:29041385_29041386insA	ENST00000294409.2	+	0	1912				GMEB1_ENST00000373816.1_3'UTR|GMEB1_ENST00000361872.4_3'UTR|GMEB1_ENST00000480454.1_3'UTR	NM_006582.3	NP_006573.2	Q9Y692	GMEB1_HUMAN	glucocorticoid modulatory element binding protein 1						transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)	11		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Breast(348;0.00502)|Renal(390;0.00555)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		GACCCTTTTTTAAAAAAAAAAA	0.342																																																	0								ENSG00000162419																																			GMEB1	SO:0001624	3_prime_UTR_variant	0				HGNC	AF099013	CCDS327.1, CCDS328.1	1p35	2008-02-05			ENSG00000162419	ENSG00000162419			4370	protein-coding gene	gene with protein product		604409				10386584, 10523663	Standard	NM_006582		Approved	P96PIF, PIF96	uc001bra.3	Q9Y692	OTTHUMG00000003647	ENST00000294409.2:c.*100->A	1.37:g.29041396_29041396dupA		Somatic	0	21	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	24	11.11	B1AT48|Q9NWH1|Q9UKD0	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000294409.2	37	NULL	CCDS327.1	1																																																																																			-	-		0.342	GMEB1-003	KNOWN	basic|CCDS	protein_coding	GMEB1	protein_coding	OTTHUMT00000010333.1	-	NM_006582			29041386	+1	no_errors	ENST00000480454	ensembl	human	known	74_37	rna	INS	0.437:0.252	A
CYP2G1P	22952	genome.wustl.edu	37	19	41397318	41397318	+	Intron	SNP	C	C	A			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr19:41397318C>A	ENST00000601627.1	+	2	119				CYP2G1P_ENST00000252909.4_RNA																							GTCTGTCTGTCTCCTTTAATA	0.428																																																	0								ENSG00000130612																																			CYP2G1P	SO:0001627	intron_variant	0			-	HGNC																												ENST00000601627.1:c.120-578C>A	19.37:g.41397318C>A		Somatic	0	36	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	16	15.79		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000601627.1	37	NULL		19																																																																																			-	-		0.428	CTC-490E21.12-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	CYP2G1P	protein_coding	OTTHUMT00000463921.1	C		-		41397318	+1	no_errors	ENST00000252909	ensembl	human	known	74_37	rna	SNP	0.003	A
CLCN2	1181	genome.wustl.edu	37	3	184071063	184071063	+	Missense_Mutation	SNP	G	G	A	rs9820367	byFrequency	TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr3:184071063G>A	ENST00000265593.4	-	17	2174	c.2003C>T	c.(2002-2004)aCc>aTc	p.T668I	CLCN2_ENST00000423355.2_3'UTR|EIF2B5_ENST00000444495.1_Intron|CLCN2_ENST00000434054.2_Missense_Mutation_p.T624I|CLCN2_ENST00000457512.1_Missense_Mutation_p.T668I|CLCN2_ENST00000475279.1_5'Flank|CLCN2_ENST00000344937.7_Missense_Mutation_p.T651I	NM_004366.5	NP_004357.3	P51788	CLCN2_HUMAN	chloride channel, voltage-sensitive 2	668			T -> S (in dbSNP:rs9820367). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17762171, ECO:0000269|PubMed:7795595}.		cell differentiation involved in salivary gland development (GO:0060689)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|retina development in camera-type eye (GO:0060041)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|voltage-gated chloride channel activity (GO:0005247)	p.T668S(1)		breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;2.22e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Lubiprostone(DB01046)	AGCCTCAGGGGTAGGGGGACC	0.617																																																	1	Substitution - Missense(1)	stomach(1)						ENSG00000114859						92.0	103.0	99.0					3																	184071063		2203	4300	6503	CLCN2	SO:0001583	missense	0			-	HGNC	S77770	CCDS3263.1, CCDS54690.1, CCDS54691.1, CCDS54692.1	3q27.1	2013-09-19	2012-02-23		ENSG00000114859	ENSG00000114859		"""Ion channels / Chloride channels : Voltage-sensitive"""	2020	protein-coding gene	gene with protein product		600570	"""chloride channel 2"""			7795595	Standard	NM_004366		Approved	CLC2, EJM6, ClC-2	uc003foi.4	P51788	OTTHUMG00000156747	ENST00000265593.4:c.2003C>T	3.37:g.184071063G>A	ENSP00000265593:p.Thr668Ile	Somatic	0	60	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	35	15	34.31	B4DQT9|B4DZ58|E9PBD9|E9PCD2|O14864|Q6IPA9|Q8WU13	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Cl-channel_volt-gated,pfam_CBS_dom,superfamily_Cl-channel_core,prints_Cl-channel_volt-gated,prints_Cl-channel-2	p.T668I	ENST00000265593.4	37	c.2003	CCDS3263.1	3	.	.	.	.	.	.	.	.	.	.	c	18.93	3.727469	0.69074	.	.	ENSG00000114859	ENST00000265593;ENST00000344937;ENST00000434054;ENST00000457512	D;D;D;D	0.84944	-1.87;-1.82;-1.92;-1.9	5.62	4.72	0.59763	.	0.518488	0.23049	N	0.052518	T	0.74473	0.3721	N	0.19112	0.55	0.80722	D	1	B;B;B;B	0.20164	0.02;0.042;0.015;0.02	B;B;B;B	0.24541	0.017;0.024;0.054;0.017	T	0.70096	-0.4966	10	0.52906	T	0.07	-12.2828	8.3489	0.32290	0.0:0.6212:0.2989:0.0799	.	624;668;651;668	E9PBD9;E9PCD2;P51788-3;P51788	.;.;.;CLCN2_HUMAN	I	668;651;624;668	ENSP00000265593:T668I;ENSP00000345056:T651I;ENSP00000400425:T624I;ENSP00000391928:T668I	ENSP00000265593:T668I	T	-	2	0	CLCN2	185553757	0.002000	0.14202	0.975000	0.42487	0.639000	0.38242	0.790000	0.26900	1.395000	0.46643	-0.215000	0.12644	ACC	-	NULL		0.617	CLCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CLCN2	protein_coding	OTTHUMT00000345571.1	G		-		184071063	-1	no_errors	ENST00000265593	ensembl	human	known	74_37	missense	SNP	0.990	A
P2RX2	22953	genome.wustl.edu	37	12	133198160	133198160	+	Intron	SNP	G	G	A	rs199514327		TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr12:133198160G>A	ENST00000389110.3	+	10	1099				P2RX2_ENST00000449132.2_Intron|P2RX2_ENST00000352418.4_Intron|P2RX2_ENST00000351222.4_Intron|P2RX2_ENST00000343948.4_Missense_Mutation_p.G366R|P2RX2_ENST00000348800.5_Intron|P2RX2_ENST00000350048.5_Intron	NM_170682.2|NM_170683.2|NM_174873.1	NP_733782.1|NP_733783.1|NP_777362.1	Q9UBL9	P2RX2_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 2						behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of hypoxic conditions in blood by carotid body chemoreceptor signaling (GO:0003029)|ion transmembrane transport (GO:0034220)|neuromuscular junction development (GO:0007528)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to hypoxia (GO:0001666)|sensory perception of sound (GO:0007605)|sensory perception of taste (GO:0050909)|skeletal muscle fiber development (GO:0048741)|urinary bladder smooth muscle contraction (GO:0014832)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|dendritic spine (GO:0043197)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadmium ion binding (GO:0046870)|cobalt ion binding (GO:0050897)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|identical protein binding (GO:0042802)|ligand-gated ion channel activity (GO:0015276)|mercury ion binding (GO:0045340)|nickel cation binding (GO:0016151)|phosphatidylinositol binding (GO:0035091)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|kidney(2)|large_intestine(2)|liver(2)|lung(8)|ovary(1)|prostate(3)	20	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0767)		OV - Ovarian serous cystadenocarcinoma(86;2.32e-08)|Epithelial(86;8.62e-08)|all cancers(50;4.5e-06)		CAGCGGGTGCGGGGGGTCCAC	0.582																																																	0								ENSG00000187848						39.0	45.0	43.0					12																	133198160		2203	4300	6503	P2RX2	SO:0001627	intron_variant	0			-	HGNC	AF109387	CCDS31930.1, CCDS31931.1, CCDS31932.1, CCDS31933.1, CCDS31934.1, CCDS31935.1, CCDS61286.1, CCDS73548.1	12q24.33	2013-03-22			ENSG00000187848	ENSG00000187848		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	15459	protein-coding gene	gene with protein product		600844	"""deafness, autosomal dominant 41"""	DFNA41		10570044, 7523952, 23345450	Standard	XM_005266154		Approved	P2X2	uc001ukk.1	Q9UBL9	OTTHUMG00000168018	ENST00000389110.3:c.1062+34G>A	12.37:g.133198160G>A		Somatic	0	43	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	14	23	37.84	A6NGB4|A6NH93|A6NHC2|A6NHU3|A6NIG9|Q6V9R6|Q9NR37|Q9NR38|Q9UHD5|Q9UHD6|Q9UHD7|Q9Y637|Q9Y638	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_P2X_purnocptor,prints_P2X2_purnocptor,prints_P2X_purnocptor,tigrfam_P2X_purnocptor	p.G366R	ENST00000389110.3	37	c.1096	CCDS31931.1	12	.	.	.	.	.	.	.	.	.	.	G	0.025	-1.378800	0.01204	.	.	ENSG00000187848	ENST00000343948	T	0.05855	3.38	4.24	-1.39	0.08997	.	0.858235	0.09425	U	0.803884	T	0.02533	0.0077	.	.	.	0.09310	N	0.999999	P	0.41624	0.757	B	0.27076	0.076	T	0.42982	-0.9419	8	.	.	.	.	2.6482	0.04991	0.1658:0.263:0.4368:0.1344	.	366	Q9UBL9-4	.	R	366	ENSP00000343339:G366R	.	G	+	1	0	P2RX2	131708233	0.000000	0.05858	0.001000	0.08648	0.239000	0.25481	-0.978000	0.03778	0.076000	0.16826	0.555000	0.69702	GGG	-	NULL		0.582	P2RX2-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	P2RX2	protein_coding	OTTHUMT00000397542.1	G		rs199514327		133198160	+1	no_errors	ENST00000343948	ensembl	human	known	74_37	missense	SNP	0.000	A
OCIAD1	54940	genome.wustl.edu	37	4	48835496	48835496	+	Missense_Mutation	SNP	G	G	C			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr4:48835496G>C	ENST00000381473.3	+	3	555	c.137G>C	c.(136-138)aGa>aCa	p.R46T	OCIAD1_ENST00000444354.2_Missense_Mutation_p.R46T|OCIAD1_ENST00000509122.1_Intron|OCIAD1_ENST00000506801.1_Intron|OCIAD1_ENST00000508293.1_Missense_Mutation_p.R46T|OCIAD1_ENST00000264312.7_Missense_Mutation_p.R46T|OCIAD1_ENST00000513391.2_Missense_Mutation_p.R46T|OCIAD1_ENST00000396448.2_Missense_Mutation_p.R46T|OCIAD1_ENST00000512981.1_3'UTR|OCIAD1_ENST00000425583.2_Missense_Mutation_p.R46T	NM_001079839.2	NP_001073308.1	Q9NX40	OCAD1_HUMAN	OCIA domain containing 1	46	OCIA.					endosome (GO:0005768)|membrane (GO:0016020)|mitochondrion (GO:0005739)				breast(2)|large_intestine(2)|lung(2)|prostate(1)|skin(2)	9						TTCTGGTTCAGATGTGAGTTC	0.333																																																	0								ENSG00000109180						50.0	52.0	52.0					4																	48835496		2203	4300	6503	OCIAD1	SO:0001583	missense	0			-	HGNC	AF324350	CCDS3484.1, CCDS43228.1, CCDS47052.1	4p11	2010-03-19			ENSG00000109180	ENSG00000109180			16074	protein-coding gene	gene with protein product						11162530, 18328549	Standard	NM_017830		Approved	FLJ20455, TPA018, OCIA, Asrij	uc010igk.3	Q9NX40	OTTHUMG00000102095	ENST00000381473.3:c.137G>C	4.37:g.48835496G>C	ENSP00000370882:p.Arg46Thr	Somatic	0	45	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	26	39	40.00	C9K030|G8JLN7|Q9BZE8	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_OCIA	p.R46T	ENST00000381473.3	37	c.137	CCDS3484.1	4	.	.	.	.	.	.	.	.	.	.	G	22.9	4.352063	0.82132	.	.	ENSG00000109180	ENST00000504654;ENST00000509664;ENST00000514981;ENST00000508996;ENST00000507210;ENST00000264312;ENST00000396448;ENST00000512236;ENST00000509164;ENST00000511102;ENST00000381473;ENST00000444354;ENST00000509963;ENST00000425583;ENST00000508293;ENST00000513391	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36;-0.36	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	D	0.82388	0.5026	M	0.81112	2.525	0.44890	D	0.997908	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.984;0.984;0.999	D	0.84688	0.0721	10	0.72032	D	0.01	-17.4095	15.8864	0.79251	0.0:0.0:1.0:0.0	.	46;46;46	Q9NX40-3;Q9NX40-2;Q9NX40	.;.;OCAD1_HUMAN	T	46	ENSP00000423381:R46T;ENSP00000422171:R46T;ENSP00000423845:R46T;ENSP00000424252:R46T;ENSP00000420917:R46T;ENSP00000264312:R46T;ENSP00000379725:R46T;ENSP00000426386:R46T;ENSP00000426902:R46T;ENSP00000427389:R46T;ENSP00000370882:R46T;ENSP00000399656:R46T;ENSP00000425633:R46T;ENSP00000416943:R46T;ENSP00000423002:R46T;ENSP00000423909:R46T	ENSP00000264312:R46T	R	+	2	0	OCIAD1	48530253	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.398000	0.66308	2.546000	0.85860	0.655000	0.94253	AGA	-	pfam_OCIA		0.333	OCIAD1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	OCIAD1	protein_coding	OTTHUMT00000361812.3	G	NM_017830	-		48835496	+1	no_errors	ENST00000264312	ensembl	human	known	74_37	missense	SNP	1.000	C
SPTA1	6708	genome.wustl.edu	37	1	158581004	158581004	+	3'UTR	SNP	T	T	C			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr1:158581004T>C	ENST00000368147.4	-	0	7490				SPTA1_ENST00000485680.1_5'UTR	NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1						actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TGCCCCCCAGTAAATTTCCCA	0.463																																																	0								ENSG00000163554						41.0	43.0	42.0					1																	158581004		1910	4124	6034	SPTA1	SO:0001624	3_prime_UTR_variant	0			-	HGNC	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.*50A>G	1.37:g.158581004T>C		Somatic	0	32	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	10	17	37.04	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000368147.4	37	NULL	CCDS41423.1	1																																																																																			-	-		0.463	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SPTA1	protein_coding	OTTHUMT00000051851.3	T	NM_003126	-		158581004	-1	no_errors	ENST00000485680	ensembl	human	known	74_37	rna	SNP	0.000	C
