#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_ ensembl_gene_id	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_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_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	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_dbSNP	i_default_gene_name	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_name_source	i_gene_type	i_havana_transcript	i_n_alt_count	i_n_alt_count_full	i_n_alt_count_val	i_n_ref_count	i_n_ref_count_full	i_n_ref_count_val	i_normal_vaf	i_normal_vaf_val	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_t_alt_count_full	i_t_alt_count_val	i_t_ref_count_full	i_t_ref_count_val	i_tier	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_tumor_vaf	i_tumor_vaf_val	i_type	i_ucsc_cons	i_variant	t_alt_count	t_ref_count
TP53	7157	genome.wustl.edu	37	17	7578235	7578235	+	Missense_Mutation	SNP	T	T	C			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr17:7578235T>C	ENST00000269305.4	-	6	803	c.614A>G	c.(613-615)tAt>tGt	p.Y205C	TP53_ENST00000455263.2_Missense_Mutation_p.Y205C|TP53_ENST00000574684.1_Intron|TP53_ENST00000359597.4_Missense_Mutation_p.Y205C|TP53_ENST00000413465.2_Missense_Mutation_p.Y205C|TP53_ENST00000445888.2_Missense_Mutation_p.Y205C|TP53_ENST00000420246.2_Missense_Mutation_p.Y205C	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	205	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Y -> C (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1459726}.|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in sporadic cancers; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|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 transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Y205C(68)|p.Y205S(14)|p.Y205F(8)|p.0?(8)|p.Y112C(5)|p.?(5)|p.Y73C(5)|p.Y73S(1)|p.Y112S(1)|p.E204fs*39(1)|p.E204_N210delEYLDDRN(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTCATCCAAATACTCCACACG	0.542		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			ENSG00000141510																									Pancreas(47;798 1329 9957 10801)		yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	117	Substitution - Missense(102)|Whole gene deletion(8)|Unknown(5)|Deletion - In frame(1)|Deletion - Frameshift(1)	lung(20)|upper_aerodigestive_tract(19)|central_nervous_system(10)|large_intestine(9)|biliary_tract(8)|breast(6)|ovary(6)|haematopoietic_and_lymphoid_tissue(5)|endometrium(5)|urinary_tract(5)|bone(5)|soft_tissue(4)|oesophagus(4)|stomach(3)|liver(3)|pancreas(2)|vulva(1)|skin(1)|prostate(1)											136.0	121.0	126.0					17																	7578235		2203	4300	6503	SO:0001583	missense	0	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	-	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.614A>G	17.37:g.7578235T>C	ENSP00000269305:p.Tyr205Cys		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	pfam_p53_D-bd,pfam_p53_tetrameristn,pfam_p53_transactivation_domain,superfamily_p53-like_TF_D-bd,superfamily_p53_tetrameristn,prints_p53_tumour_suppressor	p.Y205C	ENST00000269305.4	37	c.614	CCDS11118.1	17	.	.	.	.	.	.	.	.	.	.	T	17.85	3.490024	0.64074	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99872	-7.36;-7.36;-7.36;-7.36;-7.36;-7.36;-7.36;-7.36	5.41	4.33	0.51752	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99840	0.9927	M	0.88906	2.99	0.58432	D	0.999999	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.995;0.998;0.995;0.997;0.999;0.997;0.996	D	0.97320	0.9943	10	0.87932	D	0	-5.8058	9.707	0.40222	0.0:0.0827:0.0:0.9173	.	166;205;205;112;205;205;205	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	C	205;205;205;205;205;205;194;112;73;112;73	ENSP00000410739:Y205C;ENSP00000352610:Y205C;ENSP00000269305:Y205C;ENSP00000398846:Y205C;ENSP00000391127:Y205C;ENSP00000391478:Y205C;ENSP00000425104:Y73C;ENSP00000423862:Y112C	ENSP00000269305:Y205C	Y	-	2	0	TP53	7518960	1.000000	0.71417	0.137000	0.22149	0.045000	0.14185	7.996000	0.88334	1.001000	0.39076	-0.256000	0.11100	TAT	-	TP53	-	pfam_p53_D-bd,superfamily_p53-like_TF_D-bd		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TP53	HGNC	protein_coding	OTTHUMT00000367397.1	0	0		58	58		0.00		T	NM_000546		7578235	-1	38		12		tier1	no_errors	ENST00000269305	ensembl	human	known	74_37	missense	76.00		SNP	0.989	C	38	12
ZNF568	374900	genome.wustl.edu	37	19	37488408	37488408	+	Silent	SNP	A	A	G			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr19:37488408A>G	ENST00000455427.2	+	9	1952	c.1623A>G	c.(1621-1623)gaA>gaG	p.E541E		NM_001204839.1	NP_001191768.1	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	572					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GAAGGTCAGAACTCACACATC	0.468													ENSG00000198453																																					0																																										SO:0001819	synonymous_variant	0			-	BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"""Zinc fingers, C2H2-type"", ""-"""	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000455427.2:c.1623A>G	19.37:g.37488408A>G			B4DS92|E7ER33|Q6N060|Q8NA64	Silent	SNP	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.E541	ENST00000455427.2	37	c.1623	CCDS56093.1	19																																																																																			-	ZNF568	-	smart_Znf_C2H2-like,pfscan_Znf_C2H2		0.468	ZNF568-007	KNOWN	basic|CCDS	protein_coding	ZNF568	HGNC	protein_coding	OTTHUMT00000457465.1	0	0		73	73		0.00		A	NM_198539		37488408	+1	11		125		tier1	no_errors	ENST00000455427	ensembl	human	known	74_37	silent	8.09		SNP	0.002	G	11	125
KCNC2	3747	genome.wustl.edu	37	12	75444697	75444697	+	Missense_Mutation	SNP	C	C	T	rs550561919		TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr12:75444697C>T	ENST00000549446.1	-	3	1768	c.1088G>A	c.(1087-1089)cGc>cAc	p.R363H	KCNC2_ENST00000548243.1_5'UTR|KCNC2_ENST00000298972.1_Missense_Mutation_p.R363H|KCNC2_ENST00000548513.1_Missense_Mutation_p.R363H|KCNC2_ENST00000350228.2_Missense_Mutation_p.R363H|KCNC2_ENST00000341669.3_Missense_Mutation_p.R363H|KCNC2_ENST00000550433.1_Missense_Mutation_p.R363H|KCNC2_ENST00000540018.1_Missense_Mutation_p.R363H|KCNC2_ENST00000393288.2_Missense_Mutation_p.R363H	NM_001260497.1|NM_139137.3	NP_001247426.1|NP_631875.1	Q96PR1	KCNC2_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 2	363					action potential (GO:0001508)|energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(28)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	54					Dalfampridine(DB06637)	TACAAAATGGCGGGTGAGCTT	0.453													ENSG00000166006	C|||	1	0.000199681	0.0	0.0	5008	,	,		19106	0.001		0.0	False		,,,				2504	0.0																0													51.0	46.0	48.0					12																	75444697		2203	4300	6503	SO:0001583	missense	0			-	AF268896	CCDS9005.1, CCDS9006.1, CCDS9007.1, CCDS58255.1, CCDS58256.1, CCDS58257.1	12q14.1	2012-07-05						"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6234	protein-coding gene	gene with protein product		176256				8111118, 16382104	Standard	NM_139136		Approved	Kv3.2	uc001sxg.2	Q96PR1	OTTHUMG00000169717	ENST00000549446.1:c.1088G>A	12.37:g.75444697C>T	ENSP00000449253:p.Arg363His		B7Z231|F5H030|J3KPP5|Q4LE77|Q86W09|Q8N1V9|Q96PR0	Missense_Mutation	SNP	pfam_Ion_trans_dom,pfam_T1-type_BTB,pfam_2pore_dom_K_chnl_dom,superfamily_BTB/POZ_fold,smart_BTB/POZ-like,prints_K_chnl,prints_K_chnl_volt-dep_Kv3,prints_K_chnl_volt-dep_Kv	p.R363H	ENST00000549446.1	37	c.1088	CCDS9007.1	12	.	.	.	.	.	.	.	.	.	.	C	25.4	4.637692	0.87760	.	.	ENSG00000166006	ENST00000550433;ENST00000548513;ENST00000549446;ENST00000341669;ENST00000298972;ENST00000350228;ENST00000540018;ENST00000393288	D;D;D;D;D;D;D;D	0.98602	-5.02;-5.02;-5.02;-5.02;-5.02;-5.02;-5.02;-5.02	6.06	6.06	0.98353	Ion transport (1);	0.000000	0.64402	D	0.000003	D	0.99102	0.9691	M	0.84585	2.705	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;0.997;1.0;0.996;0.999	D	0.99593	1.0976	10	0.87932	D	0	.	20.6397	0.99537	0.0:1.0:0.0:0.0	.	363;363;363;363;363	F5H030;Q96PR1-2;Q96PR1;Q96PR1-4;Q96PR1-3	.;.;KCNC2_HUMAN;.;.	H	363	ENSP00000448301:R363H;ENSP00000449941:R363H;ENSP00000449253:R363H;ENSP00000340121:R363H;ENSP00000298972:R363H;ENSP00000319877:R363H;ENSP00000438423:R363H;ENSP00000376966:R363H	ENSP00000298972:R363H	R	-	2	0	KCNC2	73730964	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.792000	0.85828	2.880000	0.98712	0.650000	0.86243	CGC	-	KCNC2	-	pfam_Ion_trans_dom,prints_K_chnl,prints_K_chnl_volt-dep_Kv		0.453	KCNC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	KCNC2	HGNC	protein_coding	OTTHUMT00000405581.2	0	0		17	17		0.00		C	NM_153748		75444697	-1	6		8		tier1	no_errors	ENST00000549446	ensembl	human	known	74_37	missense	42.86		SNP	1.000	T	6	8
PIK3CA	5290	genome.wustl.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279		TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr3:178952085A>G	ENST00000263967.3	+	21	3297	c.3140A>G	c.(3139-3141)cAt>cGt	p.H1047R	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1047	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (in BC; unknown pathological significance). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16353168}.|H -> R (in CLOVE, KERSEB, CRC, BC and OC; also found in an endometrial carcinoma sample; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane). {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|H -> Y (in MCAP; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H1047R(1387)|p.H1047L(194)|p.H1047P(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AATGATGCACATCATGGTGGC	0.378	H1047L(EFM19_BREAST)|H1047R(BT20_BREAST)|H1047R(CAL29_URINARY_TRACT)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(HCC1954_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(MCAS_OVARY)|H1047R(MDAMB453_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(RKO_LARGE_INTESTINE)|H1047R(SKOV3_OVARY)|H1047R(T47D_BREAST)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)			ENSG00000121879																									Colon(199;1504 1750 3362 26421 31210 32040)			Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	1582	Substitution - Missense(1582)	breast(961)|large_intestine(245)|endometrium(114)|ovary(77)|urinary_tract(36)|upper_aerodigestive_tract(26)|lung(19)|central_nervous_system(19)|stomach(19)|haematopoietic_and_lymphoid_tissue(11)|thyroid(10)|NS(9)|liver(7)|kidney(6)|soft_tissue(6)|skin(4)|prostate(4)|pituitary(3)|pancreas(3)|meninges(1)|cervix(1)|bone(1)											99.0	89.0	92.0					3																	178952085		1912	4130	6042	SO:0001583	missense	0			-		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3140A>G	3.37:g.178952085A>G	ENSP00000263967:p.His1047Arg		Q14CW1|Q99762	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,pfam_PI3K_adapt-bd_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,superfamily_C2_dom,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.H1047R	ENST00000263967.3	37	c.3140	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506328	0.44558	.	.	ENSG00000121879	ENST00000263967	T	0.80214	-1.35	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.62466	0.2430	N	0.08118	0	0.80722	D	1	P	0.38597	0.639	B	0.28011	0.085	T	0.67526	-0.5648	10	0.40728	T	0.16	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	R	1047	ENSP00000263967:H1047R	ENSP00000263967:H1047R	H	+	2	0	PIK3CA	180434779	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	CAT	rs121913279	PIK3CA	-	superfamily_Kinase-like_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	0	0		19	19		0.00		A			178952085	+1	41		1		tier1	no_errors	ENST00000263967	ensembl	human	known	74_37	missense	97.62		SNP	1.000	G	41	1
NKAPL	222698	genome.wustl.edu	37	6	28227274	28227274	+	Missense_Mutation	SNP	G	G	A			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr6:28227274G>A	ENST00000343684.3	+	1	177	c.125G>A	c.(124-126)cGc>cAc	p.R42H	ZKSCAN4_ENST00000423974.2_5'Flank	NM_001007531.1	NP_001007532.1	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	42										breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						GGCTGTTCCCGCTCTCACTCC	0.652													ENSG00000189134																																					0													44.0	46.0	45.0					6																	28227274		2203	4300	6503	SO:0001583	missense	0			-	BC038240	CCDS34353.1	6p21.33	2008-02-05	2007-08-16	2007-08-16	ENSG00000189134	ENSG00000189134			21584	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 194"""	C6orf194			Standard	NM_001007531		Approved	bA424I5.1	uc003nkt.4	Q5M9Q1	OTTHUMG00000014517	ENST00000343684.3:c.125G>A	6.37:g.28227274G>A	ENSP00000345716:p.Arg42His		Q3MIV1|Q9H4Q7	Missense_Mutation	SNP	pfam_DUF926	p.R42H	ENST00000343684.3	37	c.125	CCDS34353.1	6	.	.	.	.	.	.	.	.	.	.	G	11.63	1.696038	0.30052	.	.	ENSG00000189134	ENST00000343684	T	0.18502	2.21	3.99	2.1	0.27182	.	1.245590	0.05707	N	0.595259	T	0.03178	0.0093	N	0.19112	0.55	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.42916	-0.9423	10	0.23891	T	0.37	0.8902	5.9432	0.19203	0.2595:0.0:0.7405:0.0	.	42	Q5M9Q1	NKAPL_HUMAN	H	42	ENSP00000345716:R42H	ENSP00000345716:R42H	R	+	2	0	NKAPL	28335253	0.000000	0.05858	0.000000	0.03702	0.076000	0.17211	0.294000	0.19047	0.416000	0.25844	-0.192000	0.12808	CGC	-	NKAPL	-	NULL		0.652	NKAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NKAPL	HGNC	protein_coding	OTTHUMT00000040185.1	0	0		28	28		0.00		G			28227274	+1	31		26		tier1	no_errors	ENST00000343684	ensembl	human	known	74_37	missense	54.39		SNP	0.000	A	31	26
TMEM44	93109	genome.wustl.edu	37	3	194317814	194317815	+	Intron	INS	-	-	GCGTGCACACACCCACATGCACAC	rs71179376|rs201153308	byFrequency	TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr3:194317814_194317815insGCGTGCACACACCCACATGCACAC	ENST00000392432.2	-	10	1523				TMEM44_ENST00000273580.7_Intron|TMEM44_ENST00000473092.1_Intron|TMEM44_ENST00000381975.3_Intron|TMEM44_ENST00000347147.4_Intron	NM_001166305.1	NP_001159777.1	Q2T9K0	TMM44_HUMAN	transmembrane protein 44							integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|urinary_tract(1)	8	all_cancers(143;1.41e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;9.06e-06)		cacatgggcatgcgtgcacaca	0.55													ENSG00000145014		1109	0.221446	0.0378	0.2824	5008	,	,		22761	0.1964		0.4672	False		,,,				2504	0.1994																0																																										SO:0001627	intron_variant	0				AL833026	CCDS3308.1, CCDS33921.1, CCDS3308.2, CCDS54698.1, CCDS54699.1	3q29	2005-08-16			ENSG00000145014	ENSG00000145014			25120	protein-coding gene	gene with protein product							Standard	NM_138399		Approved	DKFZp686O18124	uc010hzn.3	Q2T9K0	OTTHUMG00000156023	ENST00000392432.2:c.1317+7200->GTGTGCATGTGGGTGTGTGCACGC	3.37:g.194317814_194317815insGCGTGCACACACCCACATGCACAC			A1L3V7|B7ZLZ5|B7ZLZ6|C9JJ62|E9PGA9|Q0P6F7|Q6ZT47|Q8IXR1|Q8N4G3	R	INS	-	NULL	ENST00000392432.2	37	NULL	CCDS54699.1	3																																																																																				TMEM44	-	-		0.550	TMEM44-002	KNOWN	basic|CCDS	protein_coding	TMEM44	HGNC	protein_coding	OTTHUMT00000342750.1									-	NM_138399		194317815	-1					tier1	no_errors	ENST00000467284	ensembl	human	putative	74_37	rna			INS	0.000:0.000	GCGTGCACACACCCACATGCACAC		
CYFIP2	26999	genome.wustl.edu	37	5	156810368	156810368	+	Splice_Site	SNP	G	G	A			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr5:156810368G>A	ENST00000521420.1	+	27	3220		c.e27+1		CYFIP2_ENST00000377576.3_Splice_Site|CYFIP2_ENST00000347377.6_Splice_Site|CYFIP2_ENST00000541131.1_Splice_Site|CYFIP2_ENST00000318218.6_Splice_Site|CYFIP2_ENST00000522463.1_Splice_Site|CYFIP2_ENST00000435847.2_Splice_Site|CTB-47B11.3_ENST00000508443.1_RNA|CYFIP2_ENST00000442283.2_Splice_Site|CTB-47B11.3_ENST00000520658.1_RNA					cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GACCCCTCAGGTACCAATCTT	0.547													ENSG00000055163																																					0													23.0	26.0	25.0					5																	156810368		1861	4095	5956	SO:0001630	splice_region_variant	0			-	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"""p53 inducible protein"""	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.3129+1G>A	5.37:g.156810368G>A				Splice_Site	SNP	-	e29+1	ENST00000521420.1	37	c.3282+1		5	.	.	.	.	.	.	.	.	.	.	G	17.13	3.310410	0.60414	.	.	ENSG00000055163	ENST00000318218;ENST00000522463;ENST00000521420;ENST00000347377;ENST00000377576;ENST00000541131;ENST00000435847	.	.	.	4.88	4.88	0.63580	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.0478	0.89338	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CYFIP2	156742946	1.000000	0.71417	0.999000	0.59377	0.582000	0.36321	9.676000	0.98643	2.254000	0.74563	0.563000	0.77884	.	-	CYFIP2	-	-		0.547	CYFIP2-001	NOVEL	basic	protein_coding	CYFIP2	HGNC	protein_coding	OTTHUMT00000373710.1	0	0		36	36		0.00		G	NM_001037332	Intron	156810368	+1	10		29		tier1	no_errors	ENST00000318218	ensembl	human	known	74_37	splice_site	25.64		SNP	1.000	A	10	29
