#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ENSG_ID	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ens_Gene	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GMAF	i_HGNC	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_Normal_Alt_Count	i_Normal_Ref_Count	i_Normal_VAF	i_ORegAnno_bin	i_PurityEst	i_RNA_Tum_Ref_count	i_RNA_Tum_VAF	i_RNA_Tum_Var_count	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Tier	i_Tumor_Alt_Count	i_Tumor_Ref_Count	i_Tumor_VAF	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_WGS_Norm_Ref_count	i_WGS_Norm_VAF	i_WGS_Norm_Var_count	i_WGS_Tum_Ref_count	i_WGS_Tum_VAF	i_WGS_Tum_Var_count	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_deletion_substructures	i_domain	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_rs_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
MICAL3	57553	genome.wustl.edu	37	22	18301218	18301218	+	Silent	SNP	G	G	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr22:18301218G>T	ENST00000441493.2	-	26	4561	c.4209C>A	c.(4207-4209)acC>acA	p.T1403T	MICAL3_ENST00000580469.1_5'Flank	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1403	Pro-rich.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		GGGACCGGGGGGTTGGCAGGG	0.672																																																	0								ENSG00000243156						75.0	86.0	82.0					22																	18301218		1926	4120	6046	MICAL3	SO:0001819	synonymous_variant	0			-	HGNC	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.4209C>A	22.37:g.18301218G>T		Somatic	0	37	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	29	12.12	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_DUF3585,pfam_CH-domain,pfam_CAMSAP_CH,pfam_Znf_LIM,pfam_mOase_FAD-bd,superfamily_CH-domain,smart_CH-domain,smart_Znf_LIM,pfscan_CH-domain,pfscan_Znf_LIM,prints_Rng_hydrolase-like	p.T1403	ENST00000441493.2	37	c.4209	CCDS46659.1	22	.	.	.	.	.	.	.	.	.	.	G	0.016	-1.512906	0.00975	.	.	ENSG00000093100	ENST00000252134	.	.	.	4.42	-5.7	0.02421	.	.	.	.	.	T	0.46795	0.1411	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46816	-0.9164	4	.	.	.	.	5.9118	0.19033	0.5076:0.0:0.2951:0.1973	.	.	.	.	H	385	.	.	P	-	2	0	XXbac-B461K10.4	16681218	0.774000	0.28592	0.003000	0.11579	0.003000	0.03518	-0.156000	0.10100	-1.089000	0.03073	-1.436000	0.01078	CCC	-	NULL		0.672	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	MICAL3	protein_coding	OTTHUMT00000447351.1	G		-		18301218	-1	no_errors	ENST00000441493	ensembl	human	known	74_37	silent	SNP	0.396	T
C1orf177	163747	genome.wustl.edu	37	1	55279609	55279609	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr1:55279609G>T	ENST00000371273.3	+	7	900	c.885G>T	c.(883-885)agG>agT	p.R295S	C1orf177_ENST00000358193.3_Missense_Mutation_p.R295S	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	295										breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						CTACAGAGAGGATTTACTGGG	0.522																																																	0								ENSG00000162398						75.0	80.0	78.0					1																	55279609		2203	4300	6503	C1orf177	SO:0001583	missense	0			-	HGNC	AK097520	CCDS599.1, CCDS44153.1	1p32.3	2012-07-25			ENSG00000162398	ENSG00000162398			26854	protein-coding gene	gene with protein product							Standard	NM_152607		Approved	FLJ40201	uc001cyb.4	Q3ZCV2	OTTHUMG00000009986	ENST00000371273.3:c.885G>T	1.37:g.55279609G>T	ENSP00000360320:p.Arg295Ser	Somatic	0	44	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	33	10.53	B7WPL2|Q8N7Y9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.R295S	ENST00000371273.3	37	c.885	CCDS44153.1	1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.968120	0.53614	.	