ENTPD1	953	genome.wustl.edu	37	10	97515949	97515949	+	5'UTR	DEL	G	G	-	rs200451742	byFrequency	TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr10:97515949delG	ENST00000371205.4	+	0	236				ENTPD1_ENST00000539125.1_5'UTR|ENTPD1_ENST00000543964.1_Intron|ENTPD1_ENST00000371207.3_Intron|ENTPD1_ENST00000371203.5_5'UTR|ENTPD1-AS1_ENST00000416301.1_RNA|ENTPD1_ENST00000453258.2_Intron			P49961	ENTP1_HUMAN	ectonucleoside triphosphate diphosphohydrolase 1						ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|purine ribonucleoside diphosphate catabolic process (GO:0009181)	basal lamina (GO:0005605)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|skin(1)	16		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)		AGCAGAGGCTGGGGGGGGGAA	0.493																																																	0								ENSG00000226688						25.0	29.0	27.0					10																	97515949		2203	4300	6503	ENTPD1-AS1	SO:0001623	5_prime_UTR_variant	0				HGNC	S73813	CCDS7444.1, CCDS53556.1, CCDS53557.1, CCDS53558.1, CCDS41554.1	10q24.1	2014-03-03			ENSG00000138185	ENSG00000138185		"""CD molecules"""	3363	protein-coding gene	gene with protein product		601752		CD39		9226376, 24482476	Standard	NM_001098175		Approved	NTPDase-1, ATPDase, SPG64	uc010qoj.2	P49961	OTTHUMG00000018818	ENST00000371205.4:c.-48G>-	10.37:g.97515949delG		Somatic	0	24	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	2	16	11.11	A9Z1X8|B4DWB9|B4E1X1|B7Z599|G3XAF6|Q5T561|Q5T562|Q86VV3|Q9UQQ9|Q9Y3Q9	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000371205.4	37	NULL	CCDS7444.1	10																																																																																			-	-		0.493	ENTPD1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	ENTPD1-AS1	protein_coding	OTTHUMT00000049566.1	G	NM_001776			97515949	-1	no_errors	ENST00000416301	ensembl	human	known	74_37	rna	DEL	0.906	-
ZNF729	100287226	genome.wustl.edu	37	19	22498491	22498491	+	Missense_Mutation	SNP	C	C	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr19:22498491C>T	ENST00000601693.1	+	4	2390	c.2272C>T	c.(2272-2274)Cat>Tat	p.H758Y	ZNF729_ENST00000357491.6_Missense_Mutation_p.H758Y			A6NN14	ZN729_HUMAN	zinc finger protein 729	758					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(1)|lung(32)|ovary(3)	41						CCTTAGAAAACATAAGGTAAT	0.338																																																	0								ENSG00000196350																																			ZNF729	SO:0001583	missense	0			-	HGNC		CCDS59368.1	19p12	2014-02-14			ENSG00000196350	ENSG00000196350		"""Zinc fingers, C2H2-type"", ""-"""	32464	protein-coding gene	gene with protein product							Standard	NM_001242680		Approved		uc021urs.1	A6NN14	OTTHUMG00000182938	ENST00000601693.1:c.2272C>T	19.37:g.22498491C>T	ENSP00000469582:p.His758Tyr	Somatic	0	38	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	6	21	22.22	M0QY45	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	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.H758Y	ENST00000601693.1	37	c.2272	CCDS59368.1	19	.	.	.	.	.	.	.	.	.	.	.	13.41	2.228880	0.39399	.	.	ENSG00000196350	ENST00000357491	D	0.86769	-2.17	0.996	0.996	0.19844	.	.	.	.	.	D	0.90738	0.7093	M	0.85542	2.76	.	.	.	.	.	.	.	.	.	D	0.91547	0.5254	6	0.87932	D	0	.	8.7778	0.34774	0.0:1.0:0.0:0.0	.	.	.	.	Y	758	ENSP00000350085:H758Y	ENSP00000350085:H758Y	H	+	1	0	ZNF729	22290331	0.132000	0.22450	0.012000	0.15200	0.012000	0.07955	1.976000	0.40579	0.416000	0.25844	0.416000	0.27883	CAT	-	smart_Znf_C2H2-like,pfscan_Znf_C2H2		0.338	ZNF729-001	NOVEL	basic|appris_principal|CCDS	protein_coding	ZNF729	protein_coding	OTTHUMT00000464396.1	C	XM_496301	-		22498491	+1	no_errors	ENST00000601693	ensembl	human	novel	74_37	missense	SNP	0.700	T
ETV5	2119	genome.wustl.edu	37	3	185797767	185797767	+	Silent	SNP	G	G	A			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr3:185797767G>A	ENST00000306376.5	-	7	735	c.489C>T	c.(487-489)gcC>gcT	p.A163A	ETV5_ENST00000537818.1_Silent_p.A205A|ETV5-AS1_ENST00000453370.1_RNA|ETV5_ENST00000434744.1_Silent_p.A163A	NM_004454.2	NP_004445.1	P41161	ETV5_HUMAN	ets variant 5	163					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|locomotory behavior (GO:0007626)|male germ-line stem cell asymmetric division (GO:0048133)|neuromuscular synaptic transmission (GO:0007274)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of synapse organization (GO:0050807)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	28	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)			CAGCTGCAGGGGCATGCCCTG	0.637			T	"""TMPRSS2, SCL45A3"""	Prostate																																			Dom	yes		3	3q28	2119	ets variant gene 5		E	0								ENSG00000244405						27.0	34.0	32.0					3																	185797767		2199	4299	6498	ETV5	SO:0001819	synonymous_variant	0			-	HGNC	BC007333	CCDS33906.1	3q28	2008-09-12	2008-09-12		ENSG00000244405	ENSG00000244405			3494	protein-coding gene	gene with protein product	"""ets-related molecule"""	601600	"""ets variant gene 5 (ets-related molecule)"""			8152800	Standard	NM_004454		Approved	ERM	uc003fpz.3	P41161	OTTHUMG00000156639	ENST00000306376.5:c.489C>T	3.37:g.185797767G>A		Somatic	0	33	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	8	16	33.33	A6NH46|B7Z7D7|Q6IBN5	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_ETS_PEA3_N,pfam_Ets_dom,smart_Ets_dom,pfscan_Ets_dom,prints_Ets_dom	p.A205	ENST00000306376.5	37	c.615	CCDS33906.1	3																																																																																			-	pfam_ETS_PEA3_N		0.637	ETV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ETV5	protein_coding	OTTHUMT00000344947.1	G	NM_004454	-		185797767	-1	no_errors	ENST00000537818	ensembl	human	known	74_37	silent	SNP	0.587	A
AKAP17A	8227	genome.wustl.edu	37	X	1713021	1713021	+	Silent	SNP	C	C	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chrX:1713021C>T	ENST00000313871.3	+	2	862	c.666C>T	c.(664-666)cgC>cgT	p.R222R	AKAP17A_ENST00000381261.3_Silent_p.R222R	NM_005088.2	NP_005079.2	Q02040	AK17A_HUMAN	A kinase (PRKA) anchor protein 17A	222	RRM.				B cell activation (GO:0042113)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)			breast(2)|endometrium(5)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)	26						TGCAGTACCGCGAGTACATGG	0.607													c|||	2801	0.559305	0.5832	0.5115	5008	,	,		19903	0.5268		0.5875	False		,,,				2504	0.5654																0								ENSG00000197976			2444,1962		683,1078,442	111.0	102.0	105.0		666	-0.7	0.0	X	dbSNP_134	105	4590,4002		1181,2228,887	no	coding-synonymous	AKAP17A	NM_005088.2		1864,3306,1329	TT,TC,CC		46.5782,44.5302,45.884		222/696	1713021	7034,5964	2203	4296	6499	AKAP17A	SO:0001819	synonymous_variant	0			-	HGNC	L03426	CCDS14116.1	Xp22.33 and Yp11.32	2010-09-08	2010-09-08	2010-09-08	ENSG00000197976	ENSG00000197976		"""Pseudoautosomal regions / PAR1"", ""A-kinase anchor proteins"""	18783	protein-coding gene	gene with protein product		312095, 465000	"""chromosome X and Y open reading frame 3"", ""splicing factor, arginine/serine-rich 17A"""	CXYorf3, SFRS17A		9736779, 1438229, 19840947	Standard	NR_027383		Approved	XE7, XE7Y, DXYS155E, MGC39904, 721P, CCDC133	uc004cqa.3	Q02040	OTTHUMG00000021063	ENST00000313871.3:c.666C>T	X.37:g.1713021C>T		Somatic	0	92	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	28	15.15	Q02832|Q2TB98|Q5JQ74|Q5JQ76|Q8N6U9	Silent	SNP	NA	NA	NA	NA	NA	NA	NULL	p.R222	ENST00000313871.3	37	c.666	CCDS14116.1	X																																																																																			-	NULL		0.607	AKAP17A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	AKAP17A	protein_coding	OTTHUMT00000055609.2	C	NM_005088	-		1713021	+1	no_errors	ENST00000313871	ensembl	human	known	74_37	silent	SNP	0.764	T
DARS	1615	genome.wustl.edu	37	2	136742985	136742985	+	Missense_Mutation	SNP	C	C	A			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr2:136742985C>A	ENST00000264161.4	-	1	269	c.54G>T	c.(52-54)atG>atT	p.M18I	AC093391.2_ENST00000419808.1_RNA|DARS_ENST00000537273.1_5'UTR|AC093391.2_ENST00000438432.1_RNA|AC093391.2_ENST00000444406.1_RNA|AC093391.2_ENST00000446492.1_RNA	NM_001349.2	NP_001340.2	P14868	SYDC_HUMAN	aspartyl-tRNA synthetase	18					aspartyl-tRNA aminoacylation (GO:0006422)|gene expression (GO:0010467)|protein complex assembly (GO:0006461)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacylase activity (GO:0004046)|aspartate-tRNA ligase activity (GO:0004815)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(2)	15				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)	CCGCCGCGTCCATGATCTCCC	0.697																																																	0								ENSG00000115866						43.0	48.0	46.0					2																	136742985		2203	4300	6503	DARS	SO:0001583	missense	0			-	HGNC	J05032	CCDS2180.1	2q21.3	2011-07-01			ENSG00000115866	ENSG00000115866	6.1.1.12	"""Aminoacyl tRNA synthetases / Class II"""	2678	protein-coding gene	gene with protein product	"""aspartate tRNA ligase 1, cytoplasmic"""	603084				2674137	Standard	NM_001349		Approved		uc002tux.1	P14868	OTTHUMG00000131741	ENST00000264161.4:c.54G>T	2.37:g.136742985C>A	ENSP00000264161:p.Met18Ile	Somatic	0	111	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	42	71	37.17	A8K3J2|D3DP77|Q2TNI3|Q32Q69|Q53HV4|Q53YC5|Q68CR9|Q9BW52	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_aa-tRNA-synt_II,pfam_NA-bd_OB_tRNA,superfamily_NA-bd_OB-fold,pfscan_aa-tRNA-synth_II,prints_Asp/Asn-tRNA-synth_IIb,tigrfam_Asp-tRNA_synthase	p.M18I	ENST00000264161.4	37	c.54	CCDS2180.1	2	.	.	.	.	.	.	.	.	.	.	C	17.19	3.325285	0.60743	.	.	ENSG00000115866	ENST00000264161	D	0.82081	-1.57	4.83	4.83	0.62350	.	0.442639	0.27384	N	0.019619	T	0.67942	0.2947	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.64829	-0.6315	10	0.44086	T;T	0.13;0.13	-7.7323	13.3107	0.60378	0.0:1.0:0.0:0.0	.	18	P14868	SYDC_HUMAN	I	18	ENSP00000264161:M18I	ENSP00000264161:M18I;ENSP00000264161:M18I	M	-	3	0	DARS	136459455	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.683000	0.54663	2.500000	0.84329	0.467000	0.42956	ATG	-	NULL		0.697	DARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DARS	protein_coding	OTTHUMT00000254660.5	C	NM_001349	-		136742985	-1	no_errors	ENST00000264161	ensembl	human	known	74_37	missense	SNP	1.000	A
SETX	23064	genome.wustl.edu	37	9	135139194	135139196	+	3'UTR	DEL	TCT	TCT	-	rs371444348|rs112251805|rs111411587	byFrequency	TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	TCT	TCT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr9:135139194_135139196delTCT	ENST00000224140.5	-	0	8646_8648				SETX_ENST00000477049.1_5'UTR|SETX_ENST00000372169.2_3'UTR|SETX_ENST00000393220.1_3'UTR	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin						cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		CCTCCTCCCATCTTTTTTTTTTT	0.365																																																	0								ENSG00000107290																																			SETX	SO:0001624	3_prime_UTR_variant	0				HGNC	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"""amyotrophic lateral sclerosis 4"", ""spinocerebellar ataxia, recessive, non-Friedreich type 1"""	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.*432AGA>-	9.37:g.135139194_135139196delTCT		Somatic	0	40	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	22	12.00	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000224140.5	37	NULL	CCDS6947.1	9																																																																																			-	-		0.365	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SETX	protein_coding	OTTHUMT00000054774.3	TCT	NM_015046			135139196	-1	no_errors	ENST00000477049	ensembl	human	known	74_37	rna	DEL	0.000:0.000:0.000	-
FKBP15	23307	genome.wustl.edu	37	9	115932891	115932891	+	Missense_Mutation	SNP	G	G	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr9:115932891G>T	ENST00000238256.3	-	25	2794	c.2677C>A	c.(2677-2679)Cag>Aag	p.Q893K		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	893					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						TGGAACACCTGGTTCATGATC	0.448																																																	0								ENSG00000119321						183.0	176.0	178.0					9																	115932891		1940	4145	6085	FKBP15	SO:0001583	missense	0			-	HGNC	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.2677C>A	9.37:g.115932891G>T	ENSP00000238256:p.Gln893Lys	Somatic	0	37	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	30	11.76	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_PPIase_FKBP_dom,superfamily_Regulat_G_prot_signal_superfam,pfscan_PPIase_FKBP_dom	p.Q893K	ENST00000238256.3	37	c.2677	CCDS48007.1	9	.	.	.	.	.	.	.	.	.	.	G	10.99	1.508544	0.27036	.	.	ENSG00000119321	ENST00000446284;ENST00000238256	T;T	0.21191	2.02;2.03	5.86	4.93	0.64822	.	.	.	.	.	T	0.18593	0.0446	L	0.50333	1.59	0.25843	N	0.984037	B;B	0.18610	0.029;0.001	B;B	0.15484	0.013;0.002	T	0.26430	-1.0103	9	0.08179	T	0.78	-5.7535	12.1204	0.53887	0.0:0.0:0.7034:0.2966	.	474;893	B4DVS2;Q5T1M5	.;FKB15_HUMAN	K	918;893	ENSP00000416158:Q918K;ENSP00000238256:Q893K	ENSP00000238256:Q893K	Q	-	1	0	FKBP15	114972712	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.555000	0.45854	2.777000	0.95525	0.655000	0.94253	CAG	-	NULL		0.448	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	FKBP15	protein_coding		G	NM_015258	-		115932891	-1	no_errors	ENST00000238256	ensembl	human	known	74_37	missense	SNP	1.000	T