ZFHX4	79776	genome.wustl.edu	37	8	77766738	77766738	+	Silent	SNP	G	G	A	rs373464374		TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr8:77766738G>A	ENST00000521891.2	+	10	8029	c.7581G>A	c.(7579-7581)ccG>ccA	p.P2527P	ZFHX4_ENST00000518282.1_Silent_p.P2501P|ZFHX4_ENST00000455469.2_Silent_p.P2482P|ZFHX4_ENST00000050961.6_Silent_p.P2482P	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2482					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TTCACTCTCCGTTCTTGGAAA	0.507										HNSCC(33;0.089)			ENSG00000091656																																					0													158.0	158.0	158.0					8																	77766738		2024	4197	6221	SO:0001819	synonymous_variant	0			-		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.7581G>A	8.37:g.77766738G>A			G3V138|Q18PS0|Q6ZN20	Silent	SNP	pfam_Homeobox_dom,superfamily_Homeodomain-like,superfamily_Adenylate_cyclase-assoc_CAP_N,smart_Znf_C2H2-like,smart_Znf_U1,smart_Homeobox_dom,pfscan_Homeobox_dom,pfscan_Znf_C2H2	p.P2527	ENST00000521891.2	37	c.7581	CCDS47878.2	8																																																																																			-	ZFHX4	-	NULL		0.507	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ZFHX4	HGNC	protein_coding	OTTHUMT00000379197.2	0	0		17	17		0.00		G	NM_024721		77766738	+1	15		15		tier1	no_errors	ENST00000521891	ensembl	human	known	74_37	silent	50.00		SNP	0.850	A	15	15
MUC4	4585	genome.wustl.edu	37	3	195509535	195509535	+	Silent	SNP	A	A	T			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr3:195509535A>T	ENST00000463781.3	-	2	9375	c.8916T>A	c.(8914-8916)ggT>ggA	p.G2972G	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.G2972G|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGTGGCGTGACCTGTGGATG	0.587													ENSG00000145113																																					0													15.0	9.0	11.0					3																	195509535		664	1539	2203	SO:0001819	synonymous_variant	0			-	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8916T>A	3.37:g.195509535A>T			O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	pfam_Nidogen_extracell_dom,pfam_AMOP,pfam_VWF_type-D,smart_Nidogen_extracell_dom,smart_AMOP,smart_VWF_type-D,smart_EG-like_dom,pfscan_AMOP,pfscan_EG-like_dom	p.G2972	ENST00000463781.3	37	c.8916	CCDS54700.1	3																																																																																			-	MUC4	-	NULL		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	MUC4	HGNC	protein_coding	OTTHUMT00000324081.6	0	0		114	114		0.00		A	NM_018406		195509535	-1	16		80		tier1	no_errors	ENST00000463781	ensembl	human	known	74_37	silent	16.33		SNP	0.001	T	16	80
MUC4	4585	genome.wustl.edu	37	3	195509553	195509553	+	Silent	SNP	A	A	G			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr3:195509553A>G	ENST00000463781.3	-	2	9357	c.8898T>C	c.(8896-8898)acT>acC	p.T2966T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T2966T|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ATGCTGAGGAAGTGTCGGTGA	0.582													ENSG00000145113																																					0													11.0	8.0	9.0					3																	195509553		651	1521	2172	SO:0001819	synonymous_variant	0			-	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8898T>C	3.37:g.195509553A>G			O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	pfam_Nidogen_extracell_dom,pfam_AMOP,pfam_VWF_type-D,smart_Nidogen_extracell_dom,smart_AMOP,smart_VWF_type-D,smart_EG-like_dom,pfscan_AMOP,pfscan_EG-like_dom	p.T2966	ENST00000463781.3	37	c.8898	CCDS54700.1	3																																																																																			-	MUC4	-	NULL		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	MUC4	HGNC	protein_coding	OTTHUMT00000324081.6	1	1		112	112		0.88		A	NM_018406		195509553	-1	12		90		tier1	no_errors	ENST00000463781	ensembl	human	known	74_37	silent	11.76		SNP	0.705	G	12	90
LINC00905	148231	genome.wustl.edu	37	19	16145448	16145448	+	RNA	SNP	G	G	A			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr19:16145448G>A	ENST00000588117.2	+	0	334					NR_024335.1|NR_024336.1				long intergenic non-protein coding RNA 905																		TATTTCCTATGTAATTCTCTA	0.433													ENSG00000167459																																					0																																												0			-	BC031284, BC069223, DB461577		19p13.12	2013-05-21			ENSG00000167459	ENSG00000167459		"""Long non-coding RNAs"""	26334	non-coding RNA	RNA, long non-coding							Standard	NR_110321		Approved	FLJ25328			OTTHUMG00000182270		19.37:g.16145448G>A				R	SNP	-	NULL	ENST00000588117.2	37	NULL		19																																																																																			-	LINC00905	-	-		0.433	LINC00905-001	KNOWN	basic	lincRNA	LINC00905	HGNC	processed_transcript	OTTHUMT00000460313.2	0	0		23	23		0.00		G	NR_024335		16145448	+1	5		32		tier1	no_errors	ENST00000588117	ensembl	human	known	74_37	rna	13.51		SNP	0.080	A	5	32
AXIN2	8313	genome.wustl.edu	37	17	63533137	63533137	+	Missense_Mutation	SNP	G	G	C			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr17:63533137G>C	ENST00000307078.5	-	7	2070	c.1757C>G	c.(1756-1758)aCg>aGg	p.T586R	AXIN2_ENST00000375702.5_Intron	NM_004655.3	NP_004646.3	Q9Y2T1	AXIN2_HUMAN	axin 2	586				Missing (in Ref. 2; AAF22799). {ECO:0000305}.	bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						GCCCGGCTCCGTGCCTTTCCC	0.672									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome				ENSG00000168646																																					0													21.0	22.0	22.0					17																	63533137		2202	4297	6499	SO:0001583	missense	0	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	-	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"""conductin"", ""axil"""	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000307078.5:c.1757C>G	17.37:g.63533137G>C	ENSP00000302625:p.Thr586Arg		Q3MJ88|Q9H3M6|Q9UH84	Missense_Mutation	SNP	pfam_DIX,pfam_RGS_dom,pfam_Axin_b-cat-bd,superfamily_Regulat_G_prot_signal_superfam,smart_Regulat_G_prot_signal_superfam,smart_DIX,pfscan_DIX,pfscan_Regulat_G_prot_signal_superfam,prints_RGS_dom	p.T586R	ENST00000307078.5	37	c.1757	CCDS11662.1	17	.	.	.	.	.	.	.	.	.	.	G	13.42	2.232073	0.39399	.	.	ENSG00000168646	ENST00000307078	T	0.65916	-0.18	4.84	3.84	0.44239	.	1.123640	0.06478	N	0.732279	T	0.51839	0.1698	N	0.19112	0.55	0.32510	N	0.537702	B	0.30281	0.275	B	0.35727	0.209	T	0.52071	-0.8624	10	0.32370	T	0.25	-4.923	9.8547	0.41079	0.1791:0.0:0.8209:0.0	.	586	Q9Y2T1	AXIN2_HUMAN	R	586	ENSP00000302625:T586R	ENSP00000302625:T586R	T	-	2	0	AXIN2	60963599	0.000000	0.05858	0.106000	0.21319	0.997000	0.91878	0.125000	0.15749	0.953000	0.37825	0.462000	0.41574	ACG	-	AXIN2	-	NULL		0.672	AXIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AXIN2	HGNC	protein_coding	OTTHUMT00000445900.1	0	0		8	8		0.00		G	NM_004655		63533137	-1	9		11		tier1	no_errors	ENST00000307078	ensembl	human	known	74_37	missense	45.00		SNP	0.043	C	9	11
MT-CO1	4512	genome.wustl.edu	37	M	6874	6874	+	Missense_Mutation	SNP	T	T	C			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chrM:6874T>C	ENST00000361624.2	+	1	971	c.971T>C	c.(970-972)cTc>cCc	p.L324P	MT-CO3_ENST00000362079.2_5'Flank|MT-TM_ENST00000387377.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TC_ENST00000387405.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-CO2_ENST00000361739.1_5'Flank|MT-ATP8_ENST00000361851.1_5'Flank			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I	324					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						ATTTAGCTGACTCGCCACACT	0.473													ENSG00000198804																																					0																																										SO:0001583	missense	0			-			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395		ENST00000361624.2:c.971T>C	M.37:g.6874T>C	ENSP00000354499:p.Leu324Pro		Q34770	Missense_Mutation	SNP	pfam_Cyt_c_Oxase_su1,superfamily_Cyt_c_Oxase_su1_dom,pfscan_Cyt_c_Oxase_su1_dom,prints_Cyt_c_Oxase_su1	p.L324P	ENST00000361624.2	37	c.971		MT																																																																																			-	MT-CO1	-	pfam_Cyt_c_Oxase_su1,superfamily_Cyt_c_Oxase_su1_dom,pfscan_Cyt_c_Oxase_su1_dom,prints_Cyt_c_Oxase_su1		0.473	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	MT-CO1	HGNC	protein_coding		0	0		44	44		0.00		T	YP_003024028		6874	+1	21		1		tier1	no_errors	ENST00000361624	ensembl	human	known	74_37	missense	95.45		SNP	NULL	C	21	1
FAM27E2	100289124	genome.wustl.edu	37	9	45733681	45733681	+	Missense_Mutation	SNP	T	T	A	rs146523101|rs10909739	byFrequency	TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr9:45733681T>A	ENST00000377529.1	+	1	123	c.94T>A	c.(94-96)Ttg>Atg	p.L32M				Q5SNX5	F27E2_HUMAN	family with sequence similarity 27, member E2	32																	GCGAAAAGGATTGACAACCGG	0.567													ENSG00000204807	-|||	1884	0.376198	0.3139	0.4063	5008	,	,		14775	0.4405		0.4483	False		,,,				2504	0.2986																0																																										SO:0001583	missense	0			-			9p11.2	2013-03-15			ENSG00000204807				32013	other	unknown							Standard	NR_103712		Approved			Q5SNX5	OTTHUMG00000013305	ENST00000377529.1:c.94T>A	9.37:g.45733681T>A	ENSP00000366752:p.Leu32Met		A8E4L5	Missense_Mutation	SNP	NULL	p.L32M	ENST00000377529.1	37	c.94		9	.	.	.	.	.	.	.	.	.	.	T	10.74	1.434008	0.25813	.	.	ENSG00000204807	ENST00000377529	.	.	.	.	.	.	.	.	.	.	.	T	0.48040	0.1478	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.57843	-0.7741	2	0.72032	D	0.01	.	.	.	.	.	.	.	.	M	32	.	ENSP00000366752:L32M	L	+	1	2	FAM27E2	45623677	0.014000	0.17966	0.038000	0.18304	0.038000	0.13279	0.077000	0.14738	0.056000	0.16144	0.055000	0.15244	TTG	rs146523101	FAM27E2	-	NULL		0.567	FAM27E2-001	KNOWN	basic|appris_principal	protein_coding	FAM27E2	HGNC	protein_coding	OTTHUMT00000037095.1	0	0		55	55		0.00		T	XR_078687		45733681	+1	6		10		tier1	no_errors	ENST00000377529	ensembl	human	known	74_37	missense	37.50		SNP	0.038	A	6	10
CPT2	1376	genome.wustl.edu	37	1	53666452	53666452	+	Silent	SNP	T	T	C			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr1:53666452T>C	ENST00000371486.3	+	2	729	c.214T>C	c.(214-216)Ttg>Ctg	p.L72L	CPT2_ENST00000468572.1_3'UTR	NM_000098.2	NP_000089.1	P23786	CPT2_HUMAN	carnitine palmitoyltransferase 2	72					carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	15					L-Carnitine(DB00583)|Perhexiline(DB01074)	GAAGCCTCTCTTGAATGATGG	0.507													ENSG00000157184																																					0													129.0	116.0	121.0					1																	53666452		2203	4300	6503	SO:0001819	synonymous_variant	0			-	BC002445	CCDS575.1	1p32.3	2014-01-09	2009-03-04		ENSG00000157184	ENSG00000157184	2.3.1.21		2330	protein-coding gene	gene with protein product		600650	"""carnitine palmitoyltransferase II"""	CPT1		1339389	Standard	NM_000098		Approved	CPTASE	uc001cvb.4	P23786	OTTHUMG00000008942	ENST00000371486.3:c.214T>C	1.37:g.53666452T>C			B2R6S0|Q5SW68|Q9BQ26	Silent	SNP	pfam_Carn_acyl_trans	p.L72	ENST00000371486.3	37	c.214	CCDS575.1	1																																																																																			-	CPT2	-	pfam_Carn_acyl_trans		0.507	CPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CPT2	HGNC	protein_coding	OTTHUMT00000024757.1	0	0		114	114		0.00		T	NM_000098		53666452	+1	96		47		tier1	no_errors	ENST00000371486	ensembl	human	known	74_37	silent	67.13		SNP	0.983	C	96	47
SHPRH	257218	genome.wustl.edu	37	6	146268768	146268768	+	Missense_Mutation	SNP	T	T	C			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr6:146268768T>C	ENST00000367505.2	-	6	1337	c.1073A>G	c.(1072-1074)gAg>gGg	p.E358G	SHPRH_ENST00000367503.3_Missense_Mutation_p.E358G|SHPRH_ENST00000275233.7_Missense_Mutation_p.E358G|SHPRH_ENST00000438092.2_Missense_Mutation_p.E358G			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	358	Helicase ATP-binding; first part. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		ATTTGGGTACTCACGAATGAT	0.393													ENSG00000146414																																					0													88.0	83.0	84.0					6																	146268768		1870	4111	5981	SO:0001583	missense	0			-	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"""RING-type (C3HC4) zinc fingers"""	19336	protein-coding gene	gene with protein product		608048	"""SNF2 histone linker PHD RING helicase"""			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.1073A>G	6.37:g.146268768T>C	ENSP00000356475:p.Glu358Gly		Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	pfam_SNF2_N,pfam_Histone_H1/H5_H15,superfamily_P-loop_NTPase,superfamily_Znf_FYVE_PHD,superfamily_WW_dom,smart_Helicase_ATP-bd,smart_Histone_H1/H5_H15,smart_Znf_PHD,smart_Znf_RING,smart_Helicase_C,pfscan_Znf_RING,pfscan_Helicase_C	p.E358G	ENST00000367505.2	37	c.1073	CCDS43513.2	6	.	.	.	.	.	.	.	.	.	.	T	19.15	3.772356	0.69992	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233;ENST00000444767	D;D;D;D	0.93189	-3.18;-3.18;-3.18;-3.18	5.59	5.59	0.84812	DEAD-like helicase (1);SNF2-related (1);	0.164549	0.38663	N	0.001603	D	0.93223	0.7841	M	0.64997	1.995	0.58432	D	0.999991	P;P;P;P	0.45569	0.836;0.861;0.649;0.604	B;P;B;B	0.51297	0.319;0.665;0.237;0.22	D	0.94035	0.7304	10	0.66056	D	0.02	-7.0607	15.769	0.78149	0.0:0.0:0.0:1.0	.	247;358;358;247	Q149N8-2;Q149N8;Q149N8-4;F8WEL0	.;SHPRH_HUMAN;.;.	G	358;358;358;358;247	ENSP00000356475:E358G;ENSP00000356473:E358G;ENSP00000412797:E358G;ENSP00000275233:E358G	ENSP00000275233:E358G	E	-	2	0	SHPRH	146310461	1.000000	0.71417	0.988000	0.46212	0.868000	0.49771	8.040000	0.89188	2.118000	0.64928	0.482000	0.46254	GAG	-	SHPRH	-	pfam_SNF2_N,superfamily_P-loop_NTPase,superfamily_WW_dom,smart_Helicase_ATP-bd		0.393	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	SHPRH	HGNC	protein_coding	OTTHUMT00000042571.2	0	0		20	20		0.00		T	NM_173082		146268768	-1	21		22		tier1	no_errors	ENST00000367503	ensembl	human	known	74_37	missense	48.84		SNP	1.000	C	21	22
GGT7	2686	genome.wustl.edu	37	20	33432915	33432916	+	3'UTR	INS	-	-	CACCAC	rs143837915|rs372075951|rs79530197|rs369783775		TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr20:33432915_33432916insCACCAC	ENST00000336431.5	-	0	2248_2249				GGT7_ENST00000469018.1_5'UTR	NM_178026.2	NP_821158.2	Q9UJ14	GGT7_HUMAN	gamma-glutamyltransferase 7						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)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			NS(2)|breast(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)	20						ATGCTGACACTcaccaccacca	0.564													ENSG00000131067																																					0																																										SO:0001624	3_prime_UTR_variant	0				AL049709	CCDS13242.2	20q11.22	2008-11-24	2008-03-10	2008-03-10	ENSG00000131067	ENSG00000131067		"""Gamma-glutamyltransferases"""	4259	protein-coding gene	gene with protein product		612342	"""gamma-glutamyltransferase-like 3"""	GGTL5, GGTL3		8104871, 18357469	Standard	NM_178026		Approved	D20S101, dJ18C9.2	uc002xay.3	Q9UJ14	OTTHUMG00000032314	ENST00000336431.5:c.*216->GTGGTG	20.37:g.33432916_33432921dupCACCAC			Q8N899|Q8NF66|Q9BYP5|Q9BYP6	R	INS	-	NULL	ENST00000336431.5	37	NULL	CCDS13242.2	20																																																																																				GGT7	-	-		0.564	GGT7-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	GGT7	HGNC	protein_coding	OTTHUMT00000078816.2									-	NM_178026		33432916	-1					tier1	no_errors	ENST00000469018	ensembl	human	known	74_37	rna			INS	0.062:0.008	CACCAC		
RN7SKP189	106479180	genome.wustl.edu	37	X	144138832	144138832	+	RNA	SNP	C	C	T	rs113241063		TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chrX:144138832C>T	ENST00000365042.1	+	0	205									RNA, 7SK small nuclear pseudogene 189																		cgagtagctgcgctcccctgc	0.463													ENSG00000201912																																					0																																												0			-			Xq27.3	2013-03-19			ENSG00000201912	ENSG00000201912			45913	pseudogene	RNA, pseudogene							Standard			Approved						X.37:g.144138832C>T				R	SNP	-	NULL	ENST00000365042.1	37	NULL		X																																																																																			-	RN7SKP189	-	-		0.463	RN7SKP189-201	KNOWN	basic	misc_RNA	RN7SKP189	HGNC	misc_RNA		0	0		8	8		0.00		C			144138832	+1	6		3		tier1	no_errors	ENST00000365042	ensembl	human	known	74_37	rna	66.67		SNP	0.001	T	6	3
RAD54L2	23132	genome.wustl.edu	37	3	51667774	51667774	+	Splice_Site	SNP	C	C	T			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr3:51667774C>T	ENST00000409535.2	+	7	1132	c.1007C>T	c.(1006-1008)cCg>cTg	p.P336L	RAD54L2_ENST00000296477.3_Splice_Site_p.P30L	NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2 (S. cerevisiae)	336	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|transcription cofactor activity (GO:0003712)			NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		GCCATTGTGCCGGTAAGAGTT	0.512													ENSG00000164080																																					0													69.0	70.0	70.0					3																	51667774		2203	4300	6503	SO:0001630	splice_region_variant	0			-	AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080			29123	protein-coding gene	gene with protein product						9872452	Standard	NM_015106		Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.1008+1C>T	3.37:g.51667774C>T			Q8TB57|Q9BV54	Missense_Mutation	SNP	pfam_SNF2_N,pfam_Helicase_C,pfam_Helicase/UvrB_dom,superfamily_P-loop_NTPase,smart_Helicase_ATP-bd,smart_Helicase_C,pfscan_Helicase_ATP-bd,pfscan_Helicase_C	p.P336L	ENST00000409535.2	37	c.1007	CCDS33765.2	3	.	.	.	.	.	.	.	.	.	.	C	32	5.121456	0.94385	.	.	ENSG00000164080	ENST00000409535;ENST00000296477	D;D	0.97994	-4.65;-4.65	5.19	5.19	0.71726	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.99375	0.9780	H	0.99182	4.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98256	1.0496	10	0.87932	D	0	-11.4359	17.6911	0.88269	0.0:1.0:0.0:0.0	.	336	Q9Y4B4	ARIP4_HUMAN	L	336;30	ENSP00000386520:P336L;ENSP00000296477:P30L	ENSP00000296477:P30L	P	+	2	0	RAD54L2	51642814	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.814000	0.86154	2.396000	0.81511	0.655000	0.94253	CCG	-	RAD54L2	-	pfam_SNF2_N,pfam_Helicase/UvrB_dom,superfamily_P-loop_NTPase,smart_Helicase_ATP-bd,pfscan_Helicase_ATP-bd		0.512	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RAD54L2	HGNC	protein_coding	OTTHUMT00000328700.2	0	0		48	48		0.00		C	NM_015106	Missense_Mutation	51667774	+1	23		4		tier1	no_errors	ENST00000409535	ensembl	human	known	74_37	missense	85.19		SNP	1.000	T	23	4