.	ENSG00000162398	ENST00000358193;ENST00000371273	T;T	0.24350	1.86;1.86	4.98	0.928	0.19443	.	0.000000	0.64402	D	0.000001	T	0.43144	0.1234	M	0.71581	2.175	0.43069	D	0.994702	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.996	T	0.24764	-1.0151	10	0.87932	D	0	-0.5067	6.5195	0.22266	0.4382:0.0:0.5618:0.0	.	295;295	Q3ZCV2;Q3ZCV2-2	CA177_HUMAN;.	S	295	ENSP00000350924:R295S;ENSP00000360320:R295S	ENSP00000350924:R295S	R	+	3	2	C1orf177	55052197	1.000000	0.71417	0.998000	0.56505	0.498000	0.33706	0.717000	0.25851	0.012000	0.14892	0.561000	0.74099	AGG	-	NULL		0.522	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	C1orf177	protein_coding	OTTHUMT00000027674.1	G	NM_152607	-		55279609	+1	no_errors	ENST00000371273	ensembl	human	known	74_37	missense	SNP	0.999	T
ALG1	56052	genome.wustl.edu	37	16	5125535	5125536	+	Frame_Shift_Ins	INS	-	-	GA			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr16:5125535_5125536insGA	ENST00000262374.5	+	4	568_569	c.537_538insGA	c.(538-540)tggfs	p.W180fs	ALG1_ENST00000544428.1_Frame_Shift_Ins_p.W69fs|ALG1_ENST00000588623.1_Frame_Shift_Ins_p.W69fs	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	180					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipopolysaccharide biosynthetic process (GO:0009103)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitobiosyldiphosphodolichol beta-mannosyltransferase activity (GO:0004578)|mannosyltransferase activity (GO:0000030)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(90;0.0164)				TGCTGGCCAAGTGGTGAGAGTC	0.545																																																	0								ENSG00000033011																																			ALG1	SO:0001589	frameshift_variant	0				HGNC	AB019038	CCDS10528.1	16p13.3	2013-02-22	2013-02-22		ENSG00000033011	ENSG00000033011	2.4.1.142	"""Glycosyltransferase group 1 domain containing"""	18294	protein-coding gene	gene with protein product		605907	"""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase)"", ""asparagine-linked glycosylation 1, beta-1,4-mannosyltransferase homolog (S. cerevisiae)"""			10704531	Standard	NM_019109		Approved	HMT-1, HMAT1	uc002cym.3	Q9BT22	OTTHUMG00000129529	Exception_encountered	16.37:g.5125535_5125536insGA	ENSP00000262374:p.Trp180fs	Somatic	0	52	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	40	11.11	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Frame_Shift_Ins	INS	NA	NA	NA	NA	NA	NA	pfam_Glyco_trans_1	p.W179fs	ENST00000262374.5	37	c.537_538	CCDS10528.1	16																																																																																			-	NULL		0.545	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ALG1	protein_coding	OTTHUMT00000251716.2	-	NM_019109			5125536	+1	no_errors	ENST00000262374	ensembl	human	known	74_37	frame_shift_ins	INS	0.998:1.000	GA
NEK1	4750	genome.wustl.edu	37	4	170327851	170327851	+	Silent	SNP	G	G	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr4:170327851G>T	ENST00000439128.2	-	30	3826	c.3186C>A	c.