PNKP	11284	genome.wustl.edu	37	19	50370442	50370442	+	Frame_Shift_Del	DEL	G	G	-			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr19:50370442delG	ENST00000322344.3	-	2	129	c.20delC	c.(19-21)ccgfs	p.P7fs	PNKP_ENST00000595792.1_5'UTR|PNKP_ENST00000600573.1_Frame_Shift_Del_p.P7fs|PNKP_ENST00000600910.1_Frame_Shift_Del_p.P7fs|PNKP_ENST00000596014.1_Frame_Shift_Del_p.P7fs	NM_007254.3	NP_009185.2	Q96T60	PNKP_HUMAN	polynucleotide kinase 3'-phosphatase	7	FHA.				dephosphorylation (GO:0016311)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide phosphorylation (GO:0046939)|nucleotide-excision repair, DNA damage removal (GO:0000718)|polynucleotide 3' dephosphorylation (GO:0098506)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|damaged DNA binding (GO:0003684)|double-stranded DNA binding (GO:0003690)|endonuclease activity (GO:0004519)|nucleotide kinase activity (GO:0019201)|polynucleotide 3'-phosphatase activity (GO:0046403)|purine nucleotide binding (GO:0017076)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|urinary_tract(1)	19		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0118)|OV - Ovarian serous cystadenocarcinoma(262;0.0134)		CAAGCGGCCCGGGGCCTCCAC	0.721								Other BER factors																																									0								ENSG00000039650						9.0	11.0	11.0					19																	50370442		2022	4056	6078	PNKP	SO:0001589	frameshift_variant	0				HGNC	AF126486	CCDS12783.1	19q13.3-q13.4	2008-02-05				ENSG00000039650			9154	protein-coding gene	gene with protein product		605610				10446192, 10446193	Standard	NM_007254		Approved	PNK	uc002pqj.3	Q96T60		ENST00000322344.3:c.20delC	19.37:g.50370442delG	ENSP00000323511:p.Pro7fs	Somatic	0	11	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	2	11	15.38	Q9BUL2|Q9P1V2|Q9UKU8|Q9UNF8|Q9UNI0	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_PNK3P,superfamily_HAD-like_dom,superfamily_SMAD_FHA_domain,superfamily_P-loop_NTPase,tigrfam_PNK_3Pase_met,tigrfam_Polynucleotide_phosphatase,tigrfam_HAD-SF_hydro_IIIA	p.P7fs	ENST00000322344.3	37	c.20	CCDS12783.1	19																																																																																			-	superfamily_SMAD_FHA_domain,tigrfam_PNK_3Pase_met		0.721	PNKP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PNKP	protein_coding	OTTHUMT00000465830.1	G	NM_007254			50370442	-1	no_errors	ENST00000322344	ensembl	human	known	74_37	frame_shift_del	DEL	0.000	-
DISP2	85455	genome.wustl.edu	37	15	40661057	40661057	+	Missense_Mutation	SNP	C	C	T	rs559188294		TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr15:40661057C>T	ENST00000267889.3	+	8	2831	c.2744C>T	c.(2743-2745)cCg>cTg	p.P915L	RP11-64K12.4_ENST00000558421.1_RNA|LINC00594_ENST00000561261.1_lincRNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	915					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)		p.P915Q(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		CGGAACAGTCCGGACTACAAC	0.627																																																	1	Substitution - Missense(1)	endometrium(1)						ENSG00000140323						49.0	51.0	50.0					15																	40661057		2203	4300	6503	DISP2	SO:0001583	missense	0			-	HGNC	AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.2744C>T	15.37:g.40661057C>T	ENSP00000267889:p.Pro915Leu	Somatic	0	55	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	18	35	33.96	Q6AHW3|Q9C0C1	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfscan_SSD	p.P915L	ENST00000267889.3	37	c.2744	CCDS10056.1	15	.	.	.	.	.	.	.	.	.	.	C	0.008	-1.866601	0.00547	.	.	ENSG00000140323	ENST00000267889	T	0.09445	2.98	4.85	3.86	0.44501	.	0.360109	0.31102	N	0.008241	T	0.03053	0.0090	N	0.02345	-0.59	0.38645	D	0.951694	B	0.25048	0.117	B	0.09377	0.004	T	0.44832	-0.9302	10	0.20046	T	0.44	-0.9813	3.9102	0.09199	0.0:0.6855:0.0:0.3145	.	915	A7MBM2	DISP2_HUMAN	L	915	ENSP00000267889:P915L	ENSP00000267889:P915L	P	+	2	0	DISP2	38448349	0.353000	0.24904	0.221000	0.23827	0.080000	0.17528	3.949000	0.56668	2.544000	0.85801	0.555000	0.69702	CCG	-	NULL		0.627	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DISP2	protein_coding	OTTHUMT00000252249.1	C	NM_033510	-		40661057	+1	no_errors	ENST00000267889	ensembl	human	known	74_37	missense	SNP	0.991	T
TPR	7175	genome.wustl.edu	37	1	186314755	186314755	+	Missense_Mutation	SNP	G	G	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr1:186314755G>T	ENST00000367478.4	-	24	3466	c.3170C>A	c.(3169-3171)gCt>gAt	p.A1057D		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1057					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		ATTACTTAAAGCTGTGCTTGC	0.378			T	NTRK1	papillary thyroid																																			Dom	yes		1	1q25	7175	translocated promoter region		E	0								ENSG00000047410						182.0	166.0	171.0					1																	186314755		1911	4126	6037	TPR	SO:0001583	missense	0			-	HGNC	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.3170C>A	1.37:g.186314755G>T	ENSP00000356448:p.Ala1057Asp	Somatic	0	33	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	34	10.53	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_TPR_MLP1_2,superfamily_Prefoldin,superfamily_tRNA-bd_arm	p.A1057D	ENST00000367478.4	37	c.3170	CCDS41446.1	1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.007680	0.93287	.	.	ENSG00000047410	ENST00000367478	T	0.28454	1.61	5.31	5.31	0.75309	Tetratricopeptide, MLP1/MLP2-like (1);	0.152745	0.64402	D	0.000017	T	0.50548	0.1622	L	0.53249	1.67	0.80722	D	1	D	0.64830	0.994	D	0.65233	0.933	T	0.33727	-0.9857	10	0.35671	T	0.21	.	19.3605	0.94436	0.0:0.0:1.0:0.0	.	1057	P12270	TPR_HUMAN	D	1057	ENSP00000356448:A1057D	ENSP00000356448:A1057D	A	-	2	0	TPR	184581378	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	8.857000	0.92250	2.630000	0.89119	0.650000	0.86243	GCT	-	pfam_TPR_MLP1_2		0.378	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TPR	protein_coding	OTTHUMT00000086353.2	G	NM_003292	-		186314755	-1	no_errors	ENST00000367478	ensembl	human	known	74_37	missense	SNP	1.000	T
VPS13A	23230	genome.wustl.edu	37	9	79910710	79910710	+	Missense_Mutation	SNP	C	C	A			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr9:79910710C>A	ENST00000360280.3	+	33	4020	c.3760C>A	c.(3760-3762)Cca>Aca	p.P1254T	VPS13A_ENST00000357409.5_Missense_Mutation_p.P1254T|VPS13A_ENST00000376636.3_Missense_Mutation_p.P1215T|VPS13A_ENST00000376634.4_Missense_Mutation_p.P1254T|VPS13A_ENST00000423463.2_3'UTR	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1254					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						GAGCTCTCCCCCACCTGTTAT	0.363																																																	0								ENSG00000197969						73.0	73.0	73.0					9																	79910710		2203	4299	6502	VPS13A	SO:0001583	missense	0			-	HGNC	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.3760C>A	9.37:g.79910710C>A	ENSP00000353422:p.Pro1254Thr	Somatic	0	27	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	40	9.09	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_VPSAP_dom,pfam_Autophagy-rel_C	p.P1254T	ENST00000360280.3	37	c.3760	CCDS6655.1	9	.	.	.	.	.	.	.	.	.	.	C	16.99	3.275247	0.59649	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.14391	2.51;2.51;2.51;2.51	5.15	4.25	0.50352	.	0.000000	0.85682	D	0.000000	T	0.37892	0.1020	M	0.80616	2.505	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.97110	0.986;0.998;1.0;1.0	T	0.21381	-1.0247	10	0.31617	T	0.26	.	14.2559	0.66051	0.0:0.9279:0.0:0.0721	.	1215;1254;1254;1254	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	T	1254;1215;1254;1254	ENSP00000365821:P1254T;ENSP00000365823:P1215T;ENSP00000353422:P1254T;ENSP00000349985:P1254T	ENSP00000349985:P1254T	P	+	1	0	VPS13A	79100530	1.000000	0.71417	0.925000	0.36789	0.635000	0.38103	5.244000	0.65400	1.324000	0.45282	-0.219000	0.12488	CCA	-	NULL		0.363	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	VPS13A	protein_coding	OTTHUMT00000052753.2	C	NM_015186	-		79910710	+1	no_errors	ENST00000360280	ensembl	human	known	74_37	missense	SNP	0.998	A
NHS	4810	genome.wustl.edu	37	X	17742527	17742527	+	Missense_Mutation	SNP	C	C	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chrX:17742527C>T	ENST00000380060.3	+	5	1492	c.1154C>T	c.(1153-1155)cCc>cTc	p.P385L	NHS_ENST00000398097.3_Missense_Mutation_p.P229L	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	406					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					TCGGGTATCCCCAGAAGAGTT	0.413																																																	0								ENSG00000188158						95.0	86.0	89.0					X																	17742527		2203	4300	6503	NHS	SO:0001583	missense	0			-	HGNC		CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.1154C>T	X.37:g.17742527C>T	ENSP00000369400:p.Pro385Leu	Somatic	0	32	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	25	16.67	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.P385L	ENST00000380060.3	37	c.1154	CCDS14181.1	X	.	.	.	.	.	.	.	.	.	.	C	27.6	4.850082	0.91277	.	.	ENSG00000188158	ENST00000380060;ENST00000398097;ENST00000380057	T;T	0.60797	0.19;0.16	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.76969	0.4062	M	0.76574	2.34	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.999;0.999	T	0.78339	-0.2242	10	0.54805	T	0.06	-20.1811	18.5982	0.91236	0.0:1.0:0.0:0.0	.	406;227;229;385	B7ZVX8;C9IYM8;Q6T4R5-2;Q6T4R5	.;.;.;NHS_HUMAN	L	385;229;227	ENSP00000369400:P385L;ENSP00000381170:P229L	ENSP00000369397:P227L	P	+	2	0	NHS	17652448	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.705000	0.84606	2.422000	0.82143	0.544000	0.68410	CCC	-	NULL		0.413	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NHS	protein_coding	OTTHUMT00000059120.1	C	NM_198270	-		17742527	+1	no_errors	ENST00000380060	ensembl	human	known	74_37	missense	SNP	1.000	T
MYCBP2	23077	genome.wustl.edu	37	13	77750765	77750766	+	Splice_Site	INS	-	-	A	rs71102724		TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr13:77750765_77750766insA	ENST00000544440.2	-	36	5244		c.e36-2		MYCBP2_ENST00000357337.6_Splice_Site|MYCBP2_ENST00000360084.5_Splice_Site|MYCBP2_ENST00000407578.2_Splice_Site					MYC binding protein 2, E3 ubiquitin protein ligase									p.?(3)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		ATGTTCACTCTAAAAAAAAAAA	0.297																																																	3	Unknown(3)	lung(3)						ENSG00000005810																																			MYCBP2	SO:0001630	splice_region_variant	0				HGNC	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"""MYC binding protein 2"""			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.5227-2->T	13.37:g.77750776_77750776dupA		Somatic	0	29	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	29	12.12		Splice_Site	INS	NA	NA	NA	NA	NA	NA	-	e36-2	ENST00000544440.2	37	c.5341-3_5341-2		13																																																																																			-	-		0.297	MYCBP2-001	KNOWN	basic	protein_coding	MYCBP2	protein_coding	OTTHUMT00000045326.1	-	NM_015057		Intron	77750766	-1	no_errors	ENST00000407578	ensembl	human	known	74_37	splice_site_ins	INS	1.000:0.995	A
TEX14	56155	genome.wustl.edu	37	17	56679184	56679184	+	Missense_Mutation	SNP	A	A	G			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr17:56679184A>G	ENST00000240361.8	-	13	1764	c.1679T>C	c.(1678-1680)aTa>aCa	p.I560T	TEX14_ENST00000349033.5_Missense_Mutation_p.I554T|TEX14_ENST00000389934.3_Missense_Mutation_p.I554T			Q8IWB6	TEX14_HUMAN	testis expressed 14	560					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CTTTAGTTCTATGATTTCCAT	0.453																																																	0								ENSG00000121101						180.0	162.0	168.0					17																	56679184		2203	4300	6503	TEX14	SO:0001583	missense	0			-	HGNC	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"""cancer/testis antigen 113"""	605792	"""testis expressed sequence 14"""			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.1679T>C	17.37:g.56679184A>G	ENSP00000240361:p.Ile560Thr	Somatic	0	34	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	12	23	34.29	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_dom,superfamily_Kinase-like_dom,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_Prot_kinase_dom	p.I560T	ENST00000240361.8	37	c.1679	CCDS56042.1	17	.	.	.	.	.	.	.	.	.	.	A	5.470	0.271765	0.10349	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.77877	-1.13;-1.13;-1.09	5.8	-0.967	0.10316	.	0.458025	0.22261	N	0.062417	T	0.51329	0.1668	N	0.08118	0	0.09310	N	1	B;B;B	0.21520	0.057;0.02;0.02	B;B;B	0.21151	0.022;0.033;0.033	T	0.39742	-0.9599	10	0.48119	T	0.1	-4.1658	4.4564	0.11645	0.2126:0.2327:0.0:0.5547	.	560;554;554	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	T	560;554;554	ENSP00000240361:I560T;ENSP00000374584:I554T;ENSP00000268910:I554T	ENSP00000240361:I560T	I	-	2	0	TEX14	54034183	1.000000	0.71417	0.991000	0.47740	0.114000	0.19823	1.356000	0.34079	-0.106000	0.12110	-1.731000	0.00696	ATA	-	NULL		0.453	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TEX14	protein_coding	OTTHUMT00000445446.1	A		-		56679184	-1	no_errors	ENST00000240361	ensembl	human	known	74_37	missense	SNP	0.077	G