INTS4	92105	genome.wustl.edu	37	11	77629981	77629981	+	Missense_Mutation	SNP	A	A	T			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr11:77629981A>T	ENST00000534064.1	-	15	1842	c.1808T>A	c.(1807-1809)aTc>aAc	p.I603N		NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	603					snRNA processing (GO:0016180)	integrator complex (GO:0032039)			INTS4/GAB2(2)	NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			TTGAGGTATGATGCTGGGAGA	0.498													ENSG00000149262																																					0													97.0	96.0	97.0					11																	77629981		2200	4292	6492	SO:0001583	missense	0			-	BC015664	CCDS31644.1	11q14.1	2006-04-26			ENSG00000149262	ENSG00000149262			25048	protein-coding gene	gene with protein product		611348				16239144	Standard	NM_033547		Approved	INT4, MGC16733, MST093	uc001oys.3	Q96HW7	OTTHUMG00000166629	ENST00000534064.1:c.1808T>A	11.37:g.77629981A>T	ENSP00000434466:p.Ile603Asn		Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Missense_Mutation	SNP	pfam_HEAT,superfamily_ARM-type_fold	p.I603N	ENST00000534064.1	37	c.1808	CCDS31644.1	11	.	.	.	.	.	.	.	.	.	.	A	4.779	0.144815	0.09134	.	.	ENSG00000149262	ENST00000534064;ENST00000354849	.	.	.	4.45	4.45	0.53987	.	0.492058	0.21689	N	0.070602	T	0.22898	0.0553	N	0.14661	0.345	0.22880	N	0.998614	B	0.19583	0.037	B	0.18871	0.023	T	0.13926	-1.0491	9	0.16896	T	0.51	-5.3162	8.5872	0.33666	0.9141:0.0:0.0859:0.0	.	603	Q96HW7	INT4_HUMAN	N	603;454	.	ENSP00000346913:I454N	I	-	2	0	INTS4	77307629	0.841000	0.29509	0.089000	0.20774	0.680000	0.39746	3.775000	0.55349	1.879000	0.54435	0.528000	0.53228	ATC	-	INTS4	-	NULL		0.498	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	INTS4	HGNC	protein_coding	OTTHUMT00000390927.1	0	0		106	106		0.00		A	NM_033547		77629981	-1	17		69		tier1	no_errors	ENST00000534064	ensembl	human	known	74_37	missense	19.77		SNP	0.065	T	17	69
CHD2	1106	genome.wustl.edu	37	15	93482893	93482893	+	Missense_Mutation	SNP	G	G	C			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr15:93482893G>C	ENST00000394196.4	+	7	1705	c.637G>C	c.(637-639)Gat>Cat	p.D213H	CHD2_ENST00000536619.1_Missense_Mutation_p.D226H|CHD2_ENST00000420239.2_Missense_Mutation_p.D213H|CHD2_ENST00000557381.1_Missense_Mutation_p.D213H	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	213					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)	p.D213N(2)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			TGAGGATGATGATGATGACGA	0.443													ENSG00000173575																																					2	Substitution - Missense(2)	lung(2)											128.0	120.0	122.0					15																	93482893		2197	4298	6495	SO:0001583	missense	0			-	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.637G>C	15.37:g.93482893G>C	ENSP00000377747:p.Asp213His		C6G482|Q96IP5	Missense_Mutation	SNP	pfam_Chromo_domain,superfamily_Chromodomain-like,smart_Chromo_domain/shadow,pfscan_Chromo_domain/shadow	p.D213H	ENST00000394196.4	37	c.637	CCDS10374.2	15	.	.	.	.	.	.	.	.	.	.	G	16.99	3.274104	0.59649	.	.	ENSG00000173575	ENST00000394196;ENST00000557381;ENST00000420239;ENST00000536619	D;D;T;T	0.90620	-2.7;-2.68;0.72;0.7	5.11	5.11	0.69529	.	0.476005	0.15038	U	0.284034	D	0.89649	0.6776	L	0.46157	1.445	0.80722	D	1	P;B;P;P	0.44578	0.838;0.265;0.693;0.708	B;B;B;B	0.42798	0.364;0.224;0.398;0.351	D	0.90114	0.4194	10	0.56958	D	0.05	-18.3339	18.724	0.91705	0.0:0.0:1.0:0.0	.	226;213;213;213	B7Z3I4;O14647;O14647-2;Q6AI05	.;CHD2_HUMAN;.;.	H	213;213;213;226	ENSP00000377747:D213H;ENSP00000451366:D213H;ENSP00000406581:D213H;ENSP00000443618:D226H	ENSP00000377747:D213H	D	+	1	0	CHD2	91283897	1.000000	0.71417	0.998000	0.56505	0.595000	0.36748	8.738000	0.91569	2.664000	0.90586	0.563000	0.77884	GAT	-	CHD2	-	NULL		0.443	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	CHD2	HGNC	protein_coding	OTTHUMT00000313528.3	0	0		82	82		0.00		G	NM_001271		93482893	+1	76		25		tier1	no_errors	ENST00000420239	ensembl	human	known	74_37	missense	75.25		SNP	1.000	C	76	25
ZNF777	27153	genome.wustl.edu	37	7	149153007	149153007	+	Missense_Mutation	SNP	C	C	A	rs374336310		TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr7:149153007C>A	ENST00000247930.4	-	2	430	c.107G>T	c.(106-108)cGc>cTc	p.R36L		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	36					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(5)|lung(17)|ovary(1)|skin(2)|urinary_tract(1)	26	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			AGGAAGAACGCGGGATTGGAA	0.547													ENSG00000196453	C|||	1	0.000199681	0.0008	0.0	5008	,	,		16142	0.0		0.0	False		,,,				2504	0.0																0													76.0	82.0	80.0					7																	149153007		1881	4104	5985	SO:0001583	missense	0			-	AB033111	CCDS43675.1	7q36.1	2013-01-08			ENSG00000196453	ENSG00000196453		"""Zinc fingers, C2H2-type"", ""-"""	22213	protein-coding gene	gene with protein product							Standard	NM_015694		Approved	KIAA1285	uc003wfv.3	Q9ULD5	OTTHUMG00000158967	ENST00000247930.4:c.107G>T	7.37:g.149153007C>A	ENSP00000247930:p.Arg36Leu		Q8N2R2|Q8N659	Missense_Mutation	SNP	pfam_Znf_C2H2,pfam_Krueppel-associated_box,pfam_DUF3669_Znf,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.R36L	ENST00000247930.4	37	c.107	CCDS43675.1	7	.	.	.	.	.	.	.	.	.	.	C	10.49	1.363686	0.24684	.	.	ENSG00000196453	ENST00000247930	T	0.04862	3.54	4.6	1.52	0.23074	.	0.648597	0.13762	N	0.364535	T	0.03390	0.0098	N	0.14661	0.345	0.09310	N	1	B	0.14438	0.01	B	0.17433	0.018	T	0.40646	-0.9552	10	0.36615	T	0.2	-5.9716	3.3758	0.07237	0.0:0.527:0.2197:0.2533	.	36	Q9ULD5-2	.	L	36	ENSP00000247930:R36L	ENSP00000247930:R36L	R	-	2	0	ZNF777	148783940	0.016000	0.18221	0.265000	0.24526	0.962000	0.63368	0.129000	0.15830	1.025000	0.39708	0.563000	0.77884	CGC	-	ZNF777	-	NULL		0.547	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF777	HGNC	protein_coding	OTTHUMT00000352708.1	0	0		15	15		0.00		C	NM_015694		149153007	-1	7		1		tier1	no_errors	ENST00000247930	ensembl	human	known	74_37	missense	87.50		SNP	0.015	A	7	1
MADCAM1	8174	genome.wustl.edu	37	19	501786	501786	+	Missense_Mutation	SNP	C	C	A	rs77264553	byFrequency	TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr19:501786C>A	ENST00000215637.3	+	4	831	c.785C>A	c.(784-786)cCg>cAg	p.P262Q	AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000346144.4_Intron|MADCAM1_ENST00000587541.1_Missense_Mutation_p.P43Q|MADCAM1_ENST00000382683.4_Intron	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	262	5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.|Mucin-like.				aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		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)		ACCACCTCCCCGGAGCCTCCC	0.726													ENSG00000099866																																					0													21.0	23.0	22.0					19																	501786		2174	4254	6428	SO:0001583	missense	0			-	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.785C>A	19.37:g.501786C>A	ENSP00000215637:p.Pro262Gln		A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	pfam_Adhes-Ig-like,smart_Ig_sub,pfscan_Ig-like_dom	p.P262Q	ENST00000215637.3	37	c.785	CCDS12028.1	19	.	.	.	.	.	.	.	.	.	.	c	9.375	1.071453	0.20147	.	.	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.12147	2.71	3.07	-3.57	0.04612	.	3.584140	0.00988	N	0.003486	T	0.04907	0.0132	N	0.03608	-0.345	0.80722	P	0.0	B	0.33073	0.396	B	0.12837	0.008	T	0.24584	-1.0156	9	0.72032	D	0.01	.	3.8366	0.08897	0.3193:0.4698:0.0:0.2109	.	262	Q13477	MADCA_HUMAN	Q	286;278;270;262	ENSP00000215637:P262Q	ENSP00000215637:P262Q	P	+	2	0	MADCAM1	452786	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.770000	0.04705	-0.633000	0.05545	-0.962000	0.02626	CCG	rs77264553	MADCAM1	-	NULL		0.726	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	MADCAM1	HGNC	protein_coding	OTTHUMT00000451884.1	0	0		16	16		0.00		C	NM_130760		501786	+1	5		19		tier1	no_errors	ENST00000215637	ensembl	human	known	74_37	missense	20.83		SNP	0.000	A	5	19
LAMA5	3911	genome.wustl.edu	37	20	60888027	60888027	+	Missense_Mutation	SNP	C	C	T			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr20:60888027C>T	ENST00000252999.3	-	66	9061	c.8995G>A	c.(8995-8997)Gtg>Atg	p.V2999M		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2999	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TACAACAGCACGAGGCTGCCT	0.647													ENSG00000130702																																					0													48.0	48.0	48.0					20																	60888027		2202	4297	6499	SO:0001583	missense	0			-	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.8995G>A	20.37:g.60888027C>T	ENSP00000252999:p.Val2999Met		Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	pfam_EGF_laminin,pfam_Laminin_I,pfam_Laminin_G,pfam_Laminin_N,pfam_Laminin_II,pfam_Laminin_B_type_IV,superfamily_ConA-like_lec_gl_sf,superfamily_Galactose-bd-like,smart_Laminin_N,smart_EGF_laminin,smart_EG-like_dom,smart_Laminin_B_subgr,smart_Laminin_G,pfscan_Laminin_B_type_IV,pfscan_EGF_laminin,pfscan_Laminin_G,pfscan_Laminin_N,pfscan_TNFR/NGFR_Cys_rich_reg	p.V2999M	ENST00000252999.3	37	c.8995	CCDS33502.1	20	.	.	.	.	.	.	.	.	.	.	c	9.117	1.008115	0.19199	.	.	ENSG00000130702	ENST00000252999	T	0.79653	-1.29	4.64	-1.37	0.09056	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.516972	0.20516	U	0.090786	T	0.71307	0.3324	L	0.58101	1.795	0.09310	N	1	P	0.50156	0.932	B	0.42188	0.379	T	0.64449	-0.6405	10	0.24483	T	0.36	.	8.0733	0.30701	0.0:0.5134:0.3431:0.1436	.	2999	O15230	LAMA5_HUMAN	M	2999	ENSP00000252999:V2999M	ENSP00000252999:V2999M	V	-	1	0	LAMA5	60321422	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	0.619000	0.24388	-0.214000	0.10078	0.479000	0.44913	GTG	-	LAMA5	-	pfam_Laminin_G,superfamily_ConA-like_lec_gl_sf,smart_Laminin_G,pfscan_Laminin_G		0.647	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LAMA5	HGNC	protein_coding	OTTHUMT00000080014.2	0	0		47	47		0.00		C	NM_005560		60888027	-1	31		35		tier1	no_errors	ENST00000252999	ensembl	human	known	74_37	missense	46.97		SNP	0.000	T	31	35
C5orf55	116349	genome.wustl.edu	37	5	443336	443374	+	5'Flank	DEL	GGCGGCGGGGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	GGCGGCGGGGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	-	rs11134039|rs368689128|rs534941835|rs374353264|rs182219748|rs11134040|rs373080314|rs11274307	byFrequency	TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	GGCGGCGGGGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	GGCGGCGGGGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr5:443336_443374delGGCGGCGGGGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	ENST00000408966.2	-	0	0				EXOC3_ENST00000510441.1_3'UTR|EXOC3_ENST00000315013.5_5'Flank|EXOC3_ENST00000512944.1_5'UTR	NM_138464.2	NP_612473.1	Q8N2X6	CE055_HUMAN	chromosome 5 open reading frame 55							extracellular region (GO:0005576)				large_intestine(1)|lung(2)	3						aggcggagggggcggcgggggcggcggcggcggcggcggcggcggcggcggcggcggcg	0.787													ENSG00000180104																																					0																																										SO:0001631	upstream_gene_variant	0				BC014011	CCDS43298.1	5p15.33	2012-02-24			ENSG00000221990	ENSG00000221990			25175	protein-coding gene	gene with protein product						12477932	Standard	NM_138464		Approved		uc010ita.3	Q8N2X6	OTTHUMG00000162235		5.37:g.443336_443374delGGCGGCGGGGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	Exception_encountered		Q96CR9	R	DEL	-	NULL	ENST00000408966.2	37	NULL	CCDS43298.1	5																																																																																				EXOC3	-	-		0.787	C5orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EXOC3	HGNC	protein_coding	OTTHUMT00000368033.1									GGCGGCGGGGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	NM_138464		443374	+1					tier1	no_errors	ENST00000510441	ensembl	human	putative	74_37	rna			DEL	0.044:0.469:0.513:0.560:0.594:0.546:0.469:0.344:0.297:0.251:0.205:0.159:0.113:0.068:0.023:0.018:0.018:0.007:0.000:0.000:0.000:0.083:0.171:0.290:0.294:0.302:0.252:0.182:0.138:0.004:0.005:0.010:0.011:0.023:0.025:0.016:0.013:0.006:0.002	-		
ECT2	1894	genome.wustl.edu	37	3	172474880	172474880	+	Silent	SNP	C	C	T			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr3:172474880C>T	ENST00000392692.3	+	5	587	c.411C>T	c.(409-411)gtC>gtT	p.V137V	ECT2_ENST00000540509.1_Silent_p.V137V|ECT2_ENST00000441497.2_Silent_p.V106V|ECT2_ENST00000232458.5_Silent_p.V106V|ECT2_ENST00000427830.1_Silent_p.V106V|ECT2_ENST00000417960.1_Silent_p.V105V	NM_001258315.1	NP_001245244.1	Q9H8V3	ECT2_HUMAN	epithelial cell transforming 2	137					activation of protein kinase activity (GO:0032147)|activation of Rac GTPase activity (GO:0032863)|activation of Rho GTPase activity (GO:0032862)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular response to calcium ion (GO:0071277)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|cytokinesis (GO:0000910)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of cytokinesis (GO:0032467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of Rho GTPase activity (GO:0032321)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|centralspindlin complex (GO:0097149)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)			AGGATTCTGTCTTTAATGACC	0.363													ENSG00000114346																																					0													114.0	118.0	117.0					3																	172474880		2203	4300	6503	SO:0001819	synonymous_variant	0			-	AA206473	CCDS3220.1, CCDS58860.1	3q26.1-q26.2	2014-03-11	2014-03-11		ENSG00000114346	ENSG00000114346		"""Rho guanine nucleotide exchange factors"""	3155	protein-coding gene	gene with protein product		600586	"""epithelial cell transforming sequence 2 oncogene"""			8464478, 10579713	Standard	NM_018098		Approved	ARHGEF31	uc003fil.2	Q9H8V3	OTTHUMG00000156762	ENST00000392692.3:c.411C>T	3.37:g.172474880C>T			Q0MT80|Q2M269|Q6U836|Q9NSV8|Q9NVW9	Silent	SNP	pfam_DH-domain,pfam_BRCT_dom,superfamily_DH-domain,superfamily_BRCT_dom,smart_BRCT_dom,smart_DH-domain,pfscan_BRCT_dom,pfscan_DH-domain	p.V106	ENST00000392692.3	37	c.318	CCDS58860.1	3																																																																																			-	ECT2	-	NULL		0.363	ECT2-003	NOVEL	basic|CCDS	protein_coding	ECT2	HGNC	protein_coding	OTTHUMT00000345994.2	0	0		53	53		0.00		C	NM_018098		172474880	+1	31		89		tier1	no_errors	ENST00000427830	ensembl	human	known	74_37	silent	25.83		SNP	0.997	T	31	89
CUL7	9820	genome.wustl.edu	37	6	43006382	43006385	+	Frame_Shift_Del	DEL	TGTC	TGTC	-			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	TGTC	TGTC					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr6:43006382_43006385delTGTC	ENST00000265348.3	-	24	4571_4574	c.4486_4489delGACA	c.(4486-4491)gacatgfs	p.DM1496fs	CUL7_ENST00000535468.1_Frame_Shift_Del_p.DM1580fs|RN7SL403P_ENST00000481783.2_RNA			Q14999	CUL7_HUMAN	cullin 7	1496					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)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			TGATTGAGCATGTCTGCGGAGAGC	0.578													ENSG00000044090																																					0																																										SO:0001589	frameshift_variant	0				BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"""KIAA0076"""	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.4486_4489delGACA	6.37:g.43006382_43006385delTGTC	ENSP00000265348:p.Asp1496fs		B4DYZ0|F5H0L1|Q5T654	Frame_Shift_Del	DEL	pfam_Cullin_N,pfam_CPH_domain,pfam_APC_su10/DOC_dom,superfamily_Galactose-bd-like,superfamily_Cullin_homology,superfamily_ARM-type_fold,smart_Cullin_neddylation_domain,pfscan_Cullin_homology	p.D1580fs	ENST00000265348.3	37	c.4741_4738	CCDS4881.1	6																																																																																				CUL7	-	pfam_Cullin_N,superfamily_Cullin_homology,pfscan_Cullin_homology		0.578	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CUL7	HGNC	protein_coding	OTTHUMT00000040575.1	0	0		10	10		0.00		TGTC	NM_014780		43006385	-1	9		14		tier1	no_errors	ENST00000535468	ensembl	human	known	74_37	frame_shift_del	39.13		DEL	0.000:0.000:0.119:0.159	-	9	14