(3184-3186)acC>acA	p.T1062T	NEK1_ENST00000510533.1_Silent_p.T1018T|NEK1_ENST00000512193.1_Silent_p.T993T|NEK1_ENST00000511633.1_Silent_p.T1046T|NEK1_ENST00000507142.1_Silent_p.T1090T	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	1062					cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		CATCCATAAGGGTTCTGAACA	0.328																																																	0								ENSG00000137601						86.0	79.0	81.0					4																	170327851		1823	4087	5910	NEK1	SO:0001819	synonymous_variant	0			-	HGNC	AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"""NIMA (never in mitosis gene a)-related kinase 1"""			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.3186C>A	4.37:g.170327851G>T		Somatic	0	44	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	19	17.39	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	p.T1090	ENST00000439128.2	37	c.3270	CCDS47162.1	4																																																																																			-	NULL		0.328	NEK1-001	KNOWN	basic|CCDS	protein_coding	NEK1	protein_coding	OTTHUMT00000363157.3	G		-		170327851	-1	no_errors	ENST00000507142	ensembl	human	known	74_37	silent	SNP	0.772	T
MTMR10	54893	genome.wustl.edu	37	15	31267168	31267168	+	Silent	SNP	A	A	G			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr15:31267168A>G	ENST00000435680.1	-	4	394	c.297T>C	c.(295-297)gaT>gaC	p.D99D	MTMR10_ENST00000563714.1_Silent_p.D17D|MTMR10_ENST00000314404.8_5'Flank|MTMR10_ENST00000425768.1_Silent_p.D99D	NM_017762.2	NP_060232.2	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	99							phosphatase activity (GO:0016791)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;2.81e-11)		all cancers(64;7.26e-15)|Epithelial(43;7.2e-11)|GBM - Glioblastoma multiforme(186;0.000158)|BRCA - Breast invasive adenocarcinoma(123;0.00426)|Lung(196;0.174)		TTAAAGGGACATCGTGTTCAC	0.318																																																	0								ENSG00000166912						69.0	64.0	65.0					15																	31267168		1832	4077	5909	MTMR10	SO:0001819	synonymous_variant	0			-	HGNC	AK000320	CCDS45204.1	15q13.3	2011-06-09				ENSG00000166912		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	25999	protein-coding gene	gene with protein product						12495846	Standard	NM_017762		Approved	FLJ20313	uc001zfh.1	Q9NXD2		ENST00000435680.1:c.297T>C	15.37:g.31267168A>G		Somatic	0	51	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	21	38	35.59	Q6P4Q6	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Myotubularin_assoc,pfam_Myotubularin-like_Pase_dom	p.D99	ENST00000435680.1	37	c.297	CCDS45204.1	15																																																																																			-	NULL		0.318	MTMR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MTMR10	protein_coding	OTTHUMT00000430747.1	A	NM_017762	-		31267168	-1	no_errors	ENST00000435680	ensembl	human	known	74_37	silent	SNP	1.000	G
TOPBP1	11073	genome.wustl.edu	37	3	133337269	133337269	+	Missense_Mutation	SNP	C	C	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr3:133337269C>T	ENST00000260810.5	-	21	3511	c.3380G>A	c.(3379-3381)cGt>cAt	p.R1127H		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1127					cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						TACTGTCTGACGAGACTGCCT	0.423								Other conserved DNA damage response genes																													Ovarian(21;193 658 4424 15423 17362)												0								ENSG00000163781						136.0	127.0	130.0					3																	133337269		1923	4148	6071	TOPBP1	SO:0001583	missense	0			-	HGNC	AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.3380G>A	3.37:g.133337269C>T	ENSP00000260810:p.Arg1127His	Somatic	0	39	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	19	50	27.14	B7Z7W8|Q7LGC1|Q9UEB9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_BRCT_dom,superfamily_BRCT_dom,superfamily_Secretoglobin,smart_BRCT_dom,pfscan_BRCT_dom	p.R1127H	ENST00000260810.5	37	c.3380	CCDS46919.1	3	.	.	.	.	