LMO2	4005	genome.wustl.edu	37	11	33902977	33902977	+	Missense_Mutation	SNP	T	T	C			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr11:33902977T>C	ENST00000330381.2	+	1	789	c.329T>C	c.(328-330)gTc>gCc	p.V110A	LMO2_ENST00000257818.2_Intron																							CTCCAACAAGTCATTTCCATC	0.468																																																	0								ENSG00000184566																																			AC132216.1	SO:0001583	missense	0			-	Clone_based_ensembl_gene																												ENST00000330381.2:c.329T>C	11.37:g.33902977T>C	ENSP00000332722:p.Val110Ala	Somatic	0	19	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	9	43.75		Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.V110A	ENST00000330381.2	37	c.329		11	.	.	.	.	.	.	.	.	.	.	T	5.671	0.308327	0.10733	.	.	ENSG00000184566	ENST00000330381	.	.	.	4.52	0.193	0.15139	.	.	.	.	.	T	0.55114	0.1900	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.55244	-0.8171	5	0.87932	D	0	.	2.4638	0.04547	0.2063:0.2774:0.0:0.5163	.	.	.	.	A	110	.	ENSP00000332722:V110A	V	+	2	0	AC132216.1	33859553	0.997000	0.39634	0.954000	0.39281	0.036000	0.12997	0.119000	0.15626	0.182000	0.20032	0.383000	0.25322	GTC	-	NULL		0.468	AC132216.1-201	KNOWN	basic|appris_principal	protein_coding	ENSG00000184566	protein_coding		T		-		33902977	+1	no_errors	ENST00000330381	ensembl	human	known	74_37	missense	SNP	0.896	C
NARS2	79731	genome.wustl.edu	37	11	78154811	78154811	+	Intron	DEL	A	A	-			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr11:78154811delA	ENST00000281038.5	-	12	1540				NARS2_ENST00000528850.1_Intron|RP11-452H21.1_ENST00000534168.1_RNA	NM_001243251.1|NM_024678.5	NP_001230180.1|NP_078954.4	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)						asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)	27	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	CAACCTAAGGAAAAAAAAAAA	0.393																																																	0								ENSG00000254420						35.0	37.0	36.0					11																	78154811		2200	4292	6492	RP11-452H21.1	SO:0001627	intron_variant	0				Clone_based_vega_gene	BC007800	CCDS8261.1, CCDS58164.1	11q14.1	2011-07-01	2007-02-23		ENSG00000137513	ENSG00000137513	6.1.1.22	"""Aminoacyl tRNA synthetases / Class II"""	26274	protein-coding gene	gene with protein product	"""asparagine tRNA ligase 2, mitochondrial (putative)"""	612803				15779907	Standard	NM_024678		Approved	FLJ23441, SLM5	uc001ozi.3	Q96I59	OTTHUMG00000166702	ENST00000281038.5:c.1165-7T>-	11.37:g.78154811delA		Somatic	0	16	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	29	14.71	G3V178	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000281038.5	37	NULL	CCDS8261.1	11																																																																																			-	-		0.393	NARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000254420	protein_coding	OTTHUMT00000391138.2	A	NM_024678			78154811	+1	no_errors	ENST00000534168	ensembl	human	known	74_37	rna	DEL	0.000	-
KRT8P47	644743	genome.wustl.edu	37	1	44570004	44570004	+	lincRNA	SNP	T	T	G			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr1:44570004T>G	ENST00000434244.1	+	0	2001																											AGCTGCCGCCTAAGGTTGTTG	0.572																																																	0								ENSG00000230615																																			RP5-1198O20.4			0			-	Clone_based_vega_gene																													1.37:g.44570004T>G		Somatic	0	29	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	19	17.39		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000434244.1	37	NULL		1																																																																																			-	-		0.572	RP5-1198O20.4-001	KNOWN	basic	lincRNA	ENSG00000230615	lincRNA	OTTHUMT00000022875.2	T		-		44570004	+1	no_errors	ENST00000434244	ensembl	human	known	74_37	rna	SNP	1.000	G
RCVRN	5957	genome.wustl.edu	37	17	9801316	9801317	+	3'UTR	INS	-	-	GTGTGTGC	rs531533066|rs376748693	byFrequency	TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr17:9801316_9801317insGTGTGTGC	ENST00000226193.5	-	0	1138_1139				RCVRN_ENST00000570909.3_5'UTR	NM_002903.2	NP_002894.1	P35243	RECO_HUMAN	recoverin						phototransduction, visible light (GO:0007603)|positive regulation of guanylate cyclase activity (GO:0031284)|regulation of calcium ion transport (GO:0051924)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	dendrite (GO:0030425)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	12						tgtgtgtgtgtgcgcgcgcgtg	0.589																																																	0								ENSG00000109047																																			RCVRN	SO:0001624	3_prime_UTR_variant	0				HGNC	BC001720	CCDS11151.1	17p13.1	2013-01-10		2006-09-26	ENSG00000109047	ENSG00000109047		"""EF-hand domain containing"""	9937	protein-coding gene	gene with protein product		179618		RCV1		1387789, 12507501, 1467959, 12789533	Standard	NM_002903		Approved		uc002gme.1	P35243	OTTHUMG00000130268	ENST00000226193.5:c.*96->GCACACAC	17.37:g.9801316_9801317insGTGTGTGC		Somatic	NA	NA	NA		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	Q53XL0	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000226193.5	37	NULL	CCDS11151.1	17																																																																																			-	-		0.589	RCVRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RCVRN	protein_coding	OTTHUMT00000252600.2	-	NM_002903			9801317	-1	no_errors	ENST00000570909	ensembl	human	putative	74_37	rna	INS	0.000:0.000	GTGTGTGC
TGM1	7051	genome.wustl.edu	37	14	24727837	24727837	+	Missense_Mutation	SNP	A	A	C			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr14:24727837A>C	ENST00000206765.6	-	8	1325	c.1202T>G	c.(1201-1203)tTc>tGc	p.F401C	TGM1_ENST00000544573.1_Intron	NM_000359.2	NP_000350.1	P22735	TGM1_HUMAN	transglutaminase 1	401			F -> V (in ARCI1).		cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|organ morphogenesis (GO:0009887)|peptide cross-linking (GO:0018149)	cell-cell adherens junction (GO:0005913)|cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|intrinsic component of membrane (GO:0031224)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)	24				GBM - Glioblastoma multiforme(265;0.0186)	L-Glutamine(DB00130)	GGCGGAGTTGAAGTTGGTGAC	0.572																																																	0								ENSG00000092295						186.0	161.0	169.0					14																	24727837		2203	4300	6503	TGM1	SO:0001583	missense	0			-	HGNC	D90287	CCDS9622.1	14q11.2	2013-05-02	2013-05-02		ENSG00000092295	ENSG00000092295	2.3.2.13	"""Transglutaminases"""	11777	protein-coding gene	gene with protein product	"""K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase"""	190195	"""transglutaminase 1 (K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase)"""	ICR2		11390390	Standard	NM_000359		Approved	TGASE, TGK, LI, LI1	uc001wod.3	P22735	OTTHUMG00000029329	ENST00000206765.6:c.1202T>G	14.37:g.24727837A>C	ENSP00000206765:p.Phe401Cys	Somatic	0	57	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	16	19	45.71	B4DWR7|Q197M4	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Transglutaminase_C,pfam_Transglutaminase_N,pfam_Transglutaminase-like,superfamily_Ig_E-set,superfamily_Transglutaminase_C,smart_Transglutaminase-like	p.F401C	ENST00000206765.6	37	c.1202	CCDS9622.1	14	.	.	.	.	.	.	.	.	.	.	A	16.12	3.031984	0.54790	.	.	ENSG00000092295	ENST00000206765	D	0.97430	-4.38	4.69	3.46	0.39613	Transglutaminase-like (2);	0.047647	0.85682	D	0.000000	D	0.98356	0.9454	H	0.94423	3.535	0.80722	D	1	D	0.63880	0.993	P	0.61533	0.89	D	0.98378	1.0557	10	0.87932	D	0	-29.0993	9.0433	0.36331	0.8349:0.0:0.0:0.1651	.	401	P22735	TGM1_HUMAN	C	401	ENSP00000206765:F401C	ENSP00000206765:F401C	F	-	2	0	TGM1	23797677	0.994000	0.37717	1.000000	0.80357	0.989000	0.77384	0.359000	0.20233	2.111000	0.64477	0.459000	0.35465	TTC	-	pfam_Transglutaminase-like,smart_Transglutaminase-like		0.572	TGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TGM1	protein_coding	OTTHUMT00000073160.6	A	NM_000359	-		24727837	-1	no_errors	ENST00000206765	ensembl	human	known	74_37	missense	SNP	1.000	C
MYH15	22989	genome.wustl.edu	37	3	108174661	108174661	+	Silent	SNP	C	C	A			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr3:108174661C>A	ENST00000273353.3	-	21	2300	c.2244G>T	c.(2242-2244)gtG>gtT	p.V748V	MYH15_ENST00000495753.2_5'UTR	NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	748	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TTCTGCTGCTCACAAACTTGC	0.363																																																	0								ENSG00000144821						164.0	154.0	157.0					3																	108174661		1851	4085	5936	MYH15	SO:0001819	synonymous_variant	0			-	HGNC	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.2244G>T	3.37:g.108174661C>A		Somatic	0	47	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	25	10.71		Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Myosin_head_motor_dom,pfam_Myosin_tail,pfam_Myosin_N,superfamily_P-loop_NTPase,superfamily_Prefoldin,superfamily_Lambda_DNA-bd_dom,smart_Myosin_head_motor_dom,prints_Myosin_head_motor_dom	p.V748	ENST00000273353.3	37	c.2244	CCDS43127.1	3																																																																																			-	pfam_Myosin_head_motor_dom,superfamily_P-loop_NTPase,smart_Myosin_head_motor_dom		0.363	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MYH15	protein_coding	OTTHUMT00000353935.1	C	XM_036988	-		108174661	-1	no_errors	ENST00000273353	ensembl	human	known	74_37	silent	SNP	0.632	A
DLX1	1745	genome.wustl.edu	37	2	172952850	172952850	+	Silent	SNP	C	C	G	rs200336628	byFrequency	TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr2:172952850C>G	ENST00000361725.4	+	3	1085	c.633C>G	c.(631-633)ccC>ccG	p.P211P	DLX1_ENST00000550686.1_3'UTR|DLX1_ENST00000341900.6_3'UTR	NM_178120.4	NP_835221.2	P56177	DLX1_HUMAN	distal-less homeobox 1	211					cerebral cortex GABAergic interneuron fate commitment (GO:0021893)|embryonic skeletal system development (GO:0048706)|hippocampus development (GO:0021766)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|proximal/distal pattern formation (GO:0009954)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|subpallium development (GO:0021544)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|lung(4)|prostate(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.216)			GCTCCCCACCCGTGCCGCCCG	0.627																																																	0								ENSG00000144355						65.0	77.0	73.0					2																	172952850		2203	4300	6503	DLX1	SO:0001819	synonymous_variant	0			-	HGNC	BC013010	CCDS2247.2, CCDS33328.1	2q31.1	2011-06-20	2005-12-22		ENSG00000144355	ENSG00000144355		"""Homeoboxes / ANTP class : NKL subclass"""	2914	protein-coding gene	gene with protein product		600029	"""distal-less homeo box 1"""			7907794	Standard	NM_001038493		Approved		uc002uhl.3	P56177	OTTHUMG00000073951	ENST00000361725.4:c.633C>G	2.37:g.172952850C>G		Somatic	0	47	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	9	23	28.12	D3DPD7|Q53ZU4|Q7Z724|Q8IYB2	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Homeobox_dom,superfamily_Homeodomain-like,smart_Homeobox_dom,pfscan_Homeobox_dom,prints_HTH_motif,prints_Homeobox_metazoa	p.P211	ENST00000361725.4	37	c.633	CCDS2247.2	2																																																																																			-	NULL		0.627	DLX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DLX1	protein_coding	OTTHUMT00000405916.1	C	XM_087198	-		172952850	+1	no_errors	ENST00000361725	ensembl	human	known	74_37	silent	SNP	0.001	G