ANKRD12	23253	genome.wustl.edu	37	18	9255635	9255635	+	Missense_Mutation	SNP	G	G	T			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr18:9255635G>T	ENST00000262126.4	+	9	2610	c.2370G>T	c.(2368-2370)atG>atT	p.M790I	ANKRD12_ENST00000383440.2_Missense_Mutation_p.M767I|ANKRD12_ENST00000400020.3_Missense_Mutation_p.M767I	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	790						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						CTTTGGGTATGAGTGCCATTG	0.328													ENSG00000101745																																					0													77.0	82.0	80.0					18																	9255635		2199	4297	6496	SO:0001583	missense	0			-	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"""Ankyrin repeat domain containing"""	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.2370G>T	18.37:g.9255635G>T	ENSP00000262126:p.Met790Ile		O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,prints_Ankyrin_rpt	p.M790I	ENST00000262126.4	37	c.2370	CCDS11843.1	18	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.202729	0.00296	.	.	ENSG00000101745	ENST00000383440;ENST00000262126;ENST00000400020	T;T	0.62105	0.05;0.05	5.22	-3.01	0.05463	.	1.695100	0.02653	N	0.106664	T	0.25158	0.0611	N	0.00707	-1.245	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.08743	-1.0707	10	0.35671	T	0.21	-24.9841	0.3235	0.00307	0.358:0.2277:0.2033:0.2111	.	417;767;790	Q9NXU3;Q6UB98-2;Q6UB98	.;.;ANR12_HUMAN	I	767;790;61	ENSP00000372932:M767I;ENSP00000262126:M790I	ENSP00000262126:M790I	M	+	3	0	ANKRD12	9245635	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	0.044000	0.13992	-0.460000	0.07003	-0.384000	0.06662	ATG	-	ANKRD12	-	NULL		0.328	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ANKRD12	HGNC	protein_coding	OTTHUMT00000254478.2	0	0		13	13		0.00		G	NM_015208		9255635	+1	12		7		tier1	no_errors	ENST00000262126	ensembl	human	known	74_37	missense	63.16		SNP	0.000	T	12	7
DCLK1	9201	genome.wustl.edu	37	13	36445375	36445375	+	Missense_Mutation	SNP	G	G	T			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr13:36445375G>T	ENST00000360631.3	-	5	1137	c.926C>A	c.(925-927)gCc>gAc	p.A309D	DCLK1_ENST00000255448.4_Missense_Mutation_p.A309D|DCLK1_ENST00000379892.4_Missense_Mutation_p.A309D			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	309	Pro/Ser-rich.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		GCTGGTGGAGGCAGGGGACTT	0.532													ENSG00000133083																																					0													180.0	170.0	173.0					13																	36445375		2203	4300	6503	SO:0001583	missense	0			-	AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"""doublecortin and CaM kinase-like 1"""	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.926C>A	13.37:g.36445375G>T	ENSP00000353846:p.Ala309Asp		B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Missense_Mutation	SNP	pfam_Prot_kinase_dom,pfam_Doublecortin_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Doublecortin_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Doublecortin_dom,pfscan_Prot_kinase_dom	p.A309D	ENST00000360631.3	37	c.926		13	.	.	.	.	.	.	.	.	.	.	G	15.96	2.987624	0.53934	.	.	ENSG00000133083	ENST00000255448;ENST00000360631;ENST00000539451;ENST00000379892	T;T;T	0.68903	-0.36;-0.35;1.77	5.43	5.43	0.79202	.	0.127130	0.52532	D	0.000079	T	0.64659	0.2618	L	0.57536	1.79	0.48901	D	0.999725	B	0.17038	0.02	B	0.17979	0.02	T	0.59637	-0.7417	10	0.17832	T	0.49	.	19.5966	0.95541	0.0:0.0:1.0:0.0	.	309	O15075-2	.	D	309	ENSP00000255448:A309D;ENSP00000353846:A309D;ENSP00000369222:A309D	ENSP00000255448:A309D	A	-	2	0	DCLK1	35343375	1.000000	0.71417	0.910000	0.35882	0.992000	0.81027	6.879000	0.75572	2.698000	0.92095	0.655000	0.94253	GCC	-	DCLK1	-	NULL		0.532	DCLK1-010	KNOWN	basic	protein_coding	DCLK1	HGNC	protein_coding	OTTHUMT00000044487.1	0	0		54	54		0.00		G	NM_004734		36445375	-1	16		32		tier1	no_errors	ENST00000360631	ensembl	human	known	74_37	missense	33.33		SNP	0.998	T	16	32
ACTRT1	139741	genome.wustl.edu	37	X	127185556	127185556	+	Silent	SNP	G	G	A			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chrX:127185556G>A	ENST00000371124.3	-	1	826	c.630C>T	c.(628-630)gcC>gcT	p.A210A		NM_138289.3	NP_612146.1	Q8TDG2	ACTT1_HUMAN	actin-related protein T1	210						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.A210A(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|skin(3)	34						TATTTACCACGGCCTTGTTGA	0.532													ENSG00000123165																																					1	Substitution - coding silent(1)	lung(1)											120.0	115.0	117.0					X																	127185556		2203	4300	6503	SO:0001819	synonymous_variant	0			-	AF440739	CCDS14611.1	Xq25	2008-02-05	2005-11-22		ENSG00000123165	ENSG00000123165			24027	protein-coding gene	gene with protein product		300487				12243744	Standard	NM_138289		Approved	AIP1, KIAA0705, ARIP1, Arp-T1	uc004eum.3	Q8TDG2	OTTHUMG00000022359	ENST00000371124.3:c.630C>T	X.37:g.127185556G>A			Q6X7C1|Q96L10	Silent	SNP	pfam_Actin-related,smart_Actin-related,prints_Actin-related	p.A210	ENST00000371124.3	37	c.630	CCDS14611.1	X																																																																																			-	ACTRT1	-	pfam_Actin-related,smart_Actin-related		0.532	ACTRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ACTRT1	HGNC	protein_coding	OTTHUMT00000058192.1	0	0		71	71		0.00		G	NM_138289		127185556	-1	51		20		tier1	no_errors	ENST00000371124	ensembl	human	known	74_37	silent	71.83		SNP	0.000	A	51	20
PRTG	283659	genome.wustl.edu	37	15	55976085	55976085	+	Missense_Mutation	SNP	C	C	T			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr15:55976085C>T	ENST00000389286.4	-	3	489	c.442G>A	c.(442-444)Gaa>Aaa	p.E148K	RP11-420M1.2_ENST00000561155.1_RNA	NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		ACTCCACCTTCGTGGACCTCA	0.413													ENSG00000166450																																					0													90.0	88.0	89.0					15																	55976085		1872	4105	5977	SO:0001583	missense	0			-	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26373	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 5"""	613261	"""protogenin homolog (Gallus gallus)"""				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.442G>A	15.37:g.55976085C>T	ENSP00000373937:p.Glu148Lys			Missense_Mutation	SNP	pfam_Fibronectin_type3,pfam_Ig_I-set,pfam_Immunoglobulin,superfamily_Fibronectin_type3,smart_Ig_sub,smart_Ig_sub2,smart_Fibronectin_type3,pfscan_Fibronectin_type3,pfscan_Ig-like_dom	p.E148K	ENST00000389286.4	37	c.442	CCDS42040.1	15	.	.	.	.	.	.	.	.	.	.	C	22.4	4.290786	0.80914	.	.	ENSG00000166450	ENST00000389286	T	0.79845	-1.31	5.66	5.66	0.87406	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);	0.068857	0.56097	U	0.000031	T	0.79305	0.4423	M	0.74647	2.275	0.80722	D	1	D	0.55172	0.97	B	0.42959	0.403	T	0.77797	-0.2453	10	0.07813	T	0.8	-12.0999	16.8992	0.86109	0.0:1.0:0.0:0.0	.	148	Q2VWP7	PRTG_HUMAN	K	148	ENSP00000373937:E148K	ENSP00000373937:E148K	E	-	1	0	PRTG	53763377	1.000000	0.71417	0.958000	0.39756	0.939000	0.58152	4.613000	0.61176	2.649000	0.89929	0.557000	0.71058	GAA	-	PRTG	-	pfam_Ig_I-set,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like_dom		0.413	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PRTG	HGNC	protein_coding	OTTHUMT00000419357.1	0	0		29	29		0.00		C	NM_173814		55976085	-1	3		23		tier1	no_errors	ENST00000389286	ensembl	human	known	74_37	missense	11.54		SNP	0.996	T	3	23
BAI3	577	genome.wustl.edu	37	6	69348841	69348841	+	Missense_Mutation	SNP	C	C	G			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr6:69348841C>G	ENST00000370598.1	+	3	1095	c.274C>G	c.(274-276)Cat>Gat	p.H92D		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	92	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				TCAGTTTGATCATTTTTCCCA	0.333													ENSG00000135298																																					0													53.0	59.0	57.0					6																	69348841		2201	4300	6501	SO:0001583	missense	0			-	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"""-"", ""GPCR / Class B : Orphans"""	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.274C>G	6.37:g.69348841C>G	ENSP00000359630:p.His92Asp		B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	pfam_GPCR_2_secretin-like,pfam_DUF3497,pfam_Thrombospondin_1_rpt,pfam_GPS_dom,superfamily_Thrombospondin_1_rpt,smart_Thrombospondin_1_rpt,smart_GPCR_2_extracellular_dom,smart_GPS_dom,pfscan_CUB_dom,pfscan_GPS_dom,pfscan_Thrombospondin_1_rpt,pfscan_GPCR_2_extracellular_dom,pfscan_GPCR_2-like,prints_GPCR_2_brain-spec_angio_inhib,prints_GPCR_2_secretin-like	p.H92D	ENST00000370598.1	37	c.274	CCDS4968.1	6	.	.	.	.	.	.	.	.	.	.	C	11.40	1.628782	0.28978	.	.	ENSG00000135298	ENST00000370598	T	0.49432	0.78	5.32	5.32	0.75619	CUB (1);	0.000000	0.85682	D	0.000000	T	0.55273	0.1910	L	0.50333	1.59	0.80722	D	1	P	0.50156	0.932	P	0.61397	0.888	T	0.51942	-0.8641	10	0.46703	T	0.11	.	19.3677	0.94471	0.0:1.0:0.0:0.0	.	92	O60242	BAI3_HUMAN	D	92	ENSP00000359630:H92D	ENSP00000359630:H92D	H	+	1	0	BAI3	69405562	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.442000	0.80503	2.634000	0.89283	0.655000	0.94253	CAT	-	BAI3	-	pfscan_CUB_dom		0.333	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BAI3	HGNC	protein_coding	OTTHUMT00000041120.1	0	0		38	38		0.00		C			69348841	+1	7		28		tier1	no_errors	ENST00000370598	ensembl	human	known	74_37	missense	20.00		SNP	1.000	G	7	28
MAP3K9	4293	genome.wustl.edu	37	14	71199867	71199867	+	Missense_Mutation	SNP	T	T	C			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr14:71199867T>C	ENST00000554752.2	-	11	2218	c.2219A>G	c.(2218-2220)aAg>aGg	p.K740R	MAP3K9_ENST00000553414.1_Missense_Mutation_p.K473R|MAP3K9_ENST00000381250.4_Missense_Mutation_p.K717R|MAP3K9_ENST00000555993.2_Missense_Mutation_p.K754R|MAP3K9_ENST00000554146.1_Missense_Mutation_p.K468R	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	740					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		ACCGCCCCGCTTGAGGCTGTT	0.657													ENSG00000006432																									GBM(114;411 1587 13539 28235 50070)												0													40.0	45.0	43.0					14																	71199867		2203	4300	6503	SO:0001583	missense	0			-	AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.2219A>G	14.37:g.71199867T>C	ENSP00000451612:p.Lys740Arg		A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Missense_Mutation	SNP	pirsf_MAPKKK9/10/11,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_dom,pfam_SH3_2,pfam_SH3_domain,superfamily_Kinase-like_dom,superfamily_SH3_domain,superfamily_Regulat_G_prot_signal_superfam,smart_SH3_domain,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,prints_SH3_domain,pfscan_SH3_domain,pfscan_Prot_kinase_dom	p.K754R	ENST00000554752.2	37	c.2261		14	.	.	.	.	.	.	.	.	.	.	T	11.80	1.747409	0.30955	.	.	ENSG00000006432	ENST00000554752;ENST00000005198;ENST00000553414;ENST00000381250;ENST00000554146;ENST00000542284	T;T;T;T	0.35421	1.31;1.31;1.31;1.31	4.77	4.77	0.60923	.	0.137931	0.56097	D	0.000028	T	0.25754	0.0627	L	0.28115	0.83	0.30206	N	0.798196	P;B;B;B	0.39071	0.658;0.003;0.084;0.313	B;B;B;B	0.38954	0.286;0.017;0.103;0.174	T	0.09037	-1.0693	10	0.10902	T	0.67	.	14.4699	0.67509	0.0:0.0:0.0:1.0	.	468;740;754;473	G3V4P9;P80192;P80192-4;G3V347	.;M3K9_HUMAN;.;.	R	740;754;473;717;468;456	ENSP00000451612:K740R;ENSP00000451038:K473R;ENSP00000370649:K717R;ENSP00000451921:K468R	ENSP00000005198:K754R	K	-	2	0	MAP3K9	70269620	1.000000	0.71417	1.000000	0.80357	0.753000	0.42808	3.927000	0.56499	2.007000	0.58848	0.459000	0.35465	AAG	-	MAP3K9	-	pirsf_MAPKKK9/10/11		0.657	MAP3K9-001	KNOWN	basic	protein_coding	MAP3K9	HGNC	protein_coding	OTTHUMT00000412550.2	0	0		20	20		0.00		T			71199867	-1	16		28		tier1	no_errors	ENST00000555993	ensembl	human	known	74_37	missense	36.36		SNP	1.000	C	16	28
LINC00955	285492	genome.wustl.edu	37	4	3589656	3589669	+	Frame_Shift_Del	DEL	ACTCCCAGATGCAG	ACTCCCAGATGCAG	-	rs537957602|rs376169500|rs370505811|rs201651178	byFrequency	TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	ACTCCCAGATGCAG	ACTCCCAGATGCAG					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr4:3589656_3589669delACTCCCAGATGCAG	ENST00000514422.1	+	2	310_323	c.24_37delACTCCCAGATGCAG	c.(22-39)gcactcccagatgcagacfs	p.LPDAD9fs						long intergenic non-protein coding RNA 955																		GTGCACCTGCACTCCCAGATGCAGACTTCCTGGT	0.547													ENSG00000216560																																					0																																										SO:0001589	frameshift_variant	0				AK092743		4p16.3	2014-04-09			ENSG00000216560	ENSG00000216560			26644	other	unknown							Standard	NR_040045		Approved	FLJ35424			OTTHUMG00000159817	ENST00000514422.1:c.24_37delACTCCCAGATGCAG	4.37:g.3589656_3589669delACTCCCAGATGCAG	ENSP00000427553:p.Leu9fs			Frame_Shift_Del	DEL	NULL	p.D11fs	ENST00000514422.1	37	c.24_37		4																																																																																				LINC00955	-	NULL		0.547	LINC00955-001	NOVEL	basic|appris_principal	protein_coding	LINC00955	HGNC	protein_coding	OTTHUMT00000357538.6									ACTCCCAGATGCAG			3589669	+1					tier1	no_errors	ENST00000514422	ensembl	human	novel	74_37	frame_shift_del			DEL	0.086:0.080:0.080:0.088:0.143:0.156:0.154:0.145:0.135:0.135:0.134:0.130:0.136:0.162	-		
RGL1	23179	genome.wustl.edu	37	1	183881229	183881229	+	Missense_Mutation	SNP	T	T	C			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr1:183881229T>C	ENST00000360851.3	+	15	1754	c.1576T>C	c.(1576-1578)Tct>Cct	p.S526P	RGL1_ENST00000539189.1_Missense_Mutation_p.S497P|RGL1_ENST00000304685.4_Missense_Mutation_p.S561P|RGL1_ENST00000536277.1_Missense_Mutation_p.S524P			Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation stimulator-like 1	526					cellular lipid metabolic process (GO:0044255)|positive regulation of Ral GTPase activity (GO:0032852)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(5)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(17)|ovary(4)|prostate(3)|stomach(1)	51						GTTTCTAGGGTCTGACATGAT	0.478													ENSG00000143344																																					0													74.0	70.0	71.0					1																	183881229		2203	4300	6503	SO:0001583	missense	0			-	AF186780	CCDS1359.1, CCDS72992.1	1q25.2	2008-02-05			ENSG00000143344	ENSG00000143344			30281	protein-coding gene	gene with protein product		605667				10760592, 10231032	Standard	XM_005245010		Approved	RGL	uc001gqm.3	Q9NZL6	OTTHUMG00000035328	ENST00000360851.3:c.1576T>C	1.37:g.183881229T>C	ENSP00000354097:p.Ser526Pro		Q5SXQ2|Q5SXQ6|Q9HBY3|Q9HBY4|Q9NZL5|Q9UG43|Q9Y2G6	Missense_Mutation	SNP	pfam_RasGRF_CDC25,pfam_Ras-like_Gua-exchang_fac_N,pfam_Ras-assoc,superfamily_Ras_GEF_dom,smart_Ras-like_Gua-exchang_fac_N,smart_RasGRF_CDC25,smart_Ras-assoc,pfscan_Ras-assoc,pfscan_RasGRF_CDC25,pfscan_Ras-like_Gua-exchang_fac_N	p.S561P	ENST00000360851.3	37	c.1681		1	.	.	.	.	.	.	.	.	.	.	T	10.98	1.503342	0.26949	.	.	ENSG00000143344	ENST00000304685;ENST00000367531;ENST00000536277;ENST00000543395;ENST00000360851;ENST00000539189	T;T;T;T;T	0.53857	0.61;0.61;0.62;0.6;0.62	5.32	1.52	0.23074	Ras guanine nucleotide exchange factor, domain (1);	0.651138	0.15608	N	0.253526	T	0.38214	0.1032	L	0.43152	1.355	0.39600	D	0.969728	B;B;B;B;B	0.09022	0.002;0.001;0.001;0.001;0.001	B;B;B;B;B	0.08055	0.003;0.001;0.002;0.001;0.001	T	0.16188	-1.0411	10	0.41790	T	0.15	.	3.5612	0.07882	0.1339:0.0738:0.1399:0.6524	.	497;524;331;526;561	F5H6U6;B7Z2W5;F5H3C3;Q9NZL6;Q5SXQ6	.;.;.;RGL1_HUMAN;.	P	561;561;524;331;526;497	ENSP00000303192:S561P;ENSP00000356501:S561P;ENSP00000438662:S524P;ENSP00000354097:S526P;ENSP00000437355:S497P	ENSP00000303192:S561P	S	+	1	0	RGL1	182147852	0.017000	0.18338	0.749000	0.31150	0.572000	0.35998	0.084000	0.14891	0.001000	0.14605	0.402000	0.26972	TCT	-	RGL1	-	superfamily_Ras_GEF_dom		0.478	RGL1-002	KNOWN	basic|appris_candidate	protein_coding	RGL1	HGNC	protein_coding	OTTHUMT00000085742.1	0	0		46	46		0.00		T	NM_015149		183881229	+1	8		55		tier1	no_errors	ENST00000304685	ensembl	human	known	74_37	missense	12.70		SNP	0.853	C	8	55
ZSCAN30	100101467	genome.wustl.edu	37	18	32862463	32862467	+	Intron	DEL	TTTAT	TTTAT	-	rs147465480	byFrequency	TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	TTTAT	TTTAT					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr18:32862463_32862467delTTTAT	ENST00000420878.3	-	1	149				ZSCAN30_ENST00000333206.5_Intron|ZSCAN30_ENST00000592278.1_Intron|ZSCAN30_ENST00000589178.1_Intron|ZSCAN30_ENST00000383091.2_Intron|RP11-158H5.7_ENST00000586922.2_lincRNA	NM_001166012.1	NP_001159484.1	Q86W11	ZSC30_HUMAN	zinc finger and SCAN domain containing 30						transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(5)|lung(3)|urinary_tract(1)	9						cctagaattatttattttatgttta	0.366													ENSG00000268573		1258	0.251198	0.1384	0.3862	5008	,	,		22152	0.1498		0.3897	False		,,,				2504	0.2699																0																																										SO:0001627	intron_variant	0				AY234408	CCDS42427.1, CCDS74207.1	18q12.2	2013-01-08	2010-07-23	2010-07-23	ENSG00000186814	ENSG00000186814		"""-"", ""Zinc fingers, C2H2-type"""	33517	protein-coding gene	gene with protein product			"""zinc finger protein 397 opposite strand"", ""ZNF397 opposite strand"""	ZNF397OS		12801647	Standard	NM_001166012		Approved	ZNF917	uc002kym.3	Q86W11		ENST00000420878.3:c.306+7580ATAAA>-	18.37:g.32862468_32862472delTTTAT			B4E0N0|Q6ZNB3|Q96PN3	R	DEL	-	NULL	ENST00000420878.3	37	NULL	CCDS42427.1	18																																																																																				RP11-158H5.7	-	-		0.366	ZSCAN30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	ENSG00000268573	Clone_based_vega_gene	protein_coding	OTTHUMT00000442510.1									TTTAT	NM_001112734		32862467	-1					tier1	no_errors	ENST00000586922	ensembl	human	known	74_37	rna			DEL	0.018:0.019:0.019:0.018:0.020	-		