.	.	.	.	.	.	C	15.17	2.753721	0.49362	.	.	ENSG00000163781	ENST00000260810	T	0.12774	2.65	6.17	5.3	0.74995	.	0.044840	0.85682	D	0.000000	T	0.13543	0.0328	L	0.45137	1.4	0.53688	D	0.999973	B;B	0.27192	0.171;0.171	B;B	0.20184	0.023;0.028	T	0.02404	-1.1164	10	0.39692	T	0.17	.	15.01	0.71542	0.0:0.9327:0.0:0.0673	.	1040;1127	A0AV47;Q92547	.;TOPB1_HUMAN	H	1127	ENSP00000260810:R1127H	ENSP00000260810:R1127H	R	-	2	0	TOPBP1	134819959	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	4.430000	0.59907	2.941000	0.99782	0.655000	0.94253	CGT	-	NULL		0.423	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TOPBP1	protein_coding	OTTHUMT00000357254.1	C	NM_007027	-		133337269	-1	no_errors	ENST00000260810	ensembl	human	known	74_37	missense	SNP	1.000	T
CRLF3	51379	genome.wustl.edu	37	17	29124397	29124397	+	Silent	SNP	A	A	G			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr17:29124397A>G	ENST00000324238.6	-	3	481	c.357T>C	c.(355-357)ggT>ggC	p.G119G	CRLF3_ENST00000577725.1_Intron|CRLF3_ENST00000544695.1_Silent_p.G3G	NM_015986.3	NP_057070.3	Q8IUI8	CRLF3_HUMAN	cytokine receptor-like factor 3	119					G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of cell growth (GO:0030308)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	17		all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)				CTCCCACACCACCAAGCATGG	0.408																																					Pancreas(30;346 881 29244 33464 41299)												0								ENSG00000176390						121.0	106.0	112.0					17																	29124397		2203	4300	6503	CRLF3	SO:0001819	synonymous_variant	0			-	HGNC	AF120151	CCDS32607.1	17q11.2	2008-05-02				ENSG00000176390			17177	protein-coding gene	gene with protein product		614853					Standard	NM_015986		Approved	CREME9, CYTOR4	uc002hfr.4	Q8IUI8		ENST00000324238.6:c.357T>C	17.37:g.29124397A>G		Somatic	0	37	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	36	9.76	A6NJF3|B2R8C3|Q2MLY7|Q9UNI3|Q9Y6M8	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.V50A	ENST00000324238.6	37	c.149	CCDS32607.1	17																																																																																			-	NULL		0.408	CRLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CRLF3	protein_coding	OTTHUMT00000444354.1	A		-		29124397	-1	no_errors	ENST00000578692	ensembl	human	known	74_37	missense	SNP	0.980	G
CXCL14	9547	genome.wustl.edu	37	5	134914193	134914193	+	Missense_Mutation	SNP	A	A	G			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr5:134914193A>G	ENST00000337225.5	-	2	601	c.137T>C	c.(136-138)aTc>aCc	p.I46T	CTC-321K16.1_ENST00000514446.1_RNA|CXCL14_ENST00000512158.1_Missense_Mutation_p.I34T|CTC-321K16.1_ENST00000509372.1_RNA	NM_004887.4	NP_004878.2	O95715	CXL14_HUMAN	chemokine (C-X-C motif) ligand 14	46					cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inner ear development (GO:0048839)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	chemokine activity (GO:0008009)			large_intestine(2)|lung(2)|prostate(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GCTGTAGCGGATCTTGGGTCC	0.597																																																	0								ENSG00000145824						148.0	139.0	142.0					5																	134914193		2203	4300	6503	CXCL14	SO:0001583	missense	0			-	HGNC	AF073957	CCDS4188.1	5q31	2010-04-30	2002-08-22	2002-08-23	ENSG00000145824	ENSG00000145824			10640	protein-coding gene	gene with protein product	"""breast and kidney"""	604186	"""small inducible cytokine subfamily B (Cys-X-Cys), member 14 (BRAK)"""	SCYB14		10049774	Standard	NM_004887		Approved	BRAK, NJAC, bolekine, Kec, MIP-2g, BMAC, KS1	uc003lay.3	O95715	OTTHUMG00000129139	ENST00000337225.5:c.137T>C	5.37:g.134914193A>G	ENSP00000337065:p.Ile46Thr	Somatic	0	62	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	26	102	20.31	B3KQU8|Q6UW97|Q86U69|Q9BTR1|Q9NS21	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Chemokine_IL8-like_dom,superfamily_Chemokine_IL8-like_dom	p.I46T	ENST00000337225.5	37	c.137	CCDS4188.1	5	.	