CCT6A	908	genome.wustl.edu	37	7	56129482	56129482	+	Missense_Mutation	SNP	G	G	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr7:56129482G>T	ENST00000275603.4	+	12	1609	c.1390G>T	c.(1390-1392)Gtt>Ttt	p.V464F	SNORA15_ENST00000384439.1_RNA|SUMF2_ENST00000413756.1_5'Flank|SUMF2_ENST00000437307.2_5'Flank|SUMF2_ENST00000395435.2_5'Flank|SUMF2_ENST00000434526.2_5'Flank|SUMF2_ENST00000395436.2_5'Flank|CCT6A_ENST00000462133.1_3'UTR|CCT6A_ENST00000540286.1_Missense_Mutation_p.V433F|CCT6A_ENST00000335503.3_Missense_Mutation_p.V419F|SUMF2_ENST00000275607.9_5'Flank|SUMF2_ENST00000342190.6_5'Flank	NM_001762.3	NP_001753.1	P40227	TCPZ_HUMAN	chaperonin containing TCP1, subunit 6A (zeta 1)	464					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|cervix(2)|endometrium(1)|large_intestine(4)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)	15	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GGAAACATTAGTTAAAATTCA	0.358																																																	0								ENSG00000146731						49.0	48.0	48.0					7																	56129482		2203	4300	6503	CCT6A	SO:0001583	missense	0			-	HGNC	M94083	CCDS5523.1, CCDS34640.1	7p11.2	2011-09-02			ENSG00000146731	ENSG00000146731		"""Heat Shock Proteins / Chaperonins"""	1620	protein-coding gene	gene with protein product		104613		CCT6		1352881, 8034610	Standard	NM_001762		Approved	TTCP20, TCPZ, Cctz, HTR3, TCP20	uc003trl.1	P40227	OTTHUMG00000022842	ENST00000275603.4:c.1390G>T	7.37:g.56129482G>T	ENSP00000275603:p.Val464Phe	Somatic	0	42	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	49	12.50	A6NCD2|Q3KP28|Q75LP4|Q96S46	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Cpn60/TCP-1,superfamily_Cpn60/TCP-1,superfamily_GroEL-like_apical_dom,prints_Chaperone_TCP-1,prints_Chaprnin_Cpn60,tigrfam_Chap_CCT_zeta	p.V464F	ENST00000275603.4	37	c.1390	CCDS5523.1	7	.	.	.	.	.	.	.	.	.	.	G	13.70	2.315383	0.40996	.	.	ENSG00000146731	ENST00000275603;ENST00000335503;ENST00000540286;ENST00000539340	T;T;T	0.78481	-1.18;-1.18;-1.18	4.96	4.08	0.47627	.	0.205916	0.41294	N	0.000918	T	0.81791	0.4897	M	0.90309	3.105	0.53688	D	0.999976	B;B;B	0.18610	0.029;0.008;0.02	B;B;B	0.26969	0.038;0.075;0.038	T	0.80982	-0.1139	10	0.87932	D	0	-11.2745	12.0307	0.53396	0.0854:0.0:0.9146:0.0	.	433;419;464	B4DPJ8;A6NCD2;P40227	.;.;TCPZ_HUMAN	F	464;419;433;322	ENSP00000275603:V464F;ENSP00000352019:V419F;ENSP00000438488:V433F	ENSP00000275603:V464F	V	+	1	0	CCT6A	56096976	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.996000	0.76263	1.088000	0.41272	0.456000	0.33151	GTT	-	pfam_Cpn60/TCP-1,superfamily_Cpn60/TCP-1,tigrfam_Chap_CCT_zeta		0.358	CCT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CCT6A	protein_coding	OTTHUMT00000251526.2	G	NM_001762	-		56129482	+1	no_errors	ENST00000275603	ensembl	human	known	74_37	missense	SNP	1.000	T
CYP3A7	1551	genome.wustl.edu	37	7	99314839	99314839	+	Missense_Mutation	SNP	C	C	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr7:99314839C>T	ENST00000336374.2	-	6	484	c.482G>A	c.(481-483)aGg>aAg	p.R161K		NM_000765.3	NP_000756.2	P24462	CP3A7_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 7	161					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxygen binding (GO:0019825)			autonomic_ganglia(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	32	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Alfentanil(DB00802)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amlodipine(DB00381)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atorvastatin(DB01076)|Buprenorphine(DB00921)|Buspirone(DB00490)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clotrimazole(DB00257)|Cocaine(DB00907)|Codeine(DB00318)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diltiazem(DB00343)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Eplerenone(DB00700)|Erythromycin(DB00199)|Estradiol(DB00783)|Ethosuximide(DB00593)|Ethylmorphine(DB01466)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluticasone Propionate(DB00588)|Fluvoxamine(DB00176)|Gestodene(DB06730)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nifedipine(DB01115)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Testosterone(DB00624)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	TGCTTCCCGCCTCAGATTTCT	0.502																																																	0								ENSG00000160870						162.0	146.0	151.0					7																	99314839		2203	4300	6503	CYP3A7	SO:0001583	missense	0			-	HGNC	AF315325	CCDS5673.1	7q21-q22.1	2007-12-14	2003-01-14		ENSG00000160870	ENSG00000160870		"""Cytochrome P450s"""	2640	protein-coding gene	gene with protein product		605340	"""cytochrome P450, subfamily IIIA, polypeptide 7"""			2722762	Standard	NM_000765		Approved	CP37, P450-HFLA		P24462	OTTHUMG00000156726	ENST00000336374.2:c.482G>A	7.37:g.99314839C>T	ENSP00000337450:p.Arg161Lys	Somatic	0	51	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	39	15.22	A4D288|Q9H241	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Cyt_P450,superfamily_Cyt_P450,prints_Cyt_P450_E_CYP3A,prints_Cyt_P450_E_grp-I,prints_Cyt_P450_E_grp-II,prints_Cyt_P450_E_grp-IV,prints_Cyt_P450,prints_Cyt_P450_B	p.R161K	ENST00000336374.2	37	c.482	CCDS5673.1	7	.	.	.	.	.	.	.	.	.	.	C	2.943	-0.218383	0.06101	.	.	ENSG00000160870	ENST00000292414;ENST00000336374	T	0.69040	-0.37	3.98	2.02	0.26589	.	0.517672	0.23237	N	0.050394	T	0.38214	0.1032	N	0.12853	0.265	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.11494	-1.0585	10	0.12103	T	0.63	.	3.923	0.09251	0.2031:0.5865:0.0:0.2103	.	161	P24462	CP3A7_HUMAN	K	161	ENSP00000337450:R161K	ENSP00000292414:R161K	R	-	2	0	CYP3A7	99152775	0.059000	0.20769	0.026000	0.17262	0.226000	0.24999	0.537000	0.23144	0.715000	0.32103	0.462000	0.41574	AGG	-	pfam_Cyt_P450,superfamily_Cyt_P450		0.502	CYP3A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CYP3A7	protein_coding	OTTHUMT00000345484.1	C		-		99314839	-1	no_errors	ENST00000336374	ensembl	human	known	74_37	missense	SNP	0.046	T
APC2	10297	genome.wustl.edu	37	19	1457894	1457895	+	Intron	INS	-	-	GGGGGGGGG	rs374378343|rs113990038|rs71174372		TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr19:1457894_1457895insGGGGGGGGG	ENST00000535453.1	+	9	2920				CTB-25B13.12_ENST00000588225.1_RNA|APC2_ENST00000233607.2_Intron|APC2_ENST00000238483.4_Intron			P02655	APOC2_HUMAN	adenomatosis polyposis coli 2						cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|kidney(4)|large_intestine(2)|lung(5)|pancreas(1)|skin(2)	18		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGCGGGTTGCGGGACCTTCGG	0.619																																																	0								ENSG00000267317																																			CTB-25B13.12	SO:0001627	intron_variant	0				Clone_based_vega_gene		CCDS12068.1	19p13.3	2013-02-14			ENSG00000115266	ENSG00000115266		"""Armadillo repeat containing"""	24036	protein-coding gene	gene with protein product	"""adenomatous polyposis coli like"""	612034				9823329, 10021369	Standard	XM_005259475		Approved	APCL	uc002lsr.1	O95996		ENST00000535453.1:c.1208-69->GGGGGGGGG	19.37:g.1457894_1457895insGGGGGGGGG		Somatic	NA	NA	NA		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000535453.1	37	NULL	CCDS12068.1	19																																																																																			-	-		0.619	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	ENSG00000267317	protein_coding	OTTHUMT00000449539.2	-	NM_005883			1457895	-1	no_errors	ENST00000588225	ensembl	human	known	74_37	rna	INS	0.000:0.000	GGGGGGGGG
ANKRD27	84079	genome.wustl.edu	37	19	33137460	33137460	+	Missense_Mutation	SNP	A	A	G			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr19:33137460A>G	ENST00000306065.4	-	4	433	c.275T>C	c.(274-276)gTg>gCg	p.V92A	ANKRD27_ENST00000587352.1_Missense_Mutation_p.V92A	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	92					early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					GAGAATGGGCACTGAGAGAAG	0.433																																																	0								ENSG00000105186						86.0	88.0	88.0					19																	33137460		2203	4300	6503	ANKRD27	SO:0001583	missense	0			-	HGNC	AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"""Ankyrin repeat domain containing"""	25310	protein-coding gene	gene with protein product	"""Vps9 domain and ankyrin-repeat-containing protein"""					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.275T>C	19.37:g.33137460A>G	ENSP00000304292:p.Val92Ala	Somatic	0	24	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	17	29.17	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Ankyrin_rpt,pfam_VPS9,superfamily_Ankyrin_rpt-contain_dom,smart_VPS9_subgr,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_VPS9,prints_Ankyrin_rpt	p.V92A	ENST00000306065.4	37	c.275	CCDS32986.1	19	.	.	.	.	.	.	.	.	.	.	A	22.6	4.311343	0.81358	.	.	ENSG00000105186	ENST00000306065	T	0.64803	-0.12	5.24	5.24	0.73138	.	0.000000	0.51477	D	0.000090	T	0.70298	0.3208	L	0.46157	1.445	0.42323	D	0.992269	D	0.64830	0.994	P	0.59171	0.853	T	0.74228	-0.3733	10	0.72032	D	0.01	-25.4491	15.1942	0.73071	1.0:0.0:0.0:0.0	.	92	Q96NW4	ANR27_HUMAN	A	92	ENSP00000304292:V92A	ENSP00000304292:V92A	V	-	2	0	ANKRD27	37829300	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.953000	0.87836	1.997000	0.58415	0.445000	0.29226	GTG	-	NULL		0.433	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ANKRD27	protein_coding	OTTHUMT00000450329.1	A	NM_032139	-		33137460	-1	no_errors	ENST00000306065	ensembl	human	known	74_37	missense	SNP	1.000	G
SHOX2	6474	genome.wustl.edu	37	3	157820535	157820535	+	Missense_Mutation	SNP	G	G	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr3:157820535G>T	ENST00000425436.3	-	2	512	c.487C>A	c.(487-489)Cac>Aac	p.H163N	SHOX2_ENST00000554685.1_5'UTR|SHOX2_ENST00000389589.4_Missense_Mutation_p.H187N|SHOX2_ENST00000441443.2_Missense_Mutation_p.H34N|SHOX2_ENST00000490689.2_Missense_Mutation_p.H34N|SHOX2_ENST00000483851.2_Missense_Mutation_p.H163N	NM_001163678.1|NM_006884.3	NP_001157150.1|NP_006875.2	O60902	SHOX2_HUMAN	short stature homeobox 2	163					cardiac atrium morphogenesis (GO:0003209)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte development (GO:0002063)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint morphogenesis (GO:0060272)|heart development (GO:0007507)|heart valve development (GO:0003170)|muscle tissue morphogenesis (GO:0060415)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of axonogenesis (GO:0050772)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of chondrocyte differentiation (GO:0032330)|skeletal system development (GO:0001501)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(10)|skin(3)|upper_aerodigestive_tract(1)	20			Lung(72;0.00318)|LUSC - Lung squamous cell carcinoma(72;0.0043)			TCGGGATAGTGGGTCTCGTCA	0.597																																																	0								ENSG00000168779						155.0	127.0	137.0					3																	157820535		2203	4300	6503	SHOX2	SO:0001583	missense	0			-	HGNC	AJ002368	CCDS33884.1, CCDS43164.1, CCDS33884.2, CCDS54664.1	3q25.32	2011-06-20			ENSG00000168779	ENSG00000168779		"""Homeoboxes / PRD class"""	10854	protein-coding gene	gene with protein product		602504				9482898, 9466998	Standard	NM_006884		Approved	SHOT, OG12X, OG12	uc003fbs.3	O60902	OTTHUMG00000158755	ENST00000425436.3:c.487C>A	3.37:g.157820535G>T	ENSP00000398704:p.His163Asn	Somatic	0	64	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	40	9.09	O60465|O60467|O60903	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Homeobox_dom,pfam_OAR_dom,superfamily_Homeodomain-like,smart_Homeobox_dom,pfscan_OAR_dom,pfscan_Homeobox_dom,prints_HTH_motif	p.H187N	ENST00000425436.3	37	c.559	CCDS43164.1	3	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.9|29.9	5.042309|5.042309	0.93685|0.93685	.|.	.|.	ENSG00000168779;ENSG00000168779;ENSG00000168779;ENSG00000168779;ENSG00000168779;ENSG00000258518|ENSG00000168779	ENST00000425436;ENST00000490689;ENST00000389589;ENST00000313019;ENST00000441443;ENST00000483851|ENST00000555977	D;D;D;D;D|.	0.95377|.	-3.69;-3.69;-3.69;-3.69;-3.69|.	5.49|5.49	5.49|5.49	0.81192|0.81192	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);|.	0.059016|.	0.64402|.	D|.	0.000004|.	T|T	0.75243|0.75243	0.3823|0.3823	M|M	0.68317|0.68317	2.08|2.08	0.80722|0.80722	D|D	1|1	P;D;D|.	0.89917|.	0.879;0.999;1.0|.	P;D;D|.	0.87578|.	0.503;0.998;0.998|.	T|T	0.73424|0.73424	-0.3987|-0.3987	10|5	0.87932|.	D|.	0|.	.|.	19.3593|19.3593	0.94428|0.94428	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	163;187;163|.	O60902-2;O60902-3;O60902|.	.;.;SHOX2_HUMAN|.	N|Q	187;34;163;34;34;163|66	ENSP00000398704:H187N;ENSP00000451888:H34N;ENSP00000374240:H163N;ENSP00000397099:H34N;ENSP00000419362:H163N|.	ENSP00000327294:H34N|.	H|P	-|-	1|2	0|0	SHOX2;AC112502.1|SHOX2	159303229|159303229	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	9.869000|9.869000	0.99810|0.99810	2.576000|2.576000	0.86940|0.86940	0.655000|0.655000	0.94253|0.94253	CAC|CCA	-	pfam_Homeobox_dom,superfamily_Homeodomain-like,smart_Homeobox_dom,pfscan_Homeobox_dom		0.597	SHOX2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	SHOX2	protein_coding	OTTHUMT00000352057.2	G		-		157820535	-1	no_errors	ENST00000389589	ensembl	human	known	74_37	missense	SNP	1.000	T