LSS	4047	genome.wustl.edu	37	21	47635208	47635208	+	Silent	SNP	G	G	A			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr21:47635208G>A	ENST00000397728.3	-	9	975	c.897C>T	c.(895-897)ctC>ctT	p.L299L	LSS_ENST00000356396.4_Silent_p.L299L|LSS_ENST00000464357.1_5'Flank|LSS_ENST00000522411.1_Silent_p.L288L|LSS_ENST00000457828.2_Silent_p.L219L	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	299					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					ACAGGTTGAGGAGCGCTACAG	0.612													ENSG00000160285																									Pancreas(114;955 2313 34923 50507)												0													68.0	55.0	59.0					21																	47635208		2202	4299	6501	SO:0001819	synonymous_variant	0			-	U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.897C>T	21.37:g.47635208G>A			B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Silent	SNP	pfam_Prenyltrans,superfamily_Terpenoid_cyclase/PrenylTrfase,tigrfam_Squalene_cyclase	p.L299	ENST00000397728.3	37	c.897	CCDS13733.1	21																																																																																			-	LSS	-	superfamily_Terpenoid_cyclase/PrenylTrfase,tigrfam_Squalene_cyclase		0.612	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LSS	HGNC	protein_coding	OTTHUMT00000207274.2	0	0		57	57		0.00		G			47635208	-1	22		14		tier1	no_errors	ENST00000356396	ensembl	human	known	74_37	silent	61.11		SNP	0.370	A	22	14
GCNT2	2651	genome.wustl.edu	37	6	10629469	10629469	+	3'UTR	SNP	A	A	T			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr6:10629469A>T	ENST00000379597.3	+	0	4394				GCNT2_ENST00000316170.3_3'UTR|GCNT2_ENST00000265012.4_3'UTR|GCNT2_ENST00000397423.2_3'UTR			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)						maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		TTAATGTTGGAAGAGCATAGT	0.393													ENSG00000111846																																					0																																										SO:0001624	3_prime_UTR_variant	0			-	L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"""Blood group antigens"", ""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4204	protein-coding gene	gene with protein product	"""Ii blood group"", ""unassigned linkage group 3"""	600429	"""glucosaminyl (N-acetyl) transferase 5"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)"", ""cataract, congenital"""	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.*2629A>T	6.37:g.10629469A>T				R	SNP	-	NULL	ENST00000379597.3	37	NULL	CCDS34338.1	6																																																																																			-	GCNT2	-	-		0.393	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GCNT2	HGNC	protein_coding	OTTHUMT00000327912.3	0	0		47	47		0.00		A	NM_145649		10629469	+1	18		66		tier1	no_errors	ENST00000397423	ensembl	human	known	74_37	rna	21.18		SNP	0.001	T	18	66
LTBP1	4052	genome.wustl.edu	37	2	33589422	33589422	+	Splice_Site	SNP	C	C	T			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr2:33589422C>T	ENST00000404816.2	+	30	4892	c.4539C>T	c.(4537-4539)aaC>aaT	p.N1513N	LTBP1_ENST00000402934.1_Splice_Site_p.N1132N|LTBP1_ENST00000407925.1_Splice_Site_p.N1187N|LTBP1_ENST00000404525.1_Splice_Site_p.N1134N|LTBP1_ENST00000354476.3_Splice_Site_p.N1514N|LTBP1_ENST00000418533.2_Splice_Site_p.N1145N|LTBP1_ENST00000272273.5_Splice_Site_p.N411N|LTBP1_ENST00000390003.4_Splice_Site_p.N1188N			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1513					extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				CTGAGTCAAACGGTATGTTTC	0.403													ENSG00000049323																																					0													79.0	74.0	75.0					2																	33589422		2203	4300	6503	SO:0001630	splice_region_variant	0			-		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.4540+1C>T	2.37:g.33589422C>T			A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	pfam_EGF-like_Ca-bd_dom,pfam_TB_dom,pfam_EG-like_dom,superfamily_TB_dom,smart_EG-like_dom,smart_EGF-like_Ca-bd_dom,pfscan_EG-like_dom	p.N1514	ENST00000404816.2	37	c.4542	CCDS33177.2	2																																																																																			-	LTBP1	-	NULL		0.403	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	LTBP1	HGNC	protein_coding	OTTHUMT00000326227.2	0	0		44	44		0.00		C	NM_206943	Silent	33589422	+1	29		53		tier1	no_errors	ENST00000354476	ensembl	human	known	74_37	silent	35.37		SNP	0.998	T	29	53
ITPK1	3705	genome.wustl.edu	37	14	93483134	93483134	+	Missense_Mutation	SNP	G	G	A			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr14:93483134G>A	ENST00000267615.6	-	4	306	c.133C>T	c.(133-135)Cgg>Tgg	p.R45W	ITPK1_ENST00000556603.2_Missense_Mutation_p.R45W|ITPK1_ENST00000555495.1_5'UTR|ITPK1_ENST00000354313.3_Missense_Mutation_p.R45W|ITPK1_ENST00000556954.1_5'UTR			Q13572	ITPK1_HUMAN	inositol-tetrakisphosphate 1-kinase	45					blood coagulation (GO:0007596)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|inositol trisphosphate metabolic process (GO:0032957)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|inositol tetrakisphosphate 1-kinase activity (GO:0047325)|inositol-1,3,4,5,6-pentakisphosphate 1-phosphatase activity (GO:0052825)|inositol-1,3,4,6-tetrakisphosphate 1-phosphatase activity (GO:0052831)|inositol-1,3,4,6-tetrakisphosphate 6-phosphatase activity (GO:0052830)|inositol-1,3,4-trisphosphate 5-kinase activity (GO:0052726)|inositol-1,3,4-trisphosphate 6-kinase activity (GO:0052725)|inositol-3,4,6-trisphosphate 1-kinase activity (GO:0052835)|isomerase activity (GO:0016853)|magnesium ion binding (GO:0000287)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)	11		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		TCGATCGGCCGGCTAAGGTTC	0.577													ENSG00000100605																																					0													90.0	76.0	81.0					14																	93483134		2203	4300	6503	SO:0001583	missense	0			-	U51336	CCDS9907.1, CCDS45157.1	14q32.12	2012-08-16	2011-04-28		ENSG00000100605	ENSG00000100605	2.7.1.134		6177	protein-coding gene	gene with protein product		601838	"""inositol 1,3,4-triphosphate 5/6 kinase"""			8662638, 11042108	Standard	NM_014216		Approved		uc001ybh.3	Q13572	OTTHUMG00000171226	ENST00000267615.6:c.133C>T	14.37:g.93483134G>A	ENSP00000267615:p.Arg45Trp		Q9BTL6|Q9H2E7	Missense_Mutation	SNP	pfam_Inositol_tetrakis-P_1-kinase	p.R45W	ENST00000267615.6	37	c.133	CCDS9907.1	14	.	.	.	.	.	.	.	.	.	.	G	17.47	3.397604	0.62177	.	.	ENSG00000100605	ENST00000354313;ENST00000405174;ENST00000556603;ENST00000267615;ENST00000311458;ENST00000556185;ENST00000555553;ENST00000553452;ENST00000557309	.	.	.	5.25	3.21	0.36854	.	0.181065	0.47852	D	0.000214	T	0.56455	0.1986	L	0.61036	1.89	0.36118	D	0.845293	D;D	0.76494	0.999;0.993	P;B	0.50192	0.634;0.287	T	0.69003	-0.5260	9	0.66056	D	0.02	-15.8496	11.5472	0.50700	0.0:0.0:0.4156:0.5844	.	45;45	Q13572;Q13572-2	ITPK1_HUMAN;.	W	45;75;45;45;45;63;45;45;45	.	ENSP00000267615:R45W	R	-	1	2	ITPK1	92552887	1.000000	0.71417	0.990000	0.47175	0.639000	0.38242	3.542000	0.53625	1.174000	0.42811	0.561000	0.74099	CGG	-	ITPK1	-	pfam_Inositol_tetrakis-P_1-kinase		0.577	ITPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ITPK1	HGNC	protein_coding	OTTHUMT00000412421.2	0	0		24	24		0.00		G	NM_014216		93483134	-1	20		24		tier1	no_errors	ENST00000267615	ensembl	human	known	74_37	missense	45.45		SNP	1.000	A	20	24
FAM95B1	100133036	genome.wustl.edu	37	9	42472104	42472104	+	Intron	SNP	C	C	T			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr9:42472104C>T	ENST00000421686.2	+	11	1457				FAM95B1_ENST00000592873.1_RNA																							GTGGTTCTGCCCATTGCTGGA	0.542													ENSG00000223839																																					0																																										SO:0001627	intron_variant	0			-																												ENST00000421686.2:c.224-1832C>T	9.37:g.42472104C>T				R	SNP	-	NULL	ENST00000421686.2	37	NULL		9																																																																																			-	FAM95B1	-	-		0.542	RP11-146D12.2-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	FAM95B1	HGNC	protein_coding	OTTHUMT00000129789.5	1	1		146	146		0.68		C			42472104	+1	7		73		tier1	no_errors	ENST00000592873	ensembl	human	known	74_37	rna	8.75		SNP	0.012	T	7	73
TTC37	9652	genome.wustl.edu	37	5	94864706	94864706	+	Splice_Site	SNP	T	T	C			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr5:94864706T>C	ENST00000358746.2	-	12	1291	c.993A>G	c.(991-993)caA>caG	p.Q331Q		NM_014639.3	NP_055454.1	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	331						cytoplasm (GO:0005737)|nucleus (GO:0005634)|Ski complex (GO:0055087)|transcriptionally active chromatin (GO:0035327)				breast(2)|endometrium(6)|kidney(3)|large_intestine(13)|liver(1)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	47						CAAAAATACCTTGACTGCATG	0.373													ENSG00000198677																																					0													80.0	69.0	73.0					5																	94864706		2203	4300	6503	SO:0001630	splice_region_variant	0			-	AB002370	CCDS4072.1	5q15	2014-09-17	2008-06-11	2008-06-11	ENSG00000198677	ENSG00000198677		"""Tetratricopeptide (TTC) repeat domain containing"""	23639	protein-coding gene	gene with protein product		614589	"""KIAA0372"""	KIAA0372		9205841	Standard	NM_014639		Approved		uc003klb.3	Q6PGP7	OTTHUMG00000121165	ENST00000358746.2:c.994+1A>G	5.37:g.94864706T>C			O15077|Q6PJI3	Silent	SNP	pfam_TPR_1,smart_TPR_repeat,pfscan_TPR_repeat,pfscan_TPR-contain_dom	p.Q331	ENST00000358746.2	37	c.993	CCDS4072.1	5																																																																																			-	TTC37	-	smart_TPR_repeat,pfscan_TPR-contain_dom		0.373	TTC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TTC37	HGNC	protein_coding	OTTHUMT00000241651.1	0	0		27	27		0.00		T	NM_014639	Silent	94864706	-1	19		10		tier1	no_errors	ENST00000358746	ensembl	human	known	74_37	silent	65.52		SNP	1.000	C	19	10
NAV2	89797	genome.wustl.edu	37	11	20119223	20119224	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	AA	AA					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr11:20119223_20119224delAA	ENST00000396087.3	+	34	6389_6390	c.6290_6291delAA	c.(6289-6291)gaafs	p.E2097fs	NAV2_ENST00000349880.4_Frame_Shift_Del_p.E2038fs|NAV2_ENST00000527559.2_Frame_Shift_Del_p.E2026fs|NAV2_ENST00000540292.1_Frame_Shift_Del_p.E2028fs|NAV2_ENST00000311043.8_Frame_Shift_Del_p.E1102fs|NAV2_ENST00000360655.4_Frame_Shift_Del_p.E1974fs|NAV2_ENST00000533917.1_Frame_Shift_Del_p.E1102fs|NAV2_ENST00000396085.1_Frame_Shift_Del_p.E2041fs	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	2097					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						AACACTTCCGAAACACCGGAGC	0.49													ENSG00000166833																																					0																																										SO:0001589	frameshift_variant	0				AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.6290_6291delAA	11.37:g.20119223_20119224delAA	ENSP00000379396:p.Glu2097fs		A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Frame_Shift_Del	DEL	pfam_CH-domain,superfamily_CH-domain,superfamily_P-loop_NTPase,smart_CH-domain,smart_AAA+_ATPase,pfscan_CH-domain	p.E2097fs	ENST00000396087.3	37	c.6290_6291	CCDS58126.1	11																																																																																				V2	-	NULL		0.490	NAV2-001	KNOWN	basic|CCDS	protein_coding	V2	HGNC	protein_coding	OTTHUMT00000324112.1	0	0		103	103		0.00		AA	NM_145117		20119224	+1	21		100		tier1	no_errors	ENST00000396087	ensembl	human	known	74_37	frame_shift_del	17.36		DEL	1.000:1.000	-	21	100
YIPF7	285525	genome.wustl.edu	37	4	44626623	44626623	+	Silent	SNP	T	T	A			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr4:44626623T>A	ENST00000332990.5	-	5	691	c.675A>T	c.(673-675)tcA>tcT	p.S225S	YIPF7_ENST00000415895.4_Silent_p.S201S	NM_182592.2	NP_872398.2	Q8N8F6	YIPF7_HUMAN	Yip1 domain family, member 7	225						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(9)|upper_aerodigestive_tract(1)	12						CTTACTGCAGTGAAAAGAACA	0.522													ENSG00000177752																																					0													44.0	49.0	47.0					4																	44626623		2089	4229	6318	SO:0001819	synonymous_variant	0			-	AK096895	CCDS54766.1	4p13	2008-08-07			ENSG00000177752	ENSG00000177752		"""Yip1 domain family"""	26825	protein-coding gene	gene with protein product							Standard	NM_182592		Approved	FLJ39576, FinGER9	uc021xnx.1	Q8N8F6	OTTHUMG00000160467	ENST00000332990.5:c.675A>T	4.37:g.44626623T>A			Q3SY21|Q3SY22	Silent	SNP	pfam_Yip1	p.S225	ENST00000332990.5	37	c.675	CCDS54766.1	4	.	.	.	.	.	.	.	.	.	.	T	0.547	-0.850989	0.02651	.	.	ENSG00000177752	ENST00000415895	.	.	.	5.0	-2.03	0.07365	.	.	.	.	.	T	0.39279	0.1072	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.26643	-1.0097	4	.	.	.	-9.5724	1.6218	0.02715	0.1123:0.2042:0.2322:0.4512	.	.	.	.	S	202	.	.	T	-	1	0	YIPF7	44321380	0.005000	0.15991	0.572000	0.28498	0.077000	0.17291	-0.991000	0.03728	-0.474000	0.06862	-1.137000	0.01932	ACT	-	YIPF7	-	pfam_Yip1		0.522	YIPF7-201	KNOWN	basic|CCDS	protein_coding	YIPF7	HGNC	protein_coding		0	0		22	22		0.00		T	NM_182592		44626623	-1	14		3		tier1	no_errors	ENST00000332990	ensembl	human	known	74_37	silent	82.35		SNP	0.331	A	14	3
PBX2P1	5088	genome.wustl.edu	37	3	142897134	142897136	+	RNA	DEL	TTT	TTT	-	rs553879413|rs36138113|rs541447224	byFrequency	TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	TTT	TTT					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr3:142897134_142897136delTTT	ENST00000560287.1	+	0	2008_2010									pre-B-cell leukemia homeobox 2 pseudogene 1																		GGGGTTGAACttttttttttttt	0.384													ENSG00000244171																																					0																																												0						3q24	2014-03-25	2007-01-30	2007-01-30	ENSG00000244171	ENSG00000244171		"""Homeoboxes / TALE class"""	8635	pseudogene	pseudogene			"""pre-B-cell leukemia transcription factor pseudogene 1"""	PBX2, PBXP1		1682799	Standard	NG_002434		Approved				OTTHUMG00000159350		3.37:g.142897143_142897145delTTT				R	DEL	-	NULL	ENST00000560287.1	37	NULL		3																																																																																				PBX2P1	-	-		0.384	PBX2P1-002	KNOWN	basic	processed_transcript	PBX2P1	HGNC	pseudogene	OTTHUMT00000417717.1	0	0		39	39		0.00		TTT	NG_002434		142897136	+1	7		39		tier1	no_errors	ENST00000560287	ensembl	human	known	74_37	rna	15.22		DEL	0.986:0.988:0.989	-	7	39
OR8G5	219865	genome.wustl.edu	37	11	124135362	124135362	+	Missense_Mutation	SNP	T	T	G			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr11:124135362T>G	ENST00000524943.2	+	1	640	c.640T>G	c.(640-642)Tgt>Ggt	p.C214G	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	214						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)						Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0523)		CCATTATTTCTGTGATCTTAT	0.358													ENSG00000255298																									Ovarian(169;523 1969 8640 31295 51256)												0													235.0	226.0	229.0					11																	124135362		1874	4138	6012	SO:0001583	missense	0			-	BK004516	CCDS66256.1	11q24.1	2014-04-17		2004-03-10	ENSG00000255298	ENSG00000255298		"""GPCR / Class A : Olfactory receptors"""	19622	protein-coding gene	gene with protein product				OR8G5P, OR8G6			Standard	NM_001005198		Approved			Q8NG78	OTTHUMG00000186059	ENST00000524943.2:c.640T>G	11.37:g.124135362T>G	ENSP00000477014:p.Cys214Gly		B2RND3|Q6IEU6	Missense_Mutation	SNP	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	p.C214G	ENST00000524943.2	37	c.640		11																																																																																			-	OR8G5	-	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt		0.358	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	OR8G5	HGNC	protein_coding	OTTHUMT00000387283.2	0	0		71	71		0.00		T	NM_001005198		124135362	+1	45		8		tier1	no_errors	ENST00000524943	ensembl	human	known	74_37	missense	84.91		SNP	1.000	G	45	8
ILVBL	10994	genome.wustl.edu	37	19	15235791	15235791	+	Missense_Mutation	SNP	G	G	C			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr19:15235791G>C	ENST00000263383.3	-	2	219	c.80C>G	c.(79-81)gCc>gGc	p.A27G	AC003956.1_ENST00000598450.1_RNA|ILVBL_ENST00000531635.1_Intron|ILVBL_ENST00000534378.1_Intron	NM_006844.3	NP_006835.2	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	27						integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|thiamine pyrophosphate binding (GO:0030976)|transferase activity (GO:0016740)			NS(3)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)	26						CAGCAAGGCGGCCACCAGCGT	0.677													ENSG00000105135																																					0													9.0	10.0	10.0					19																	15235791		2175	4268	6443	SO:0001583	missense	0			-	U61263	CCDS12325.1	19p13.1	2008-07-16			ENSG00000105135	ENSG00000105135			6041	protein-coding gene	gene with protein product	"""acetolactate synthase homolog"""	605770				8954801	Standard	NM_006844		Approved	209L8, AHAS, ILV2H, MGC1269, FLJ39061, MGC19535	uc002nam.3	A1L0T0	OTTHUMG00000165630	ENST00000263383.3:c.80C>G	19.37:g.15235791G>C	ENSP00000263383:p.Ala27Gly		O43341|Q96F08|Q99651|Q9BWN5|Q9UEB2	Missense_Mutation	SNP	pfam_Thiamin_PyroP_enz_TPP-bd_dom,pfam_TPP_enzyme-bd_C,pfam_Thiamin_PyroP_enz_cen_dom	p.A27G	ENST00000263383.3	37	c.80	CCDS12325.1	19	.	.	.	.	.	.	.	.	.	.	G	14.30	2.494325	0.44352	.	.	ENSG00000105135	ENST00000263383;ENST00000269733;ENST00000527093;ENST00000533747	T	0.32023	1.47	4.32	2.21	0.28008	.	0.442645	0.24363	N	0.039161	T	0.14013	0.0339	N	0.08118	0	0.26664	N	0.971866	B	0.02656	0.0	B	0.01281	0.0	T	0.18398	-1.0338	10	0.31617	T	0.26	-3.9097	8.2998	0.32008	0.1954:0.0:0.8046:0.0	.	27	A1L0T0	ILVBL_HUMAN	G	27	ENSP00000263383:A27G	ENSP00000263383:A27G	A	-	2	0	ILVBL	15096791	0.002000	0.14202	0.780000	0.31762	0.944000	0.59088	1.148000	0.31614	0.481000	0.27557	0.561000	0.74099	GCC	-	ILVBL	-	NULL		0.677	ILVBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ILVBL	HGNC	protein_coding	OTTHUMT00000385439.1	0	0		33	33		0.00		G	NM_006844		15235791	-1	6		23		tier1	no_errors	ENST00000263383	ensembl	human	known	74_37	missense	20.69		SNP	0.746	C	6	23
PLEKHA4	57664	genome.wustl.edu	37	19	49362197	49362197	+	Missense_Mutation	SNP	G	G	A			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr19:49362197G>A	ENST00000263265.6	-	8	1447	c.892C>T	c.(892-894)Cgc>Tgc	p.R298C	PLEKHA4_ENST00000596713.1_5'UTR|PLEKHA4_ENST00000355496.5_Missense_Mutation_p.R298C	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	298	Pro-rich.					cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		GGTCCTCGGCGGGGAGTAGGG	0.662													ENSG00000105559																																					0													40.0	46.0	44.0					19																	49362197		2182	4255	6437	SO:0001583	missense	0			-	AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"""Pleckstrin homology (PH) domain containing"""	14339	protein-coding gene	gene with protein product		607769	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"""			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.892C>T	19.37:g.49362197G>A	ENSP00000263265:p.Arg298Cys		Q8N4M8|Q8N658	Missense_Mutation	SNP	pfam_Pleckstrin_homology,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	p.R298C	ENST00000263265.6	37	c.892	CCDS12737.1	19	.	.	.	.	.	.	.	.	.	.	G	22.6	4.314910	0.81358	.	.	ENSG00000105559	ENST00000263265;ENST00000355496	T;T	0.15952	3.0;2.38	4.78	4.78	0.61160	.	0.122950	0.40222	N	0.001158	T	0.18923	0.0454	L	0.27053	0.805	0.47819	D	0.999526	D;D	0.71674	0.993;0.998	P;P	0.50896	0.653;0.65	T	0.00542	-1.1680	10	0.51188	T	0.08	.	13.5286	0.61609	0.0:0.0:1.0:0.0	.	298;298	Q9H4M7-2;Q9H4M7	.;PKHA4_HUMAN	C	298	ENSP00000263265:R298C;ENSP00000347683:R298C	ENSP00000263265:R298C	R	-	1	0	PLEKHA4	54054009	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	2.199000	0.42715	2.671000	0.90904	0.455000	0.32223	CGC	-	PLEKHA4	-	NULL		0.662	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLEKHA4	HGNC	protein_coding	OTTHUMT00000466216.1	0	0		29	29		0.00		G			49362197	-1	17		22		tier1	no_errors	ENST00000263265	ensembl	human	known	74_37	missense	43.59		SNP	1.000	A	17	22
KAT6B	23522	genome.wustl.edu	37	10	76735646	76735646	+	Silent	SNP	C	C	G			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr10:76735646C>G	ENST00000287239.4	+	8	2040	c.1551C>G	c.(1549-1551)ccC>ccG	p.P517P	KAT6B_ENST00000372724.1_Intron|KAT6B_ENST00000372725.1_Intron|KAT6B_ENST00000372711.1_Intron|KAT6B_ENST00000372714.1_Intron	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	517	Negatively regulates HAT activity.|Ser-rich.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										CTTCTTCTCCCTCTCCCCAGA	0.547													ENSG00000156650																																					0													71.0	69.0	70.0					10																	76735646		2203	4300	6503	SO:0001819	synonymous_variant	0			-	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	17582	protein-coding gene	gene with protein product	"""MOZ-related factor"""	605880	"""MYST histone acetyltransferase (monocytic leukemia) 4"""	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.1551C>G	10.37:g.76735646C>G			O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Silent	SNP	pfam_MOZ_SAS,pfam_Znf_PHD-finger,pfam_Histone_H1/H5_H15,superfamily_Acyl_CoA_acyltransferase,superfamily_Znf_FYVE_PHD,smart_Histone_H1/H5_H15,smart_Znf_PHD,pfscan_Znf_PHD-finger	p.P517	ENST00000287239.4	37	c.1551	CCDS7345.1	10																																																																																			-	KAT6B	-	NULL		0.547	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	KAT6B	HGNC	protein_coding	OTTHUMT00000048771.1	0	0		71	71		0.00		C	NM_012330		76735646	+1	53		25		tier1	no_errors	ENST00000287239	ensembl	human	known	74_37	silent	67.95		SNP	1.000	G	53	25
SRGAP2-AS1	100873165	genome.wustl.edu	37	1	121138853	121138853	+	lincRNA	SNP	G	G	A	rs184767318		TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr1:121138853G>A	ENST00000417218.1	+	0	240				RP11-343N15.1_ENST00000437515.1_lincRNA																							GCCGAGGGGTGCTCCTGGTCC	0.692													ENSG00000227082																																					0																																												0			-																													1.37:g.121138853G>A				R	SNP	-	NULL	ENST00000417218.1	37	NULL		1																																																																																			rs184767318	AL592494.5	-	-		0.692	AL592494.5-001	KNOWN	basic	lincRNA	ENSG00000227082	Clone_based_vega_gene	lincRNA	OTTHUMT00000036739.1	0	0		15	15		0.00		G			121138853	+1	5		9		tier1	no_errors	ENST00000417218	ensembl	human	known	74_37	rna	35.71		SNP	0.951	A	5	9
ABCC11	85320	genome.wustl.edu	37	16	48234247	48234247	+	Silent	SNP	C	C	T			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr16:48234247C>T	ENST00000394747.1	-	14	2371	c.2022G>A	c.(2020-2022)gaG>gaA	p.E674E	ABCC11_ENST00000356608.2_Silent_p.E674E|ABCC11_ENST00000537808.1_Silent_p.E674E|ABCC11_ENST00000394748.1_Silent_p.E674E|ABCC11_ENST00000353782.5_Silent_p.E674E	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	674	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	TAATGCACTCCTCAAAAATGT	0.592													ENSG00000121270																																					0													116.0	99.0	105.0					16																	48234247		2201	4300	6501	SO:0001819	synonymous_variant	0			-	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"""ATP binding cassette transporters / subfamily C"""	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.2022G>A	16.37:g.48234247C>T			Q8TDJ0|Q96JA6|Q9BX80	Silent	SNP	pfam_ABC_transptr_TM_dom,pfam_ABC_transporter-like,superfamily_P-loop_NTPase,superfamily_ABC1_TM_dom,smart_AAA+_ATPase,pfscan_ABC_transporter-like,pfscan_ABC1_TM_dom	p.E674	ENST00000394747.1	37	c.2022	CCDS10732.1	16																																																																																			-	ABCC11	-	superfamily_P-loop_NTPase,smart_AAA+_ATPase,pfscan_ABC_transporter-like		0.592	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	ABCC11	HGNC	protein_coding	OTTHUMT00000429984.1	0	0		77	77		0.00		C	NM_032583		48234247	-1	10		70		tier1	no_errors	ENST00000356608	ensembl	human	known	74_37	silent	12.50		SNP	0.959	T	10	70
DMPK	1760	genome.wustl.edu	37	19	46273040	46273042	+	3'UTR	DEL	AAT	AAT	-	rs546086975	byFrequency	TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	AAT	AAT					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr19:46273040_46273042delAAT	ENST00000291270.4	-	0	2719_2721				DMPK_ENST00000343373.4_3'UTR|DMPK_ENST00000600757.1_3'UTR|DMPK_ENST00000447742.2_3'UTR|AC074212.6_ENST00000591530.1_RNA|AC074212.6_ENST00000586251.1_RNA|AC074212.6_ENST00000586498.1_RNA|AC074212.5_ENST00000592217.2_RNA|SIX5_ENST00000317578.6_5'Flank|AC074212.5_ENST00000559756.1_RNA|SIX5_ENST00000560168.1_5'Flank|AC074212.6_ENST00000590076.1_RNA	NM_004409.3	NP_004400.4	Q09013	DMPK_HUMAN	dystrophia myotonica-protein kinase						cellular calcium ion homeostasis (GO:0006874)|muscle cell apoptotic process (GO:0010657)|nuclear envelope organization (GO:0006998)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction (GO:0014853)|regulation of heart contraction (GO:0008016)|regulation of myotube differentiation (GO:0010830)|regulation of skeletal muscle contraction by calcium ion signaling (GO:0014722)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of mitochondrial outer membrane (GO:0031307)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|myosin phosphatase regulator activity (GO:0017020)|protein serine/threonine kinase activity (GO:0004674)			endometrium(5)|kidney(1)|large_intestine(1)|lung(6)|stomach(1)|urinary_tract(2)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00616)|GBM - Glioblastoma multiforme(486;0.0825)|Epithelial(262;0.24)		GGGGACAGACAATAAATACCGAG	0.571													ENSG00000259605		2	0.000399361	0.0008	0.0014	5008	,	,		13580	0.0		0.0	False		,,,				2504	0.0				Esophageal Squamous(35;307 869 9153 24033 28903)												0																																										SO:0001624	3_prime_UTR_variant	0				L19268	CCDS12674.1, CCDS46117.1, CCDS46118.1, CCDS46119.1, CCDS74400.1	19q13.3	2014-02-05					2.7.11.1		2933	protein-coding gene	gene with protein product	"""dystrophia myotonica 1"", ""DM protein kinase"", ""myotonin protein kinase A"", ""myotonic dystrophy associated protein kinase"", ""thymopoietin homolog"""	605377	"""dystrophia myotonica 1 (includes dystrophia myotonia protein kinase)"""	DM1, DM		1546325, 1546326	Standard	NM_001288765		Approved	DMK, DM1PK, MDPK, MT-PK	uc002pdf.1	Q09013		ENST00000291270.4:c.*706ATT>-	19.37:g.46273040_46273042delAAT			E5KR08|Q16205|Q6P5Z6	R	DEL	-	NULL	ENST00000291270.4	37	NULL	CCDS12674.1	19																																																																																				AC074212.5	-	-		0.571	DMPK-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ENSG00000259605	Clone_based_vega_gene	protein_coding	OTTHUMT00000460572.1	0	0		100	100		0.00		AAT	NM_004409		46273042	+1	30		64		tier1	no_errors	ENST00000592217	ensembl	human	known	74_37	rna	31.91		DEL	1.000:1.000:1.000	-	30	64
GIN1	54826	genome.wustl.edu	37	5	102440484	102440484	+	Missense_Mutation	SNP	G	G	A			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr5:102440484G>A	ENST00000399004.2	-	4	494	c.400C>T	c.(400-402)Ctc>Ttc	p.L134F	GIN1_ENST00000511400.1_5'Flank|GIN1_ENST00000508629.1_Missense_Mutation_p.L134F	NM_017676.2	NP_060146.2	Q9NXP7	GIN1_HUMAN	gypsy retrotransposon integrase 1	134					DNA integration (GO:0015074)		nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(142;3.23e-07)|all_epithelial(76;3.64e-10)|Prostate(80;0.00914)|Ovarian(225;0.0139)|Lung NSC(167;0.0212)|Colorectal(57;0.0249)|all_lung(232;0.0283)		Epithelial(69;3.57e-14)|COAD - Colon adenocarcinoma(37;0.00794)		TCCACCTTGAGAAGGTGCTGT	0.383													ENSG00000145723																																					0													97.0	91.0	93.0					5																	102440484		1873	4112	5985	SO:0001583	missense	0			-	BC015325	CCDS43349.1	5q21.1	2008-02-11	2007-06-13	2007-06-13		ENSG00000145723			25959	protein-coding gene	gene with protein product	"""gypsy integrase 1"", ""Ty3/Gypsy integrase 1"""		"""zinc finger, H2C2 domain containing"""	ZH2C2		11470852	Standard	NM_017676		Approved	FLJ20125, GIN-1, TGIN1	uc003koa.1	Q9NXP7		ENST00000399004.2:c.400C>T	5.37:g.102440484G>A	ENSP00000381970:p.Leu134Phe		B2RXF7|B4DIV4|Q6AI03|Q96BR2	Missense_Mutation	SNP	pfam_Integrase_cat-core,pfam_Znf_H2C2_histone_UAS-bd,superfamily_RNaseH-like_dom,pfscan_Integrase_cat-core	p.L134F	ENST00000399004.2	37	c.400	CCDS43349.1	5	.	.	.	.	.	.	.	.	.	.	G	1.691	-0.503933	0.04261	.	.	ENSG00000145723	ENST00000399004;ENST00000508629	T;T	0.39997	1.05;1.05	5.74	3.93	0.45458	Ribonuclease H-like (1);	0.417238	0.20258	N	0.095928	T	0.33556	0.0867	L	0.38175	1.15	0.22292	N	0.999221	P;B	0.39535	0.677;0.435	B;B	0.42138	0.377;0.3	T	0.24870	-1.0148	10	0.72032	D	0.01	-14.714	5.0805	0.14653	0.0747:0.2488:0.5322:0.1443	.	134;134	Q9NXP7-3;Q9NXP7	.;GIN1_HUMAN	F	134	ENSP00000381970:L134F;ENSP00000427162:L134F	ENSP00000381970:L134F	L	-	1	0	GIN1	102468383	0.999000	0.42202	0.945000	0.38365	0.016000	0.09150	1.246000	0.32803	0.735000	0.32537	-0.315000	0.08773	CTC	-	GIN1	-	superfamily_RNaseH-like_dom		0.383	GIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GIN1	HGNC	protein_coding	OTTHUMT00000370478.3	0	0		35	35		0.00		G	NM_017676		102440484	-1	5		38		tier1	no_errors	ENST00000399004	ensembl	human	known	74_37	missense	11.63		SNP	0.513	A	5	38
AMY2B	280	genome.wustl.edu	37	1	104115829	104115829	+	Missense_Mutation	SNP	G	G	T			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr1:104115829G>T	ENST00000361355.4	+	5	1076	c.460G>T	c.(460-462)Ggt>Tgt	p.G154C	AMY2B_ENST00000491397.1_3'UTR	NM_020978.3	NP_066188.1	P19961	AMY2B_HUMAN	amylase, alpha 2B (pancreatic)	154					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)			breast(1)|endometrium(7)|kidney(4)|large_intestine(1)|lung(30)|prostate(1)|skin(1)|urinary_tract(1)	46		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0669)|all cancers(265;0.083)|Epithelial(280;0.094)|Lung(183;0.112)		TTTTAATGATGGTAAATGTAA	0.408													ENSG00000240038																																					0													206.0	220.0	215.0					1																	104115829		2203	4295	6498	SO:0001583	missense	0			-	M24895	CCDS782.1	1p21	2010-08-02	2006-04-27		ENSG00000240038	ENSG00000240038	3.2.1.1		478	protein-coding gene	gene with protein product		104660	"""amylase, alpha 2B; pancreatic"""	AMY2		8268204	Standard	NM_020978		Approved		uc001duq.3	P19961	OTTHUMG00000011024	ENST00000361355.4:c.460G>T	1.37:g.104115829G>T	ENSP00000354610:p.Gly154Cys		B3KTI1|B3KXB7|D3DT76|Q9UBH3	Missense_Mutation	SNP	pfam_Glyco_hydro_13_cat_dom,pfam_A-amylase_b_C,superfamily_Glycoside_hydrolase_SF,smart_Glyco_hydro_13_sub_cat_dom,smart_A-amylase_b_C,prints_Alpha_amylase	p.G154C	ENST00000361355.4	37	c.460	CCDS782.1	1	.	.	.	.	.	.	.	.	.	.	G	17.33	3.363333	0.61513	.	.	ENSG00000240038	ENST00000361355	D	0.98455	-4.94	4.58	4.58	0.56647	Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);	0.330338	0.34435	N	0.003978	D	0.97052	0.9037	M	0.77103	2.36	0.38731	D	0.953665	P	0.45902	0.868	P	0.47134	0.539	D	0.97483	1.0048	10	0.72032	D	0.01	.	9.3615	0.38199	0.0:0.1563:0.6821:0.1616	.	154	P19961	AMY2B_HUMAN	C	154	ENSP00000354610:G154C	ENSP00000354610:G154C	G	+	1	0	AMY2B	103917352	0.789000	0.28775	0.999000	0.59377	0.976000	0.68499	0.852000	0.27764	2.104000	0.64026	0.644000	0.83932	GGT	-	AMY2B	-	pfam_Glyco_hydro_13_cat_dom,superfamily_Glycoside_hydrolase_SF,smart_Glyco_hydro_13_sub_cat_dom		0.408	AMY2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AMY2B	HGNC	protein_coding	OTTHUMT00000030318.1	0	0		221	221		0.00		G	NM_020978		104115829	+1	72		211		tier1	no_errors	ENST00000361355	ensembl	human	known	74_37	missense	25.35		SNP	0.979	T	72	211
CCDC62	84660	genome.wustl.edu	37	12	123286397	123286397	+	Frame_Shift_Del	DEL	A	A	-			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr12:123286397delA	ENST00000253079.6	+	9	2048	c.1704delA	c.(1702-1704)gcafs	p.A568fs	CCDC62_ENST00000392440.2_Frame_Shift_Del_p.A329fs|CCDC62_ENST00000537566.1_Frame_Shift_Del_p.A329fs|CCDC62_ENST00000392441.4_Frame_Shift_Del_p.A568fs	NM_201435.4	NP_958843.2	Q6P9F0	CCD62_HUMAN	coiled-coil domain containing 62	568					cellular response to estradiol stimulus (GO:0071392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.51e-06)|Epithelial(86;2.65e-05)|BRCA - Breast invasive adenocarcinoma(302;0.206)		ACTCCCCGGCAAGGTGAGTAA	0.468													ENSG00000130783																																					0													180.0	188.0	185.0					12																	123286397		2201	4300	6501	SO:0001589	frameshift_variant	0					CCDS9238.1	12q24.31	2009-08-18			ENSG00000130783	ENSG00000130783			30723	protein-coding gene	gene with protein product	"""cancer/testis antigen 109"""	613481				18563714, 19126643	Standard	NM_201435		Approved	TSP-NY, FLJ40344, CT109, ERAP75	uc001udc.3	Q6P9F0	OTTHUMG00000168764	ENST00000253079.6:c.1704delA	12.37:g.123286397delA	ENSP00000253079:p.Ala568fs		A8K8V1|B3KUP3|Q6ZVF2|Q86VJ0|Q9BYZ5	Frame_Shift_Del	DEL	superfamily_Prefoldin	p.S569fs	ENST00000253079.6	37	c.1704	CCDS9238.1	12																																																																																				CCDC62	-	NULL		0.468	CCDC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CCDC62	HGNC	protein_coding	OTTHUMT00000400930.1	0	0		52	52		0.00		A	NM_032573		123286397	+1	8		53		tier1	no_errors	ENST00000253079	ensembl	human	known	74_37	frame_shift_del	13.11		DEL	0.000	-	8	53