TMPRSS13	84000	genome.wustl.edu	37	11	117789313	117789327	+	In_Frame_Del	DEL	GGGCTGGAGATGCCT	GGGCTGGAGATGCCT	-	rs577467360|rs201746372|rs200205086|rs61900346|rs371814093|rs58754377|rs201983451|rs368164118|rs201369736	byFrequency	TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	GGGCTGGAGATGCCT	GGGCTGGAGATGCCT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr11:117789313_117789327delGGGCTGGAGATGCCT	ENST00000430170.2	-	2	335_349	c.248_262delAGGCATCTCCAGCCC	c.(247-264)caggcatctccagcccgg>cgg	p.QASPA83del	TMPRSS13_ENST00000524993.1_In_Frame_Del_p.QASPA83del|TMPRSS13_ENST00000445164.2_In_Frame_Del_p.QASPA83del|TMPRSS13_ENST00000526090.1_In_Frame_Del_p.QASPA83del|TMPRSS13_ENST00000528626.1_In_Frame_Del_p.QASPA83del	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	83	13 X 5 AA repeats of A-S-P-A-[GLQR].|Ala-rich.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.Q83_A87delQASPA(1)		endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		GGAGATGCCCGGGCTGGAGATGCCTGGGCTGGAGA	0.66																																																	1	Deletion - In frame(1)	urinary_tract(1)						ENSG00000137747		,,	2974,624		1262,450,87					,,	0.0	0.0		dbSNP_126	58	5904,1944		2214,1476,234	no	coding,coding,coding	TMPRSS13	NM_001206790.1,NM_001206789.1,NM_001077263.2	,,	3476,1926,321	A1A1,A1R,RR		24.7706,17.343,22.4358	,,	,,		8878,2568				TMPRSS13	SO:0001651	inframe_deletion	0				HGNC	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"""Serine peptidases / Transmembrane"""	29808	protein-coding gene	gene with protein product		610050	"""transmembrane protease, serine 11"""	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.248_262delAGGCATCTCCAGCCC	11.37:g.117789313_117789327delGGGCTGGAGATGCCT	ENSP00000387702:p.Gln83_Ala87del	Somatic	NA	NA	NA		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	pirsf_Peptidase_S1A_TMPRSS13,pfam_Peptidase_S1,pfam_Peptidase_S1A_nudel,superfamily_Trypsin-like_Pept_dom,superfamily_Srcr_rcpt-rel,superfamily_LDrepeatLR_classA_rpt,smart_Srcr_rcpt-rel,smart_Peptidase_S1,prints_Peptidase_S1A,pfscan_SRCR,pfscan_Peptidase_S1	p.QASPA83in_frame_del	ENST00000430170.2	37	c.262_248	CCDS58185.1	11																																																																																			-	pirsf_Peptidase_S1A_TMPRSS13		0.660	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	TMPRSS13	protein_coding	OTTHUMT00000392318.1	GGGCTGGAGATGCCT	NM_032046			117789327	-1	no_errors	ENST00000445164	ensembl	human	known	74_37	in_frame_del	DEL	0.000:0.000:0.001:0.000:0.000:0.000:0.000:0.000:0.027:0.023:0.018:0.154:0.212:0.233:0.001	-
PBLD	64081	genome.wustl.edu	37	10	70045108	70045108	+	Missense_Mutation	SNP	G	G	A			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr10:70045108G>A	ENST00000358769.2	-	9	953	c.751C>T	c.(751-753)Cat>Tat	p.H251Y	PBLD_ENST00000309049.4_Missense_Mutation_p.H251Y|PBLD_ENST00000336578.1_Missense_Mutation_p.H218Y|PBLD_ENST00000432941.1_Missense_Mutation_p.H251Y|PBLD_ENST00000495025.2_Missense_Mutation_p.H251Y	NM_022129.3	NP_071412.2	P30039	PBLD_HUMAN	phenazine biosynthesis-like protein domain containing	251					biosynthetic process (GO:0009058)|maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein import into nucleus (GO:0060392)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	isomerase activity (GO:0016853)			endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	21						GTCCTACCATGCATTTCTTTC	0.408																																																	0								ENSG00000108187						110.0	113.0	112.0					10																	70045108		2203	4300	6503	PBLD	SO:0001583	missense	0			-	HGNC	AK027673	CCDS7277.2, CCDS44413.1	10q21.3	2006-11-27			ENSG00000108187	ENSG00000108187			23301	protein-coding gene	gene with protein product	MAWD binding protein	612189				11355021	Standard	XM_005270028		Approved	MAWBP, MAWDBP, FLJ14767	uc001jns.1	P30039	OTTHUMG00000073949	ENST00000358769.2:c.751C>T	10.37:g.70045108G>A	ENSP00000351619:p.His251Tyr	Somatic	0	28	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	13	18.75	A8MZJ3|C9JIM0|Q9HCC2	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Phenazine_PhzF,pirsf_Phenazine_PhzF,tigrfam_Phenazine_PhzF	p.H251Y	ENST00000358769.2	37	c.751	CCDS7277.2	10	.	.	.	.	.	.	.	.	.	.	G	4.135	0.023327	0.08006	.	.	ENSG00000108187	ENST00000336578;ENST00000358769;ENST00000309049;ENST00000432941	T;T;T;T	0.29917	1.58;1.58;1.58;1.55	5.24	5.24	0.73138	.	0.366986	0.23629	N	0.046152	T	0.14614	0.0353	N	0.11789	0.175	0.34098	D	0.661482	B;B	0.10296	0.003;0.0	B;B	0.08055	0.002;0.003	T	0.12344	-1.0551	10	0.02654	T	1	.	11.134	0.48365	0.0859:0.0:0.9141:0.0	.	251;251	C9JIM0;P30039	.;PBLD_HUMAN	Y	218;251;251;251	ENSP00000338041:H218Y;ENSP00000351619:H251Y;ENSP00000308466:H251Y;ENSP00000395534:H251Y	ENSP00000308466:H251Y	H	-	1	0	PBLD	69715114	0.996000	0.38824	0.952000	0.39060	0.992000	0.81027	2.474000	0.45154	2.446000	0.82766	0.563000	0.77884	CAT	-	pfam_Phenazine_PhzF,pirsf_Phenazine_PhzF,tigrfam_Phenazine_PhzF		0.408	PBLD-201	KNOWN	basic|appris_principal|CCDS	protein_coding	PBLD	protein_coding	OTTHUMT00000048314.1	G	NM_022129	-		70045108	-1	no_errors	ENST00000309049	ensembl	human	known	74_37	missense	SNP	0.985	A
SUGP2	10147	genome.wustl.edu	37	19	19136447	19136447	+	Missense_Mutation	SNP	G	G	C			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr19:19136447G>C	ENST00000601879.1	-	3	1007	c.710C>G	c.(709-711)gCt>gGt	p.A237G	SUGP2_ENST00000452918.2_Missense_Mutation_p.A237G|SUGP2_ENST00000598202.1_5'UTR|SUGP2_ENST00000456085.2_Intron|SUGP2_ENST00000600377.1_Missense_Mutation_p.A251G|SUGP2_ENST00000337018.6_Missense_Mutation_p.A237G			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	237					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						ACCCCCCTTAGCTGTGAGCAG	0.517																																																	0								ENSG00000064607						114.0	109.0	111.0					19																	19136447		2203	4300	6503	SUGP2	SO:0001583	missense	0			-	HGNC	AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"""G patch domain containing"""	18641	protein-coding gene	gene with protein product		607993	"""splicing factor, arginine/serine-rich 14"""	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.710C>G	19.37:g.19136447G>C	ENSP00000472286:p.Ala237Gly	Somatic	0	71	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	31	38	44.93	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Surp,pfam_G_patch_dom,superfamily_Surp,smart_Surp,smart_G_patch_dom,pfscan_Surp,pfscan_G_patch_dom	p.A237G	ENST00000601879.1	37	c.710	CCDS12392.1	19	.	.	.	.	.	.	.	.	.	.	G	13.47	2.245963	0.39697	.	.	ENSG00000064607	ENST00000337018;ENST00000330854;ENST00000452918	T;T;T	0.12465	2.7;2.68;2.7	5.11	5.11	0.69529	.	0.529889	0.18395	N	0.142559	T	0.11580	0.0282	N	0.24115	0.695	0.80722	D	1	B;B	0.27823	0.104;0.19	B;B	0.24155	0.036;0.051	T	0.09465	-1.0673	10	0.66056	D	0.02	-3.7053	15.699	0.77528	0.0:0.0:1.0:0.0	.	237;237	A8K5G0;Q8IX01	.;SUGP2_HUMAN	G	237	ENSP00000337926:A237G;ENSP00000332373:A237G;ENSP00000389380:A237G	ENSP00000332373:A237G	A	-	2	0	SUGP2	18997447	0.996000	0.38824	0.046000	0.18839	0.949000	0.60115	3.935000	0.56560	2.390000	0.81377	0.313000	0.20887	GCT	-	NULL		0.517	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	SUGP2	protein_coding	OTTHUMT00000464627.1	G	NM_001017392	-		19136447	-1	no_errors	ENST00000337018	ensembl	human	known	74_37	missense	SNP	0.783	C
ALMS1	7840	genome.wustl.edu	37	2	73613032	73613037	+	In_Frame_Del	DEL	GGAGGA	GGAGGA	-	rs61156725|rs70965731|rs72319667|rs3074417	byFrequency	TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	GGAGGA	GGAGGA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr2:73613032_73613037delGGAGGA	ENST00000264448.6	+	1	147_152	c.36_41delGGAGGA	c.(34-42)ctggaggag>ctg	p.EE27del	ALMS1_ENST00000409009.1_In_Frame_Del_p.EE27del|ALMS1_ENST00000377715.1_In_Frame_Del_p.EE27del	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	27	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)|p.E28_A29insE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGGGCGAGCTggaggaggaggaggag	0.694														3836	0.765974	0.9183	0.7176	5008	,	,		6363	0.7024		0.6819	False		,,,				2504	0.7464																2	Insertion - In frame(1)|Deletion - In frame(1)	ovary(1)|breast(1)						ENSG00000116127																																			ALMS1	SO:0001651	inframe_deletion	0				HGNC	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.36_41delGGAGGA	2.37:g.73613038_73613043delGGAGGA	ENSP00000264448:p.Glu27_Glu28del	Somatic	NA	NA	NA		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	NULL	p.EE16in_frame_del	ENST00000264448.6	37	c.36_41	CCDS42697.1	2																																																																																			-	NULL		0.694	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ALMS1	protein_coding	OTTHUMT00000327776.1	GGAGGA	NM_015120			73613037	+1	no_errors	ENST00000264448	ensembl	human	known	74_37	in_frame_del	DEL	0.989:0.996:1.000:1.000:1.000:1.000	-
LINC00200	399706	genome.wustl.edu	37	10	1205801	1205801	+	lincRNA	SNP	C	C	A	rs12763661		TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr10:1205801C>A	ENST00000425630.1	+	0	94					NR_015376.2				long intergenic non-protein coding RNA 200																		CGCAGGCCTGCGCGCCACGCG	0.637																																																	0								ENSG00000229205						31.0	36.0	34.0					10																	1205801		692	1591	2283	LINC00200			0			-	HGNC	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.1205801C>A		Somatic	0	35	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	17	22.73		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000425630.1	37	NULL		10																																																																																			-	-		0.637	LINC00200-001	KNOWN	basic	lincRNA	LINC00200	lincRNA	OTTHUMT00000046417.2	C	NR_015376	rs12763661		1205801	+1	no_errors	ENST00000425630	ensembl	human	known	74_37	rna	SNP	0.025	A
ELMOD1	55531	genome.wustl.edu	37	11	107524940	107524940	+	Missense_Mutation	SNP	G	G	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr11:107524940G>T	ENST00000265840.7	+	10	955	c.690G>T	c.(688-690)aaG>aaT	p.K230N	ELMOD1_ENST00000443271.2_Missense_Mutation_p.K222N|ELMOD1_ENST00000531234.1_Missense_Mutation_p.K224N	NM_018712.3	NP_061182.3	Q8N336	ELMD1_HUMAN	ELMO/CED-12 domain containing 1	230	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				phagocytosis (GO:0006909)|positive regulation of GTPase activity (GO:0043547)	cytoskeleton (GO:0005856)	GTPase activator activity (GO:0005096)			endometrium(2)|large_intestine(5)|liver(2)|lung(7)|pancreas(2)|prostate(1)	19		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00304)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Epithelial(105;0.00027)|all cancers(92;0.00481)		GGATGGATAAGGCAATTGGGT	0.388																																																	0								ENSG00000110675						107.0	96.0	99.0					11																	107524940		1885	4102	5987	ELMOD1	SO:0001583	missense	0			-	HGNC	AL359601	CCDS44723.1, CCDS44724.1	11q23.1	2012-10-15	2006-01-20		ENSG00000110675	ENSG00000110675			25334	protein-coding gene	gene with protein product		615456	"""ELMO domain containing 1"""			12477932	Standard	NM_018712		Approved	DKFZp547C176	uc010rvs.2	Q8N336	OTTHUMG00000166361	ENST00000265840.7:c.690G>T	11.37:g.107524940G>T	ENSP00000265840:p.Lys230Asn	Somatic	0	38	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	18	14.29	B4E167|G5E9S5|Q9NPW3	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Engulfment_cell_motility_ELMO	p.K230N	ENST00000265840.7	37	c.690	CCDS44723.1	11	.	.	.	.	.	.	.	.	.	.	G	14.57	2.575392	0.45902	.	.	ENSG00000110675	ENST00000531234;ENST00000265840;ENST00000443271	.	.	.	5.35	4.14	0.48551	Engulfment/cell motility, ELMO (2);	0.087753	0.53938	D	0.000046	T	0.40347	0.1113	L	0.29908	0.895	0.53005	D	0.999965	P;P	0.41131	0.549;0.739	B;B	0.43623	0.425;0.22	T	0.10291	-1.0636	9	0.17832	T	0.49	.	8.5942	0.33705	0.8173:0.0:0.1827:0.0	.	230;222	Q8N336;G5E9S5	ELMD1_HUMAN;.	N	224;230;222	.	ENSP00000265840:K230N	K	+	3	2	ELMOD1	107030150	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.479000	0.45197	0.866000	0.35629	-0.345000	0.07892	AAG	-	pfam_Engulfment_cell_motility_ELMO		0.388	ELMOD1-001	KNOWN	basic|CCDS	protein_coding	ELMOD1	protein_coding	OTTHUMT00000389406.1	G	NM_018712	-		107524940	+1	no_errors	ENST00000265840	ensembl	human	known	74_37	missense	SNP	1.000	T
CEPT1	10390	genome.wustl.edu	37	1	111703576	111703576	+	Intron	DEL	A	A	-	rs571497696	byFrequency	TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr1:111703576delA	ENST00000545121.1	+	4	695				CEPT1_ENST00000357172.4_Intron	NM_001007794.1	NP_001007795.1	Q9Y6K0	CEPT1_HUMAN	choline/ethanolamine phosphotransferase 1						CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	diacylglycerol cholinephosphotransferase activity (GO:0004142)|ethanolaminephosphotransferase activity (GO:0004307)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	8		all_cancers(81;2.27e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0173)|Colorectal(144;0.0375)|all cancers(265;0.0701)|LUSC - Lung squamous cell carcinoma(189;0.0888)|Epithelial(280;0.103)|COAD - Colon adenocarcinoma(174;0.141)	Choline(DB00122)	GTGATTTGGTAAAAAAAAAAA	0.299													|||unknown(HR)	1547	0.308906	0.3056	0.3242	5008	,	,		16440	0.3393		0.3181	False		,,,				2504	0.2618																0								ENSG00000134255																																			CEPT1	SO:0001627	intron_variant	0				HGNC	AF068302	CCDS830.1	1p13	2010-07-08			ENSG00000134255	ENSG00000134255	2.7.8.1, 2.7.8.2		24289	protein-coding gene	gene with protein product						10191259, 12216837	Standard	XM_005270353		Approved		uc001eah.1	Q9Y6K0	OTTHUMG00000012357	ENST00000545121.1:c.488-201A>-	1.37:g.111703576delA		Somatic	0	16	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	23	11.54	Q69YJ9|Q9P0Y8	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000545121.1	37	NULL	CCDS830.1	1																																																																																			-	-		0.299	CEPT1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	CEPT1	protein_coding	OTTHUMT00000034462.2	A	NM_006090			111703576	+1	no_errors	ENST00000480324	ensembl	human	known	74_37	rna	DEL	0.207	-