FAM83A	84985	genome.wustl.edu	37	8	124219460	124219460	+	Silent	SNP	G	G	A			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr8:124219460G>A	ENST00000518448.1	+	5	2851	c.837G>A	c.(835-837)gtG>gtA	p.V279V	FAM83A_ENST00000318462.6_Silent_p.V279V|FAM83A_ENST00000536633.1_Silent_p.V279V|FAM83A_ENST00000276699.6_Silent_p.V279V|FAM83A_ENST00000522648.1_Silent_p.V223V|FAM83A_ENST00000546351.1_Silent_p.V223V			Q86UY5	FA83A_HUMAN	family with sequence similarity 83, member A	279										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(2)|skin(1)	17	Lung NSC(37;1.55e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			GCCAGGCGGTGGAGCTGTTTG	0.647													ENSG00000147689																																					0													35.0	29.0	31.0					8																	124219460		2202	4300	6502	SO:0001819	synonymous_variant	0			-	BC052300	CCDS6339.1, CCDS6340.1, CCDS75784.1	8q24.13	2014-03-13			ENSG00000147689	ENSG00000147689			28210	protein-coding gene	gene with protein product						22886303	Standard	XM_005251087		Approved	MGC14128, BJ-TSA-9	uc003ypx.3	Q86UY5	OTTHUMG00000165083	ENST00000518448.1:c.837G>A	8.37:g.124219460G>A			Q71HL2|Q8N7I1|Q96I47	Silent	SNP	pfam_DUF1669	p.V279	ENST00000518448.1	37	c.837	CCDS6340.1	8																																																																																			-	FAM83A	-	pfam_DUF1669		0.647	FAM83A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM83A	HGNC	protein_coding	OTTHUMT00000381737.1	0	0		39	39		0.00		G	NM_032899		124219460	+1	9		66		tier1	no_errors	ENST00000318462	ensembl	human	known	74_37	silent	12.00		SNP	0.993	A	9	66
HUWE1	10075	genome.wustl.edu	37	X	53657850	53657850	+	Intron	SNP	C	C	G			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chrX:53657850C>G	ENST00000342160.3	-	11	1320				HUWE1_ENST00000218328.8_Intron|HUWE1_ENST00000262854.6_Intron			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase						base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						CCCAAACTGTCTAATACGGCC	0.398													ENSG00000086758																																					0													36.0	30.0	32.0					X																	53657850		2203	4298	6501	SO:0001627	intron_variant	0			-	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"""HECT, UBA and WWE domain containing 1"""			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.862+36G>C	X.37:g.53657850C>G			O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	R	SNP	-	NULL	ENST00000342160.3	37	NULL	CCDS35301.1	X																																																																																			-	HUWE1	-	-		0.398	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HUWE1	HGNC	protein_coding	OTTHUMT00000056766.1	0	0		92	92		0.00		C	XM_497119		53657850	-1	9		76		tier1	no_errors	ENST00000471676	ensembl	human	known	74_37	rna	10.59		SNP	0.006	G	9	76
NXF4	55999	genome.wustl.edu	37	X	101822851	101822851	+	RNA	SNP	C	C	T			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chrX:101822851C>T	ENST00000360035.2	+	0	2604					NR_002216.1				nuclear RNA export factor 4 pseudogene											endometrium(2)|lung(8)	10						TCGGCAATTCCAAGTAAGTGC	0.498													ENSG00000196970																																					0																																												0			-	AK124700		Xq22	2005-01-24			ENSG00000196970	ENSG00000196970			8074	pseudogene	pseudogene		300318	"""nuclear RNA export factor 4"""			11566096	Standard	NR_002216		Approved		uc004ejf.1		OTTHUMG00000039695		X.37:g.101822851C>T				R	SNP	-	NULL	ENST00000360035.2	37	NULL		X																																																																																			-	NXF4	-	-		0.498	NXF4-001	KNOWN	basic	processed_transcript	NXF4	HGNC	pseudogene	OTTHUMT00000095720.1	0	0		142	142		0.00		C			101822851	+1	15		106		tier1	no_errors	ENST00000360035	ensembl	human	known	74_37	rna	12.40		SNP	0.303	T	15	106
GDF10	2662	genome.wustl.edu	37	10	48429409	48429409	+	Silent	SNP	G	G	T			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr10:48429409G>T	ENST00000224605.2	-	2	742	c.477C>A	c.(475-477)ggC>ggA	p.G159G		NM_004962.3	NP_004953.1	P55107	BMP3B_HUMAN	growth differentiation factor 10	159					fat cell differentiation (GO:0045444)|growth (GO:0040007)|skeletal system development (GO:0001501)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)	growth factor activity (GO:0008083)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(20)|skin(1)	31						GCAGCGGGCGGCCTGAAGCGT	0.677													ENSG00000107623																																					0													17.0	24.0	21.0					10																	48429409		2198	4292	6490	SO:0001819	synonymous_variant	0			-	L42113	CCDS73117.1	10q11.22	2014-04-10			ENSG00000107623	ENSG00000266524		"""Endogenous ligands"""	4215	protein-coding gene	gene with protein product		601361				8679252	Standard	NM_004962		Approved	BMP-3b	uc001jfb.3	P55107	OTTHUMG00000188319	ENST00000224605.2:c.477C>A	10.37:g.48429409G>T			Q5VSQ8|Q9UCX6	Silent	SNP	pfam_TGF-b_C,pfam_TGF-b_N,smart_TGF-b_C,pirsf_BMP3/GDF10	p.G159	ENST00000224605.2	37	c.477	CCDS7220.1	10																																																																																			-	GDF10	-	pirsf_BMP3/GDF10		0.677	GDF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GDF10	HGNC	protein_coding	OTTHUMT00000047884.1	0	0		12	12		0.00		G	NM_004962		48429409	-1	15		0		tier1	no_errors	ENST00000224605	ensembl	human	known	74_37	silent	100.00		SNP	0.987	T	15	0
OLA1	29789	genome.wustl.edu	37	2	175006589	175006601	+	Frame_Shift_Del	DEL	AGCCACCTTTTCT	AGCCACCTTTTCT	-			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	AGCCACCTTTTCT	AGCCACCTTTTCT					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr2:175006589_175006601delAGCCACCTTTTCT	ENST00000409546.1	-	5	1191_1203	c.561_573delAGAAAAGGTGGCT	c.(559-573)ctagaaaaggtggctfs	p.LEKVA187fs	OLA1_ENST00000284719.3_Frame_Shift_Del_p.LEKVA167fs|OLA1_ENST00000428402.2_Frame_Shift_Del_p.LEKVA167fs|OLA1_ENST00000344357.5_Frame_Shift_Del_p.LEKVA9fs					Obg-like ATPase 1									p.A171P(1)|p.E168Q(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11						CTCCTCTCACAGCCACCTTTTCTAGTTTATCTA	0.31													ENSG00000138430																																					2	Substitution - Missense(2)	ovary(1)|breast(1)																																								SO:0001589	frameshift_variant	0					CCDS2255.1, CCDS42779.1	2q31.1	2014-06-24	2007-07-27	2007-07-27	ENSG00000138430	ENSG00000138430			28833	protein-coding gene	gene with protein product		611175	"""GTP-binding protein 9 (putative)"""	GTPBP9		17430889, 24486488	Standard	NM_013341		Approved	PTD004	uc002uih.3	Q9NTK5	OTTHUMG00000132335	ENST00000409546.1:c.561_573delAGAAAAGGTGGCT	2.37:g.175006589_175006601delAGCCACCTTTTCT	ENSP00000386350:p.Leu187fs			Frame_Shift_Del	DEL	pfam_DUF933,pfam_GTP_binding_domain,pfam_Fe2_transport_prot_B_N,superfamily_P-loop_NTPase,superfamily_TGS-like,pirsf_CHP00092,prints_GTP_binding_domain,tigrfam_CHP00092	p.E168fs	ENST00000409546.1	37	c.513_501		2																																																																																				OLA1	-	superfamily_P-loop_NTPase,pirsf_CHP00092,tigrfam_CHP00092		0.310	OLA1-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	OLA1	HGNC	protein_coding	OTTHUMT00000333877.1									AGCCACCTTTTCT	NM_013341		175006601	-1					tier1	no_errors	ENST00000284719	ensembl	human	known	74_37	frame_shift_del			DEL	0.999:1.000:1.000:1.000:1.000:0.999:0.969:1.000:1.000:1.000:1.000:1.000:1.000	-		
ESPNL	339768	genome.wustl.edu	37	2	239040214	239040214	+	Silent	SNP	C	C	T			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr2:239040214C>T	ENST00000343063.3	+	9	3122	c.2859C>T	c.(2857-2859)caC>caT	p.H953H	ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409506.1_Silent_p.H585H|ESPNL_ENST00000409169.1_Silent_p.H909H	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	953										endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		CCCTGCCTCACGCCGCCGTCC	0.682													ENSG00000144488																																					0													15.0	17.0	16.0					2																	239040214		2194	4295	6489	SO:0001819	synonymous_variant	0			-	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.2859C>T	2.37:g.239040214C>T			Q66K27|Q6ZVG1|Q8IVU2	Silent	SNP	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom	p.H953	ENST00000343063.3	37	c.2859	CCDS2525.1	2																																																																																			-	ESPNL	-	NULL		0.682	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ESPNL	HGNC	protein_coding	OTTHUMT00000257164.2	0	0		20	20		0.00		C	NM_194312		239040214	+1	8		9		tier1	no_errors	ENST00000343063	ensembl	human	known	74_37	silent	47.06		SNP	0.000	T	8	9
ZNF595	152687	genome.wustl.edu	37	4	87460	87460	+	3'UTR	SNP	G	G	T			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr4:87460G>T	ENST00000339368.6	+	0	2269							Q8IYB9	ZN595_HUMAN	zinc finger protein 595						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)	20		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		atttctgtaggtacatagtat	0.269													ENSG00000197701																																					0																																										SO:0001624	3_prime_UTR_variant	0			-	BX537887	CCDS75075.1, CCDS75076.1, CCDS75077.1	4p16.3	2013-01-08				ENSG00000272602		"""Zinc fingers, C2H2-type"", ""-"""	27196	protein-coding gene	gene with protein product						12477932	Standard	NM_182524		Approved	FLJ31740		Q8IYB9		ENST00000339368.6:c.*2266G>T	4.37:g.87460G>T				R	SNP	-	NULL	ENST00000339368.6	37	NULL		4																																																																																			-	ZNF595	-	-		0.269	ZNF595-001	KNOWN	basic	processed_transcript	ZNF595	HGNC	protein_coding	OTTHUMT00000357814.2	0	0		31	31		0.00		G	NM_182524		87460	+1	3		18		tier1	no_errors	ENST00000339368	ensembl	human	known	74_37	rna	14.29		SNP	0.001	T	3	18
DEFB106B	503841	genome.wustl.edu	37	8	7340204	7340204	+	Silent	SNP	A	A	G	rs138253070	byFrequency	TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr8:7340204A>G	ENST00000335479.2	-	2	137	c.120T>C	c.(118-120)aaT>aaC	p.N40N		NM_001040704.1	NP_001035794.1	Q8N104	D106A_HUMAN	defensin, beta 106B	40					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)									COAD - Colon adenocarcinoma(149;0.0162)|READ - Rectum adenocarcinoma(644;0.236)		TAAGTTCTTCATTTTTCCCGC	0.413													ENSG00000187082																																					0													8.0	11.0	10.0					8																	7340204		1657	3516	5173	SO:0001819	synonymous_variant	0			-		CCDS34813.1	8p23.1	2011-03-29			ENSG00000187082	ENSG00000187082		"""Defensins, beta"""	28879	protein-coding gene	gene with protein product							Standard	NM_001040704		Approved			Q8N104	OTTHUMG00000129312	ENST00000335479.2:c.120T>C	8.37:g.7340204A>G			Q2NKR0|Q496I8	Silent	SNP	NULL	p.N40	ENST00000335479.2	37	c.120	CCDS34813.1	8																																																																																			rs138253070	DEFB106B	-	NULL		0.413	DEFB106B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DEFB106B	HGNC	protein_coding	OTTHUMT00000251444.1	0	0		27	27		0.00		A			7340204	-1	8		38		tier1	no_errors	ENST00000335479	ensembl	human	known	74_37	silent	17.39		SNP	0.791	G	8	38
MMS22L	253714	genome.wustl.edu	37	6	97626435	97626435	+	Missense_Mutation	SNP	T	T	G			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr6:97626435T>G	ENST00000275053.4	-	18	2828	c.2563A>C	c.(2563-2565)Aaa>Caa	p.K855Q	MMS22L_ENST00000369251.2_Missense_Mutation_p.K815Q	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	855					double-strand break repair via homologous recombination (GO:0000724)|replication fork processing (GO:0031297)	nuclear replication fork (GO:0043596)				breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						CTTGTCAGTTTGACCAACTGT	0.279													ENSG00000146263																																					0													46.0	48.0	47.0					6																	97626435		2201	4288	6489	SO:0001583	missense	0			-		CCDS5039.1	6q16.3	2010-11-11	2010-11-11	2010-11-11	ENSG00000146263	ENSG00000146263			21475	protein-coding gene	gene with protein product		615614	"""chromosome 6 open reading frame 167"""	C6orf167		21055983, 21055984	Standard	NM_198468		Approved	dJ39B17.2	uc003ppb.3	Q6ZRQ5	OTTHUMG00000015248	ENST00000275053.4:c.2563A>C	6.37:g.97626435T>G	ENSP00000275053:p.Lys855Gln		D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Missense_Mutation	SNP	superfamily_ARM-type_fold	p.K855Q	ENST00000275053.4	37	c.2563	CCDS5039.1	6	.	.	.	.	.	.	.	.	.	.	C	9.172	1.021307	0.19433	.	.	ENSG00000146263	ENST00000275053;ENST00000369251	T;T	0.29917	1.55;1.55	5.87	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.07503	0.0189	N	0.08118	0	0.19300	N	0.999978	B;B	0.14438	0.01;0.01	B;B	0.18561	0.022;0.014	T	0.25363	-1.0134	10	0.42905	T	0.14	-7.5766	15.9117	0.79477	0.0:0.8808:0.0:0.1192	.	815;855	E2QRD4;Q6ZRQ5	.;MMS22_HUMAN	Q	855;815	ENSP00000275053:K855Q;ENSP00000358254:K815Q	ENSP00000275053:K855Q	K	-	1	0	MMS22L	97733156	0.995000	0.38212	0.423000	0.26634	0.091000	0.18340	2.870000	0.48451	0.420000	0.25954	-1.736000	0.00690	AAA	-	MMS22L	-	superfamily_ARM-type_fold		0.279	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MMS22L	HGNC	protein_coding	OTTHUMT00000041573.3	0	0		51	51		0.00		T	NM_198468		97626435	-1	27		30		tier1	no_errors	ENST00000275053	ensembl	human	known	74_37	missense	47.37		SNP	0.895	G	27	30
COL13A1	1305	genome.wustl.edu	37	10	71654434	71654434	+	Missense_Mutation	SNP	C	C	T			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr10:71654434C>T	ENST00000398978.3	+	11	1099	c.607C>T	c.(607-609)Ccc>Tcc	p.P203S	COL13A1_ENST00000398964.3_Missense_Mutation_p.P174S|COL13A1_ENST00000356340.3_Missense_Mutation_p.P203S|COL13A1_ENST00000520133.1_Missense_Mutation_p.P174S|COL13A1_ENST00000357811.3_Missense_Mutation_p.P203S|COL13A1_ENST00000398966.3_Missense_Mutation_p.P203S|COL13A1_ENST00000398969.3_Missense_Mutation_p.P165S|COL13A1_ENST00000522165.1_Missense_Mutation_p.P203S|COL13A1_ENST00000517713.1_Missense_Mutation_p.P203S|COL13A1_ENST00000398974.3_Missense_Mutation_p.P191S|COL13A1_ENST00000398968.3_Missense_Mutation_p.P203S|COL13A1_ENST00000520267.1_Missense_Mutation_p.P165S|COL13A1_ENST00000398973.3_Missense_Mutation_p.P203S|COL13A1_ENST00000398972.3_Missense_Mutation_p.P203S|COL13A1_ENST00000398971.3_Missense_Mutation_p.P203S|COL13A1_ENST00000354547.3_Missense_Mutation_p.P203S	NM_001130103.1	NP_001123575.1			collagen, type XIII, alpha 1											endometrium(5)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	28						TTTGTAGGGACCCCAGGGACA	0.493													ENSG00000197467																																					0													107.0	114.0	112.0					10																	71654434		1871	4107	5978	SO:0001583	missense	0			-	AJ293624	CCDS44419.1, CCDS44423.1, CCDS44424.1, CCDS44425.1, CCDS44427.1, CCDS44428.1, CCDS44423.2, CCDS44424.2, CCDS44425.2, CCDS44427.2, CCDS44428.2	10q22	2013-01-16			ENSG00000197467	ENSG00000197467		"""Collagens"""	2190	protein-coding gene	gene with protein product		120350					Standard	NM_001130103		Approved		uc001jql.3	Q5TAT6	OTTHUMG00000018394	ENST00000398978.3:c.607C>T	10.37:g.71654434C>T	ENSP00000381949:p.Pro203Ser			Missense_Mutation	SNP	pfam_Collagen	p.P203S	ENST00000398978.3	37	c.607	CCDS44419.1	10	.	.	.	.	.	.	.	.	.	.	C	14.76	2.631661	0.46944	.	.	ENSG00000197467	ENST00000398974;ENST00000398971;ENST00000398968;ENST00000398966;ENST00000398964;ENST00000398969;ENST00000356340;ENST00000398972;ENST00000398973;ENST00000398978;ENST00000354547;ENST00000357811;ENST00000520267;ENST00000517713;ENST00000522165;ENST00000520133	D;D;D;D;T;D;D;D;D;D;D;D;D;D;D;D	0.94828	-3.43;-3.43;-3.17;-3.17;1.02;-3.53;-3.43;-3.43;-3.43;-3.43;-3.43;-3.43;-3.53;-3.43;-3.43;-3.53	5.27	5.27	0.74061	.	0.176526	0.41194	D	0.000934	D	0.95661	0.8589	M	0.67700	2.07	0.36908	D	0.890763	B;D;D;B;D;B;B;B;D;B;B;B;B;D;D;B;B;B;D	0.76494	0.021;0.997;0.998;0.23;0.997;0.271;0.149;0.271;0.997;0.271;0.271;0.23;0.23;0.999;0.996;0.123;0.123;0.271;0.996	B;D;D;B;D;B;B;B;D;B;B;B;B;D;D;B;B;B;D	0.87578	0.013;0.995;0.994;0.077;0.995;0.126;0.034;0.126;0.995;0.126;0.126;0.045;0.077;0.998;0.991;0.034;0.034;0.126;0.991	D	0.93665	0.6985	10	0.08599	T	0.76	-3.2368	11.8247	0.52261	0.1749:0.8251:0.0:0.0	.	165;203;203;203;203;203;203;203;191;203;174;203;203;212;203;203;203;174;203	B9EGD2;Q5TAT6;Q5TAT6-5;Q5TAT6-6;E9PEG9;E7ES55;E7ES51;E7ES47;E7ES46;E7ES49;E7EWL8;Q5TAT6-3;Q5TAT6-4;E7EX21;Q5TAT6-7;Q5TAT6-8;Q5TAT6-2;E7ES56;G5E987	.;CODA1_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	S	191;203;203;203;174;165;203;203;203;203;203;203;165;203;203;174	ENSP00000381946:P191S;ENSP00000381943:P203S;ENSP00000381940:P203S;ENSP00000381938:P203S;ENSP00000381936:P174S;ENSP00000381941:P165S;ENSP00000348695:P203S;ENSP00000381944:P203S;ENSP00000381945:P203S;ENSP00000381949:P203S;ENSP00000346553:P203S;ENSP00000350463:P203S;ENSP00000428057:P165S;ENSP00000430061:P203S;ENSP00000428342:P203S;ENSP00000430173:P174S	ENSP00000346553:P203S	P	+	1	0	COL13A1	71324440	0.999000	0.42202	1.000000	0.80357	0.986000	0.74619	2.707000	0.47143	2.627000	0.88993	0.650000	0.86243	CCC	-	COL13A1	-	pfam_Collagen		0.493	COL13A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	COL13A1	HGNC	protein_coding	OTTHUMT00000048468.1	0	0		71	71		0.00		C	NM_005203		71654434	+1	9		78		tier1	no_errors	ENST00000356340	ensembl	human	known	74_37	missense	10.23		SNP	1.000	T	9	78
ELFN2	114794	genome.wustl.edu	37	22	37771877	37771888	+	5'UTR	DEL	CCTCCTCCTCCT	CCTCCTCCTCCT	-	rs553606382|rs142158248|rs111745369	byFrequency	TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	CCTCCTCCTCCT	CCTCCTCCTCCT					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr22:37771877_37771888delCCTCCTCCTCCT	ENST00000402918.2	-	0	472_483				ELFN2_ENST00000435824.1_5'UTR|RP1-63G5.8_ENST00000609322.1_RNA|RP1-63G5.5_ENST00000430883.1_RNA	NM_052906.3	NP_443138.2	Q5R3F8	PPR29_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 2						negative regulation of phosphatase activity (GO:0010923)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	35	Melanoma(58;0.0574)					ACTtcctctccctcctcctcctcctcctcctc	0.637													ENSG00000166897		18	0.00359425	0.0136	0.0	5008	,	,		16480	0.0		0.0	False		,,,				2504	0.0																0																																										SO:0001623	5_prime_UTR_variant	0				BC041596	CCDS33642.1	22q13.1	2013-02-11	2011-10-27	2011-10-27	ENSG00000166897	ENSG00000166897		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"""	29396	protein-coding gene	gene with protein product			"""leucine rich repeat containing 62"", ""extracellular leucine-rich repeat and fibronectin type III containing 2"", ""extracellular leucine-rich repeat and fibronectin type III domain containing 2"", ""protein phosphatase 1, regulatory subunit 29"""	LRRC62, PPP1R29		17868438	Standard	XR_244427		Approved	dJ63G5.3, KIAA1904	uc003asq.4	Q5R3F8	OTTHUMG00000150558	ENST00000402918.2:c.-314AGGAGGAGGAGG>-	22.37:g.37771877_37771888delCCTCCTCCTCCT			Q96PY3	R	DEL	-	NULL	ENST00000402918.2	37	NULL	CCDS33642.1	22																																																																																				ELFN2	-	-		0.637	ELFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ELFN2	HGNC	protein_coding	OTTHUMT00000318900.2									CCTCCTCCTCCT	NM_052906		37771888	-1					tier1	no_errors	ENST00000414347	ensembl	human	known	74_37	rna			DEL	0.043:0.085:0.127:0.169:0.212:0.255:0.522:0.565:0.606:0.646:0.668:0.717	-		
PPP2R1A	5518	genome.wustl.edu	37	19	52715971	52715971	+	Missense_Mutation	SNP	C	C	G			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr19:52715971C>G	ENST00000322088.6	+	5	594	c.536C>G	c.(535-537)cCc>cGc	p.P179R	PPP2R1A_ENST00000444322.2_Missense_Mutation_p.P124R|PPP2R1A_ENST00000462990.1_5'UTR	NM_014225.5	NP_055040.2	P30153	2AAA_HUMAN	protein phosphatase 2, regulatory subunit A, alpha	179	PP2A subunit B binding.|Polyoma small and medium T antigens Binding.|SV40 small T antigen binding.				apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|chromosome segregation (GO:0007059)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|inactivation of MAPK activity (GO:0000188)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|negative regulation of cell growth (GO:0030308)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine dephosphorylation (GO:0070262)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein complex assembly (GO:0006461)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of DNA replication (GO:0006275)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|response to organic substance (GO:0010033)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|second-messenger-mediated signaling (GO:0019932)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	antigen binding (GO:0003823)|protein heterodimerization activity (GO:0046982)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)	p.P179R(21)|p.P179L(5)		NS(1)|breast(4)|cervix(2)|endometrium(62)|kidney(1)|large_intestine(7)|lung(21)|ovary(32)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	135				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)		GATGACACCCCCATGGTGCGG	0.612			Mis		clear cell ovarian carcinoma								ENSG00000105568																												Dom?	yes		19	19q13.41	5518	"""protein phosphatase 2, regulatory subunit A, alpha"""		E	26	Substitution - Missense(26)	endometrium(25)|ovary(1)											61.0	52.0	55.0					19																	52715971		2203	4300	6503	SO:0001583	missense	0			-		CCDS12849.1	19q13	2010-06-18	2010-04-14		ENSG00000105568	ENSG00000105568	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9302	protein-coding gene	gene with protein product	"""protein phosphatase 2A, regulatory subunit A, alpha isoform"", ""protein phosphatase 2, 65kDa regulatory subunit A"""	605983	"""protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), alpha isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit A, alpha isoform"""				Standard	NR_033500		Approved	PR65A, PP2A-Aalpha	uc002pyp.3	P30153	OTTHUMG00000137367	ENST00000322088.6:c.536C>G	19.37:g.52715971C>G	ENSP00000324804:p.Pro179Arg		Q13773|Q6ICQ3|Q96DH3	Missense_Mutation	SNP	pfam_HEAT,superfamily_ARM-type_fold,pfscan_HEAT_type_2	p.P179R	ENST00000322088.6	37	c.536	CCDS12849.1	19	.	.	.	.	.	.	.	.	.	.	C	23.8	4.457832	0.84317	.	.	ENSG00000105568	ENST00000423369;ENST00000391791;ENST00000322088;ENST00000444322	T;T	0.16597	2.33;2.33	4.5	4.5	0.54988	Armadillo-like helical (1);Armadillo-type fold (1);	0.092820	0.45867	D	0.000326	T	0.55226	0.1907	H	0.96239	3.79	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.995;0.995	T	0.70695	-0.4801	10	0.87932	D	0	-22.0504	15.1189	0.72426	0.0:1.0:0.0:0.0	.	124;179;179	F5H3X9;A8K7B7;P30153	.;.;2AAA_HUMAN	R	169;99;179;124	ENSP00000324804:P179R;ENSP00000415067:P124R	ENSP00000324804:P179R	P	+	2	0	PPP2R1A	57407783	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.760000	0.74939	2.503000	0.84419	0.655000	0.94253	CCC	-	PPP2R1A	-	pfam_HEAT,superfamily_ARM-type_fold,pfscan_HEAT_type_2		0.612	PPP2R1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PPP2R1A	HGNC	protein_coding	OTTHUMT00000267967.2	0	0		45	45		0.00		C	NM_014225		52715971	+1	36		37		tier1	no_errors	ENST00000322088	ensembl	human	known	74_37	missense	49.32		SNP	1.000	G	36	37
SRPX	8406	genome.wustl.edu	37	X	38020241	38020242	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	TG	TG					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chrX:38020241_38020242delTG	ENST00000378533.3	-	6	825_826	c.719_720delCA	c.(718-720)acafs	p.T240fs	TM4SF2_ENST00000465127.1_Intron|SRPX_ENST00000544439.1_Frame_Shift_Del_p.T220fs|SRPX_ENST00000538295.1_Frame_Shift_Del_p.T240fs|SRPX_ENST00000343800.6_Frame_Shift_Del_p.T227fs|SRPX_ENST00000479015.1_5'Flank|SRPX_ENST00000432886.2_Frame_Shift_Del_p.T181fs	NM_006307.4	NP_006298.1	P78539	SRPX_HUMAN	sushi-repeat containing protein, X-linked	240	HYR. {ECO:0000255|PROSITE- ProRule:PRU00113}.				autophagy (GO:0006914)|cell adhesion (GO:0007155)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|phagolysosome assembly (GO:0001845)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|response to endoplasmic reticulum stress (GO:0034976)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				autonomic_ganglia(1)|breast(2)|endometrium(5)|large_intestine(5)|lung(10)|prostate(2)	25						TGTCATAGACTGTGTACTGGAT	0.421													ENSG00000101955																																					0																																										SO:0001589	frameshift_variant	0				U78093	CCDS14245.1, CCDS55400.1, CCDS55401.1, CCDS55402.1	Xp21.1	2011-01-25	2011-01-25		ENSG00000101955	ENSG00000101955			11309	protein-coding gene	gene with protein product		300187	"""sushi-repeat-containing protein, X chromosome"", ""sushi-repeat-containing protein, X-linked"""			8634708, 8634709	Standard	NM_006307		Approved	ETX1	uc004ddy.2	P78539	OTTHUMG00000021362	ENST00000378533.3:c.719_720delCA	X.37:g.38020243_38020244delTG	ENSP00000367794:p.Thr240fs		A8K065|B3KWP8|B4DDB8|B4DQH5|F5H4D7|G3V1L0|Q4VX66|Q99652|Q99913	Frame_Shift_Del	DEL	pfam_Hyalin,pfam_Sushi_SCR_CCP,superfamily_Sushi_SCR_CCP,smart_Sushi_SCR_CCP,pfscan_Hyalin,pfscan_Sushi_SCR_CCP	p.T240fs	ENST00000378533.3	37	c.720_719	CCDS14245.1	X																																																																																				SRPX	-	pfam_Hyalin,pfscan_Hyalin		0.421	SRPX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	SRPX	HGNC	protein_coding	OTTHUMT00000056243.1	0	0		48	48		0.00		TG	NM_006307		38020242	-1	27		11		tier1	no_errors	ENST00000378533	ensembl	human	known	74_37	frame_shift_del	71.05		DEL	0.413:0.998	-	27	11
KRAS	3845	genome.wustl.edu	37	12	25380275	25380275	+	Missense_Mutation	SNP	T	T	A	rs17851045		TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr12:25380275T>A	ENST00000256078.4	-	3	246	c.183A>T	c.(181-183)caA>caT	p.Q61H	KRAS_ENST00000311936.3_Missense_Mutation_p.Q61H|KRAS_ENST00000557334.1_Intron|AC087239.1_ENST00000594112.1_5'Flank	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	61			Q -> H (in lung carcinoma; dbSNP:rs17851045). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16533793, ECO:0000269|Ref.7}.|Q -> R (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61H(153)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			TGTACTCCTCTTGACCTGCTG	0.423	Q61H(CL11_LARGE_INTESTINE)|Q61H(HS766T_PANCREAS)|Q61H(NCIH1155_LUNG)|Q61H(NCIH460_LUNG)|Q61H(T3M4_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			ENSG00000133703																									Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)			Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	153	Substitution - Missense(153)	large_intestine(74)|lung(26)|pancreas(18)|haematopoietic_and_lymphoid_tissue(9)|endometrium(7)|soft_tissue(3)|biliary_tract(3)|liver(3)|cervix(2)|skin(2)|kidney(2)|stomach(1)|small_intestine(1)|ovary(1)|NS(1)											109.0	98.0	102.0					12																	25380275		2203	4300	6503	SO:0001583	missense	0	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	-	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.183A>T	12.37:g.25380275T>A	ENSP00000256078:p.Gln61His		A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,pfam_EF_GTP-bd_dom,superfamily_P-loop_NTPase,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,smart_Ran_GTPase,prints_Small_GTPase,tigrfam_Small_GTP-bd_dom	p.Q61H	ENST00000256078.4	37	c.183	CCDS8703.1	12	.	.	.	.	.	.	.	.	.	.	T	22.1	4.243092	0.79912	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	D;D	0.84146	-1.81;-1.81	5.77	5.77	0.91146	Small GTP-binding protein domain (1);	0.049057	0.85682	D	0.000000	D	0.87265	0.6134	M	0.91140	3.18	0.80722	D	1	B;B	0.33413	0.411;0.09	B;B	0.32724	0.092;0.151	D	0.87829	0.2643	10	0.72032	D	0.01	.	9.9836	0.41828	0.0:0.0752:0.0:0.9248	rs17851045	61;61	P01116-2;P01116	.;RASK_HUMAN	H	61	ENSP00000308495:Q61H;ENSP00000256078:Q61H	ENSP00000256078:Q61H	Q	-	3	2	KRAS	25271542	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.240000	0.43088	2.326000	0.78906	0.533000	0.62120	CAA	rs17851045	KRAS	-	pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,pfam_EF_GTP-bd_dom,superfamily_P-loop_NTPase,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,smart_Ran_GTPase,prints_Small_GTPase,tigrfam_Small_GTP-bd_dom		0.423	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	KRAS	HGNC	protein_coding	OTTHUMT00000412232.1	0	0		31	31		0.00		T	NM_033360		25380275	-1	34		21		tier1	no_errors	ENST00000256078	ensembl	human	known	74_37	missense	61.82		SNP	1.000	A	34	21
IQCD	115811	genome.wustl.edu	37	12	113645821	113645821	+	Missense_Mutation	SNP	T	T	C			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr12:113645821T>C	ENST00000416617.2	-	2	341	c.151A>G	c.(151-153)Agg>Ggg	p.R51G	IQCD_ENST00000299732.2_Missense_Mutation_p.R51G|IQCD_ENST00000546692.1_Missense_Mutation_p.R51G			Q96DY2	IQCD_HUMAN	IQ motif containing D	51										endometrium(2)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	12						GACATGATCCTTTTGGCCTCA	0.512													ENSG00000166578																																					0													337.0	306.0	317.0					12																	113645821		2203	4300	6503	SO:0001583	missense	0			-	BC013151	CCDS9167.1	12q24.21	2014-07-18				ENSG00000166578			25168	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 10"""					23427265, 24804578	Standard	NM_138451		Approved	DRC10, CFAP84	uc001tuu.3	Q96DY2		ENST00000416617.2:c.151A>G	12.37:g.113645821T>C	ENSP00000400669:p.Arg51Gly		Q6ZSU0	Missense_Mutation	SNP	pfam_IQ_motif_EF-hand-BS,smart_IQ_motif_EF-hand-BS,pfscan_IQ_motif_EF-hand-BS	p.R51G	ENST00000416617.2	37	c.151		12	.	.	.	.	.	.	.	.	.	.	T	18.05	3.536398	0.65085	.	.	ENSG00000166578	ENST00000299732;ENST00000416617;ENST00000546692;ENST00000392574	T;T;T	0.10382	2.88;2.88;2.88	4.58	3.4	0.38934	.	0.220091	0.38548	N	0.001650	T	0.30166	0.0756	M	0.76328	2.33	0.36600	D	0.87458	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.976	T	0.26780	-1.0093	10	0.87932	D	0	-37.6166	10.344	0.43895	0.0:0.0:0.1656:0.8344	.	51;51	F8VZV9;Q96DY2-2	.;.	G	51	ENSP00000299732:R51G;ENSP00000400669:R51G;ENSP00000446623:R51G	ENSP00000299732:R51G	R	-	1	2	IQCD	112130204	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	2.647000	0.46639	0.760000	0.33108	0.460000	0.39030	AGG	-	IQCD	-	NULL		0.512	IQCD-004	KNOWN	not_organism_supported|basic|appris_candidate_longest	protein_coding	IQCD	HGNC	protein_coding	OTTHUMT00000405327.1	0	0		136	136		0.00		T	NM_138451		113645821	-1	57		225		tier1	no_errors	ENST00000416617	ensembl	human	known	74_37	missense	20.21		SNP	1.000	C	57	225
PKHD1L1	93035	genome.wustl.edu	37	8	110477413	110477413	+	Missense_Mutation	SNP	C	C	G			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr8:110477413C>G	ENST00000378402.5	+	49	8456	c.8352C>G	c.(8350-8352)aaC>aaG	p.N2784K		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	2784					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			ACACACCGAACAAGGCTGGCT	0.413										HNSCC(38;0.096)			ENSG00000205038																																					0													87.0	90.0	89.0					8																	110477413		1953	4134	6087	SO:0001583	missense	0			-	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.8352C>G	8.37:g.110477413C>G	ENSP00000367655:p.Asn2784Lys		Q567P2|Q9UF27	Missense_Mutation	SNP	pfam_IPT,pfam_G8_domain,pfam_PA14,superfamily_Ig_E-set,superfamily_Pectin_lyase_fold/virulence,superfamily_Cupredoxin,smart_IPT,smart_PA14,smart_PbH1	p.N2784K	ENST00000378402.5	37	c.8352	CCDS47911.1	8	.	.	.	.	.	.	.	.	.	.	C	11.35	1.614294	0.28712	.	.	ENSG00000205038	ENST00000378402	D	0.87334	-2.24	5.82	-0.572	0.11745	.	0.000000	0.85682	D	0.000000	D	0.88243	0.6384	M	0.73962	2.25	0.30731	N	0.747204	P	0.41710	0.76	P	0.49597	0.616	D	0.85621	0.1264	10	0.66056	D	0.02	.	9.6703	0.40008	0.0:0.4707:0.0:0.5293	.	2784	Q86WI1	PKHL1_HUMAN	K	2784	ENSP00000367655:N2784K	ENSP00000367655:N2784K	N	+	3	2	PKHD1L1	110546589	1.000000	0.71417	0.720000	0.30636	0.042000	0.13812	1.077000	0.30741	-0.444000	0.07170	-1.028000	0.02416	AAC	-	PKHD1L1	-	NULL		0.413	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PKHD1L1	HGNC	protein_coding	OTTHUMT00000381017.1	0	0		61	61		0.00		C	NM_177531		110477413	+1	40		52		tier1	no_errors	ENST00000378402	ensembl	human	known	74_37	missense	43.48		SNP	1.000	G	40	52
CNTNAP4	85445	genome.wustl.edu	37	16	76509936	76509936	+	Missense_Mutation	SNP	C	C	G			TCGA-IW-A3M5-01A-22D-A21Q-09	TCGA-IW-A3M5-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	03ced0ce-186a-4349-8d98-572c2bc90382	e5aba172-82cb-406e-9841-d2568d14b2fc	g.chr16:76509936C>G	ENST00000476707.1	+	10	1904	c.1765C>G	c.(1765-1767)Cat>Gat	p.H589D	CNTNAP4_ENST00000377504.4_Missense_Mutation_p.H537D|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.H585D|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.H513D|CNTNAP4_ENST00000469589.1_3'UTR			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	586	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)				breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						AGCTACTTGCCATAACTGTAA	0.458													ENSG00000152910																																					0													117.0	103.0	107.0					16																	76509936		2198	4300	6498	SO:0001583	missense	0			-	AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.1765C>G	16.37:g.76509936C>G	ENSP00000417628:p.His589Asp		E9PFZ6|Q86YZ7	Missense_Mutation	SNP	pfam_Laminin_G,pfam_Coagulation_fac_5/8-C_type_dom,superfamily_Galactose-bd-like,superfamily_ConA-like_lec_gl_sf,superfamily_Fibrinogen_a/b/g_C_dom,smart_Coagulation_fac_5/8-C_type_dom,smart_Laminin_G,smart_EG-like_dom,pfscan_EG-like_dom,pfscan_Coagulation_fac_5/8-C_type_dom,pfscan_Laminin_G	p.H585D	ENST00000476707.1	37	c.1753		16	.	.	.	.	.	.	.	.	.	.	C	25.9	4.681822	0.88542	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	T;T;T;T	0.14516	2.5;2.5;2.5;2.5	5.32	5.32	0.75619	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (2);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.41396	D	0.000894	T	0.41949	0.1181	.	.	.	0.80722	D	1	D;D;D;D	0.89917	1.0;0.988;1.0;1.0	D;D;D;D	0.91635	0.994;0.963;0.994;0.999	T	0.29488	-1.0010	9	0.87932	D	0	.	19.1982	0.93698	0.0:1.0:0.0:0.0	.	513;589;561;586	E9PFZ6;E9PDN6;Q96M80;Q9C0A0	.;.;.;CNTP4_HUMAN	D	585;537;513;589	ENSP00000306893:H585D;ENSP00000439733:H537D;ENSP00000418741:H513D;ENSP00000417628:H589D	ENSP00000306893:H585D	H	+	1	0	CNTNAP4	75067437	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.497000	0.81536	2.773000	0.95371	0.655000	0.94253	CAT	-	CNTP4	-	superfamily_Fibrinogen_a/b/g_C_dom,smart_EG-like_dom,pfscan_EG-like_dom		0.458	CNTNAP4-005	PUTATIVE	basic	protein_coding	CNTP4	HGNC	protein_coding	OTTHUMT00000348216.1	0	0		37	37		0.00		C	NM_033401		76509936	+1	10		37		tier1	no_errors	ENST00000307431	ensembl	human	known	74_37	missense	21.28		SNP	1.000	G	10	37