CXXC1	30827	genome.wustl.edu	37	18	47812275	47812277	+	In_Frame_Del	DEL	CTG	CTG	-	rs527645784	byFrequency	TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	CTG	CTG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr18:47812275_47812277delCTG	ENST00000285106.6	-	5	1195_1197	c.481_483delCAG	c.(481-483)cagdel	p.Q161del	CXXC1_ENST00000412036.2_In_Frame_Del_p.Q161del|CXXC1_ENST00000587396.1_5'Flank|CXXC1_ENST00000589940.1_In_Frame_Del_p.Q161del	NM_001101654.1|NM_014593.3	NP_001095124.1|NP_055408.2	Q9P0U4	CXXC1_HUMAN	CXXC finger protein 1	161					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|histone H3-K4 methylation (GO:0051568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	24						ACCGTTTGATctgctgctgctgc	0.557														27	0.00539137	0.0151	0.0	5008	,	,		19878	0.0		0.0	False		,,,				2504	0.0072																0								ENSG00000154832																																			CXXC1	SO:0001651	inframe_deletion	0				HGNC	BC014940	CCDS11945.1, CCDS45866.1	18q12	2014-02-20	2014-02-20		ENSG00000154832	ENSG00000154832		"""Zinc fingers, PHD-type"""	24343	protein-coding gene	gene with protein product	"""CpG binding protein"", ""DNA-binding protein with PHD finger and CXXC domain"", ""zinc finger, CpG binding-type containing 1"""	609150	"""CXXC finger 1 (PHD domain)"""			10799292, 10688657	Standard	NM_014593		Approved	HsT2645, PCCX1, hCGBP, PHF18, CGBP, SPP1, CFP1, ZCGPC1	uc002ler.4	Q9P0U4	OTTHUMG00000132670	ENST00000285106.6:c.481_483delCAG	18.37:g.47812284_47812286delCTG	ENSP00000285106:p.Gln161del	Somatic	0	43	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	12	20.00	B2RC03|Q8N2W4|Q96BC8|Q9P2V7	In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_CpG-bd_C,pfam_Znf_CXXC,pfam_Znf_PHD-finger,superfamily_Znf_FYVE_PHD,smart_Znf_PHD,pfscan_Znf_PHD-finger,pfscan_Znf_CXXC	p.Q161in_frame_del	ENST00000285106.6	37	c.483_481	CCDS11945.1	18																																																																																			-	pfscan_Znf_CXXC		0.557	CXXC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	CXXC1	protein_coding	OTTHUMT00000255927.2	CTG	NM_014593			47812277	-1	no_errors	ENST00000412036	ensembl	human	known	74_37	in_frame_del	DEL	1.000:1.000:1.000	-
SIK2	23235	genome.wustl.edu	37	11	111558730	111558730	+	Missense_Mutation	SNP	C	C	A			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr11:111558730C>A	ENST00000304987.3	+	4	495	c.322C>A	c.(322-324)Ctt>Att	p.L108I		NM_015191.1	NP_056006.1	Q9H0K1	SIK2_HUMAN	salt-inducible kinase 2	108	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of insulin receptor signaling pathway (GO:0046626)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	30						TACAGACTATCTTGCTAATCA	0.368																																																	0								ENSG00000170145						86.0	84.0	85.0					11																	111558730		2201	4297	6498	SIK2	SO:0001583	missense	0			-	HGNC	AB018324	CCDS8347.1	11q23.1	2008-12-23	2008-12-23	2008-12-23	ENSG00000170145	ENSG00000170145			21680	protein-coding gene	gene with protein product		608973	"""SNF1-like kinase 2"""	SNF1LK2		15067358	Standard	NM_015191		Approved	KIAA0781, QIK, DKFZp434K1115, LOH11CR1I	uc001plt.3	Q9H0K1	OTTHUMG00000150644	ENST00000304987.3:c.322C>A	11.37:g.111558730C>A	ENSP00000305976:p.Leu108Ile	Somatic	0	28	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	7	30.00	A8K5B8|B0YJ94|O94878|Q17RV0|Q6AZE2|Q76N03|Q8NCV7|Q96CZ8	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pirsf_Ser/Thr_kinase_SIK1/2,pfscan_UBA/transl_elong_EF1B_N_euk,pfscan_Prot_kinase_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	p.L108I	ENST00000304987.3	37	c.322	CCDS8347.1	11	.	.	.	.	.	.	.	.	.	.	C	19.57	3.852424	0.71719	.	.	ENSG00000170145	ENST00000304987	T	0.67345	-0.26	6.07	5.16	0.70880	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	0.85682	D	0.000000	T	0.60792	0.2296	N	0.05158	-0.105	0.80722	D	1	P	0.45569	0.861	D	0.65323	0.934	T	0.60732	-0.7205	10	0.24483	T	0.36	.	9.8667	0.41148	0.1405:0.7902:0.0:0.0693	.	108	Q9H0K1	SIK2_HUMAN	I	108	ENSP00000305976:L108I	ENSP00000305976:L108I	L	+	1	0	SIK2	111063940	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.613000	0.61176	1.561000	0.49584	0.655000	0.94253	CTT	-	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pirsf_Ser/Thr_kinase_SIK1/2,pfscan_Prot_kinase_dom,prints_Ser-Thr/Tyr_kinase_cat_dom		0.368	SIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SIK2	protein_coding	OTTHUMT00000319352.3	C	NM_015191	-		111558730	+1	no_errors	ENST00000304987	ensembl	human	known	74_37	missense	SNP	1.000	A
LINC01205	401082	genome.wustl.edu	37	3	109178739	109178740	+	lincRNA	INS	-	-	TTCCCTTGGTTTTCTTCATAAT			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr3:109178739_109178740insTTCCCTTGGTTTTCTTCATAAT	ENST00000497996.1	+	0	388_389																											Ggtgtttataattcccttggtt	0.287																																																	0								ENSG00000228980																																			RP11-702L6.4			0				Clone_based_vega_gene																													3.37:g.109178739_109178740insTTCCCTTGGTTTTCTTCATAAT		Somatic	NA	NA	NA		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA		RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000497996.1	37	NULL		3																																																																																			-	-		0.287	RP11-702L6.4-002	KNOWN	basic	lincRNA	ENSG00000228980	lincRNA	OTTHUMT00000353892.1	-				109178740	+1	no_errors	ENST00000497996	ensembl	human	known	74_37	rna	INS	0.009:0.018	TTCCCTTGGTTTTCTTCATAAT
ATRNL1	26033	genome.wustl.edu	37	10	117486842	117486842	+	Nonsense_Mutation	SNP	G	G	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr10:117486842G>T	ENST00000355044.3	+	27	4006	c.3880G>T	c.(3880-3882)Gag>Tag	p.E1294*	ATRNL1_ENST00000423111.2_Nonsense_Mutation_p.E345*|ATRNL1_ENST00000303745.7_Nonsense_Mutation_p.E87*	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	1294					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		TGAACAAACAGAGTTTCTGCG	0.478																																																	0								ENSG00000107518						52.0	48.0	49.0					10																	117486842		2203	4300	6503	ATRNL1	SO:0001587	stop_gained	0			-	HGNC	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.3880G>T	10.37:g.117486842G>T	ENSP00000347152:p.Glu1294*	Somatic	0	41	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	18	14.29	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Nonsense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Kelch_1,pfam_Kelch_2,pfam_Plexin_repeat,pfam_CUB_dom,pfam_EGF_extracell,superfamily_C-type_lectin_fold,superfamily_CUB_dom,superfamily_Plexin-like_fold,smart_EG-like_dom,smart_CUB_dom,smart_Plexin-like_fold,smart_C-type_lectin,smart_EGF_laminin,pfscan_CUB_dom,pfscan_EG-like_dom,pfscan_EGF_laminin,pfscan_C-type_lectin	p.E1294*	ENST00000355044.3	37	c.3880	CCDS7592.1	10	.	.	.	.	.	.	.	.	.	.	G	37	6.303706	0.97458	.	.	ENSG00000107518	ENST00000355044;ENST00000423111;ENST00000303745	.	.	.	5.77	5.77	0.91146	.	0.257127	0.43579	D	0.000543	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	-7.2425	19.9795	0.97321	0.0:0.0:1.0:0.0	.	.	.	.	X	1294;345;87	.	ENSP00000307660:E87X	E	+	1	0	ATRNL1	117476832	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	6.936000	0.75892	2.720000	0.93068	0.650000	0.86243	GAG	-	NULL		0.478	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ATRNL1	protein_coding	OTTHUMT00000050507.3	G	XM_049349	-		117486842	+1	no_errors	ENST00000355044	ensembl	human	known	74_37	nonsense	SNP	1.000	T
CYP2S1	29785	genome.wustl.edu	37	19	41712320	41712320	+	Frame_Shift_Del	DEL	T	T	-			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr19:41712320delT	ENST00000310054.4	+	9	1658	c.1442delT	c.(1441-1443)cttfs	p.L481fs	CYP2S1_ENST00000542619.1_Frame_Shift_Del_p.L206fs	NM_030622.6	NP_085125.1	Q96SQ9	CP2S1_HUMAN	cytochrome P450, family 2, subfamily S, polypeptide 1	481					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(2)	14						GTCAGTGGCCTTTTCAACATT	0.602																																																	0								ENSG00000167600						136.0	127.0	130.0					19																	41712320		2203	4300	6503	CYP2S1	SO:0001589	frameshift_variant	0				HGNC	AA301039	CCDS12573.1	19q13.2	2013-11-11	2003-01-14		ENSG00000167600	ENSG00000167600		"""Cytochrome P450s"""	15654	protein-coding gene	gene with protein product		611529	"""cytochrome P450, subfamily IIS, polypeptide 1"""			11181079	Standard	NM_030622		Approved		uc002opw.3	Q96SQ9	OTTHUMG00000182721	ENST00000310054.4:c.1442delT	19.37:g.41712320delT	ENSP00000308032:p.Leu481fs	Somatic	0	24	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	2	19	9.52	Q9BZ66	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Cyt_P450,superfamily_Cyt_P450,prints_Cyt_P450_E_grp-I,prints_Cyt_P450_E_grp-IV,prints_Cyt_P450,prints_Cyt_P450_E_grp-I_CYP2A-like,prints_Cyt_P450_E_grp-I_CYP2B-like,prints_Cyt_P450_B	p.F482fs	ENST00000310054.4	37	c.1442	CCDS12573.1	19																																																																																			-	pfam_Cyt_P450,superfamily_Cyt_P450		0.602	CYP2S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CYP2S1	protein_coding	OTTHUMT00000463287.1	T				41712320	+1	no_errors	ENST00000310054	ensembl	human	known	74_37	frame_shift_del	DEL	1.000	-
DSPP	1834	genome.wustl.edu	37	4	88537288	88537288	+	Silent	SNP	C	C	T	rs368208607		TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr4:88537288C>T	ENST00000282478.7	+	4	3507	c.3474C>T	c.(3472-3474)gaC>gaT	p.D1158D	DSPP_ENST00000399271.1_Silent_p.D1158D|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1158	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagcgacagcagtgaca	0.557																																																	0								ENSG00000152591						46.0	59.0	54.0					4																	88537288		1591	2859	4450	DSPP	SO:0001819	synonymous_variant	0			-	HGNC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3474C>T	4.37:g.88537288C>T		Somatic	0	44	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	35	12.50	A8MUI0|O95815	Silent	SNP	NA	NA	NA	NA	NA	NA	NULL	p.D1158	ENST00000282478.7	37	c.3474	CCDS43248.1	4																																																																																			-	NULL		0.557	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	DSPP	protein_coding	OTTHUMT00000363616.3	C	NM_014208	-		88537288	+1	no_errors	ENST00000282478	ensembl	human	known	74_37	silent	SNP	0.959	T
AIM2	9447	genome.wustl.edu	37	1	159032487	159032487	+	Frame_Shift_Del	DEL	T	T	-	rs531843702	byFrequency	TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr1:159032487delT	ENST00000368130.4	-	6	1315	c.1027delA	c.(1027-1029)acafs	p.T343fs		NM_004833.1	NP_004824.1	O14862	AIM2_HUMAN	absent in melanoma 2	343					activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to drug (GO:0035690)|cellular response to interferon-beta (GO:0035458)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein oligomerization (GO:0032461)|pyroptosis (GO:0070269)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)			breast(1)|large_intestine(1)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(1)	16	all_hematologic(112;0.0429)					CTTCTCTATGTTTTTTTTTTG	0.398														28	0.00559105	0.0076	0.0043	5008	,	,		19188	0.002		0.003	False		,,,				2504	0.0102																0								ENSG00000163568			77,102,4087		0,0,77,0,102,1954	174.0	138.0	150.0			-1.5	0.0	1		158	80,228,7946		0,0,80,0,228,3819	no	codingComplex	AIM2	NM_004833.1		0,0,157,0,330,5773	A1A1,A1A2,A1R,A2A2,A2R,RR		3.7315,4.196,3.8898			159032487	157,330,12033	2203	4300	6503	AIM2	SO:0001589	frameshift_variant	0				HGNC	AF024714	CCDS1181.1	1q22	2008-07-18			ENSG00000163568	ENSG00000163568			357	protein-coding gene	gene with protein product		604578				9242382	Standard	NM_004833		Approved	PYHIN4	uc001ftj.1	O14862	OTTHUMG00000037183	ENST00000368130.4:c.1027delA	1.37:g.159032487delT	ENSP00000357112:p.Thr343fs	Somatic	0	37	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	31	11.43	A8K7M7|Q5T3V9|Q96FG9	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_HIN200/IF120x,pfam_DAPIN,superfamily_DEATH-like_dom,superfamily_NA-bd_OB-fold,pfscan_DAPIN,pfscan_HIN200/IF120x	p.T343fs	ENST00000368130.4	37	c.1027	CCDS1181.1	1																																																																																			-	NULL		0.398	AIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AIM2	protein_coding	OTTHUMT00000090341.1	T	NM_004833			159032487	-1	no_errors	ENST00000368130	ensembl	human	known	74_37	frame_shift_del	DEL	0.001	-
MFSD4	148808	genome.wustl.edu	37	1	205571627	205571627	+	3'UTR	SNP	C	C	A			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr1:205571627C>A	ENST00000367147.4	+	0	3676				MFSD4_ENST00000478555.1_3'UTR	NM_181644.4	NP_857595.3	Q8N468	MFSD4_HUMAN	major facilitator superfamily domain containing 4						transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			taaagcaaagcactcacaata	0.323																																																	0								ENSG00000174514																																			MFSD4	SO:0001624	3_prime_UTR_variant	0			-	HGNC	BC036549	CCDS1455.1	1q32.1	2008-02-05			ENSG00000174514	ENSG00000174514			25433	protein-coding gene	gene with protein product							Standard	NM_181644		Approved	DKFZp761N1114, FLJ34577, UNQ3064, FLJ25004	uc001hcv.4	Q8N468	OTTHUMG00000037197	ENST00000367147.4:c.*2038C>A	1.37:g.205571627C>A		Somatic	0	47	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	41	8.89	B7Z8X3|Q6UY25|Q8NAY0|Q8TCP4	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000367147.4	37	NULL	CCDS1455.1	1																																																																																			-	-		0.323	MFSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MFSD4	protein_coding	OTTHUMT00000090391.1	C	NM_181644	-		205571627	+1	no_errors	ENST00000478555	ensembl	human	known	74_37	rna	SNP	0.002	A
C10orf76	79591	genome.wustl.edu	37	10	103783275	103783275	+	Missense_Mutation	SNP	C	C	G			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr10:103783275C>G	ENST00000370033.4	-	8	747	c.628G>C	c.(628-630)Gtc>Ctc	p.V210L		NM_024541.2	NP_078817.2	Q5T2E6	CJ076_HUMAN	chromosome 10 open reading frame 76	210						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|prostate(2)|upper_aerodigestive_tract(2)	24		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		AAGAGGACGACAGCATCATAC	0.458																																																	0								ENSG00000120029						121.0	118.0	119.0					10																	103783275		1946	4147	6093	C10orf76	SO:0001583	missense	0			-	HGNC	AK023176	CCDS41563.1	10q24.32	2008-10-21			ENSG00000120029	ENSG00000120029			25788	protein-coding gene	gene with protein product						14702039	Standard	NM_024541		Approved	FLJ13114	uc009xwy.1	Q5T2E6	OTTHUMG00000018943	ENST00000370033.4:c.628G>C	10.37:g.103783275C>G	ENSP00000359050:p.Val210Leu	Somatic	0	28	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	11	9	55.00	Q2TB87|Q9H8Z9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_DUF1741,superfamily_ARM-type_fold	p.V210L	ENST00000370033.4	37	c.628	CCDS41563.1	10	.	.	.	.	.	.	.	.	.	.	C	17.65	3.442772	0.63067	.	.	ENSG00000120029	ENST00000370033	.	.	.	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.52725	0.1752	L	0.31526	0.94	0.80722	D	1	B	0.17465	0.022	B	0.15484	0.013	T	0.44065	-0.9352	9	0.27082	T	0.32	-12.3662	19.1344	0.93420	0.0:1.0:0.0:0.0	.	210	Q5T2E6	CJ076_HUMAN	L	210	.	ENSP00000359050:V210L	V	-	1	0	C10orf76	103773265	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	7.480000	0.81109	2.590000	0.87494	0.563000	0.77884	GTC	-	superfamily_ARM-type_fold		0.458	C10orf76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C10orf76	protein_coding	OTTHUMT00000050007.1	C	NM_024541	-		103783275	-1	no_errors	ENST00000370033	ensembl	human	known	74_37	missense	SNP	1.000	G
REPS1	85021	genome.wustl.edu	37	6	139265676	139265676	+	Missense_Mutation	SNP	G	G	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr6:139265676G>T	ENST00000450536.2	-	5	1286	c.712C>A	c.(712-714)Cca>Aca	p.P238T	REPS1_ENST00000415951.2_Missense_Mutation_p.P238T|REPS1_ENST00000367663.4_Missense_Mutation_p.P238T|REPS1_ENST00000409812.2_Missense_Mutation_p.P238T|REPS1_ENST00000258062.5_Missense_Mutation_p.P238T			Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1	238					receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|SH3 domain binding (GO:0017124)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	19				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)		GTACTGGTTGGTGGAGTATCT	0.448																																																	0								ENSG00000135597						193.0	179.0	184.0					6																	139265676		2203	4300	6503	REPS1	SO:0001583	missense	0			-	HGNC		CCDS5193.2, CCDS47488.1, CCDS69212.1, CCDS69213.1	6q24.1	2013-01-10			ENSG00000135597	ENSG00000135597		"""EF-hand domain containing"""	15578	protein-coding gene	gene with protein product		614825					Standard	XM_005267177		Approved		uc011edr.2	Q96D71	OTTHUMG00000015685	ENST00000450536.2:c.712C>A	6.37:g.139265676G>T	ENSP00000392065:p.Pro238Thr	Somatic	0	34	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	14	15	48.28	B7ZBZ8|B7ZBZ9|B7ZC00|J3KP76|Q5JWJ5|Q5JWJ6|Q5JWJ7|Q8NDR7|Q8WU62|Q9BXY9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	smart_EPS15_homology,pfscan_EF_hand_dom,pfscan_EPS15_homology	p.P238T	ENST00000450536.2	37	c.712		6	.	.	.	.	.	.	.	.	.	.	G	20.6	4.024739	0.75390	.	.	ENSG00000135597	ENST00000450536;ENST00000367663;ENST00000529597;ENST00000409812;ENST00000258062;ENST00000415951;ENST00000367668	T;T;T;T;T;T	0.36157	1.27;1.32;1.34;1.36;1.29;1.32	5.72	5.72	0.89469	.	0.048246	0.85682	D	0.000000	T	0.38241	0.1033	N	0.24115	0.695	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.87578	0.998;0.998;0.978;0.996	T	0.07809	-1.0753	10	0.33141	T	0.24	-12.7677	18.4242	0.90604	0.0:0.0:1.0:0.0	.	238;238;238;238	Q96D71-3;Q96D71-2;Q96D71;E9PMG1	.;.;REPS1_HUMAN;.	T	238;238;224;238;238;238;186	ENSP00000392065:P238T;ENSP00000356635:P238T;ENSP00000434251:P224T;ENSP00000386699:P238T;ENSP00000258062:P238T;ENSP00000397941:P238T	ENSP00000258062:P238T	P	-	1	0	REPS1	139307369	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.727000	0.91480	2.865000	0.98341	0.655000	0.94253	CCA	-	NULL		0.448	REPS1-001	KNOWN	basic|appris_candidate_longest	protein_coding	REPS1	protein_coding	OTTHUMT00000042447.3	G		-		139265676	-1	no_errors	ENST00000450536	ensembl	human	known	74_37	missense	SNP	1.000	T
OTUD4	54726	genome.wustl.edu	37	4	146059742	146059742	+	Missense_Mutation	SNP	G	G	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr4:146059742G>T	ENST00000447906.2	-	21	2372	c.2185C>A	c.(2185-2187)Ctg>Atg	p.L729M	OTUD4_ENST00000455611.2_Intron|OTUD4_ENST00000454497.2_Missense_Mutation_p.L664M			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4	729					protein K48-linked deubiquitination (GO:0071108)		poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(180;0.151)					CAGGCTGCCAGGTAGGCCTGG	0.483																																																	0								ENSG00000164164						59.0	64.0	63.0					4																	146059742		2203	4297	6500	OTUD4	SO:0001583	missense	0			-	HGNC		CCDS3764.1, CCDS47139.1	4q31.21	2014-02-24	2014-02-24		ENSG00000164164	ENSG00000164164		"""OTU domain containing"""	24949	protein-coding gene	gene with protein product		611744	"""OTU domain containing 4"""			1475186, 12727813, 19996094	Standard	NM_001102653		Approved	HSHIN1, KIAA1046, DUBA6	uc003ika.4	Q01804	OTTHUMG00000161480	ENST00000447906.2:c.2185C>A	4.37:g.146059742G>T	ENSP00000395487:p.Leu729Met	Somatic	0	46	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	26	13.33	B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_OTU,pfscan_OTU	p.L729M	ENST00000447906.2	37	c.2185		4	.	.	.	.	.	.	.	.	.	.	G	11.26	1.585647	0.28268	.	.	ENSG00000164164	ENST00000454497;ENST00000447906	T;T	0.38887	1.12;1.11	6.04	0.571	0.17352	.	0.324746	0.26096	N	0.026364	T	0.22859	0.0552	N	0.17082	0.46	0.80722	D	1	B;B	0.21821	0.061;0.036	B;B	0.22753	0.041;0.018	T	0.03945	-1.0990	10	0.36615	T	0.2	-1.2783	7.4244	0.27090	0.1196:0.0:0.1648:0.7157	.	729;728	G3V0I6;Q01804	.;OTUD4_HUMAN	M	664;729	ENSP00000409279:L664M;ENSP00000395487:L729M	ENSP00000395487:L729M	L	-	1	2	OTUD4	146279192	0.983000	0.35010	1.000000	0.80357	0.993000	0.82548	0.108000	0.15396	0.370000	0.24538	-0.311000	0.09066	CTG	-	NULL		0.483	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	OTUD4	protein_coding	OTTHUMT00000365117.2	G	NM_017493	-		146059742	-1	no_errors	ENST00000447906	ensembl	human	known	74_37	missense	SNP	0.980	T
GGT6	124975	genome.wustl.edu	37	17	4461459	4461459	+	Missense_Mutation	SNP	G	G	T			TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr17:4461459G>T	ENST00000574154.1	-	4	1629	c.1333C>A	c.(1333-1335)Cag>Aag	p.Q445K	MYBBP1A_ENST00000381556.2_5'Flank|MYBBP1A_ENST00000254718.4_5'Flank|GGT6_ENST00000381550.3_Missense_Mutation_p.Q451K|GGT6_ENST00000301395.3_Missense_Mutation_p.Q413K|GGT6_ENST00000573591.1_Missense_Mutation_p.Q297K			Q6P531	GGT6_HUMAN	gamma-glutamyltransferase 6	445					glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			endometrium(2)|large_intestine(1)|lung(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						TGCTGGGCCTGGGTAGGGGGC	0.627																																																	0								ENSG00000167741						91.0	80.0	83.0					17																	4461459		2203	4300	6503	GGT6	SO:0001583	missense	0			-	HGNC	AK074646	CCDS11047.1, CCDS45582.1, CCDS73942.1	17p13.2	2014-08-12	2008-03-10		ENSG00000167741	ENSG00000167741		"""Gamma-glutamyltransferases"""	26891	protein-coding gene	gene with protein product		612341	"""gamma-glutamyltransferase 6 homolog (rat)"""			18357469	Standard	NM_001122890		Approved	FLJ90165	uc002fyd.4	Q6P531	OTTHUMG00000177827	ENST00000574154.1:c.1333C>A	17.37:g.4461459G>T	ENSP00000458307:p.Gln445Lys	Somatic	0	46	0.00		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	8	27.27	B4DUH4|Q8NCM0	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_GGT_peptidase,prints_GGT_peptidase	p.Q445K	ENST00000574154.1	37	c.1333	CCDS45582.1	17	.	.	.	.	.	.	.	.	.	.	G	6.839	0.524060	0.13066	.	.	ENSG00000167741	ENST00000381550;ENST00000301395;ENST00000414312	T	0.23348	1.91	3.51	3.51	0.40186	.	0.687209	0.13089	N	0.414719	T	0.20414	0.0491	L	0.47716	1.5	0.09310	N	1	B;B;P	0.40731	0.255;0.231;0.728	B;B;B	0.38500	0.071;0.107;0.275	T	0.05321	-1.0892	10	0.09084	T	0.74	-26.312	10.7479	0.46191	0.0:0.0:1.0:0.0	.	451;445;413	B4DKN3;Q6P531;Q6P531-2	.;GGT6_HUMAN;.	K	445;413;297	ENSP00000301395:Q413K	ENSP00000301395:Q413K	Q	-	1	0	GGT6	4408208	0.015000	0.18098	0.011000	0.14972	0.392000	0.30506	1.539000	0.36104	1.964000	0.57103	0.655000	0.94253	CAG	-	NULL		0.627	GGT6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	GGT6	protein_coding	OTTHUMT00000439122.1	G	NM_153338	-		4461459	-1	no_errors	ENST00000574154	ensembl	human	known	74_37	missense	SNP	0.019	T
SPATA5	166378	genome.wustl.edu	37	4	123928724	123928751	+	Intron	DEL	TGTGTGTGTGTGTGTGTGTGTGTGTGTG	TGTGTGTGTGTGTGTGTGTGTGTGTGTG	-	rs112099221|rs368779194|rs200644187|rs148702654|rs112656406|rs200478794		TCGA-MB-A5Y8-01A-11D-A29N-09	TCGA-MB-A5Y8-10A-01D-A29N-09	TGTGTGTGTGTGTGTGTGTGTGTGTGTG	TGTGTGTGTGTGTGTGTGTGTGTGTGTG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ef3ebd13-0657-488a-b94a-c92dcb425306	2acedeb3-0a0d-4d72-b763-176d68e55d0e	g.chr4:123928724_123928751delTGTGTGTGTGTGTGTGTGTGTGTGTGTG	ENST00000274008.4	+	11	1938				SPATA5_ENST00000422835.2_Intron|AC109357.1_ENST00000401335.1_RNA	NM_145207.2	NP_660208.2	Q8NB90	SPAT5_HUMAN	spermatogenesis associated 5						cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24						tgtgtgtatatgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg	0.36																																																	0								ENSG00000216154																																			AC109357.1	SO:0001627	intron_variant	0				Clone_based_ensembl_gene	AF361489	CCDS3730.1	4q28.1	2010-04-21			ENSG00000145375	ENSG00000145375		"""ATPases / AAA-type"""	18119	protein-coding gene	gene with protein product	"""ATPase family gene 2 homolog (S. cerevisiae)"""	613940				16465403	Standard	NM_145207		Approved	SPAF, AFG2	uc003iez.4	Q8NB90	OTTHUMG00000133074	ENST00000274008.4:c.1870-20590TGTGTGTGTGTGTGTGTGTGTGTGTGTG>-	4.37:g.123928724_123928751delTGTGTGTGTGTGTGTGTGTGTGTGTGTG		Somatic	NA	NA	NA		0.7201401137352239	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	C9JT97|Q86XW1|Q8NI20|Q8TDL7	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000274008.4	37	NULL	CCDS3730.1	4																																																																																			-	-		0.360	SPATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000216154	protein_coding	OTTHUMT00000256714.2	TGTGTGTGTGTGTGTGTGTGTGTGTGTG	NM_145207			123928751	-1	no_errors	ENST00000401335	ensembl	human	novel	74_37	rna	DEL	0.008:0.004:0.004:0.003:0.003:0.003:0.005:0.006:0.007:0.007:0.007:0.006:0.005:0.003:0.004:0.003:0.005:0.006:0.012:0.017:0.021:0.026:0.029:0.032:0.035:0.037:0.038:0.039	-