.	.	.	.	.	.	.	.	.	A	26.3	4.724197	0.89298	.	.	ENSG00000145824	ENST00000337225;ENST00000512158	T;T	0.09073	3.02;3.02	5.12	5.12	0.69794	Chemokine interleukin-8-like domain (2);	0.000000	0.85682	D	0.000000	T	0.27731	0.0682	M	0.69823	2.125	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.01356	-1.1376	10	0.87932	D	0	1.3637	13.4744	0.61299	1.0:0.0:0.0:0.0	.	46	O95715	CXL14_HUMAN	T	46;34	ENSP00000337065:I46T;ENSP00000423783:I34T	ENSP00000337065:I46T	I	-	2	0	CXCL14	134942092	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.026000	0.88783	1.927000	0.55829	0.482000	0.46254	ATC	-	pfam_Chemokine_IL8-like_dom,superfamily_Chemokine_IL8-like_dom		0.597	CXCL14-201	KNOWN	basic|appris_principal|CCDS	protein_coding	CXCL14	protein_coding		A	NM_004887	-		134914193	-1	no_errors	ENST00000337225	ensembl	human	known	74_37	missense	SNP	1.000	G
ALG1	56052	genome.wustl.edu	37	16	5125537	5125538	+	Splice_Site	INS	-	-	A			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr16:5125537_5125538insA	ENST00000262374.5	+	4	570	c.539_539insA	c.(538-540)tgg>tAgg	p.W180fs	ALG1_ENST00000544428.1_Splice_Site_p.W69fs|ALG1_ENST00000588623.1_Splice_Site_p.W69fs	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	180					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipopolysaccharide biosynthetic process (GO:0009103)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitobiosyldiphosphodolichol beta-mannosyltransferase activity (GO:0004578)|mannosyltransferase activity (GO:0000030)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(90;0.0164)				CTGGCCAAGTGGTGAGAGTCTA	0.545																																																	0								ENSG00000033011																																			ALG1	SO:0001630	splice_region_variant	0				HGNC	AB019038	CCDS10528.1	16p13.3	2013-02-22	2013-02-22		ENSG00000033011	ENSG00000033011	2.4.1.142	"""Glycosyltransferase group 1 domain containing"""	18294	protein-coding gene	gene with protein product		605907	"""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase)"", ""asparagine-linked glycosylation 1, beta-1,4-mannosyltransferase homolog (S. cerevisiae)"""			10704531	Standard	NM_019109		Approved	HMT-1, HMAT1	uc002cym.3	Q9BT22	OTTHUMG00000129529	ENST00000262374.5:c.539+1->A	16.37:g.5125537_5125538insA		Somatic	0	49	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	39	11.36	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Frame_Shift_Ins	INS	NA	NA	NA	NA	NA	NA	pfam_Glyco_trans_1	p.W180fs	ENST00000262374.5	37	c.539_540	CCDS10528.1	16																																																																																			-	NULL		0.545	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ALG1	protein_coding	OTTHUMT00000251716.2	-	NM_019109		Frame_Shift_Ins	5125538	+1	no_errors	ENST00000262374	ensembl	human	known	74_37	frame_shift_ins	INS	1.000:1.000	A
PKMYT1	9088	genome.wustl.edu	37	16	3026988	3026988	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr16:3026988G>T	ENST00000262300.8	-	3	563	c.55C>A	c.(55-57)Cca>Aca	p.P19T	PKMYT1_ENST00000574730.1_Intron|PKMYT1_ENST00000573944.1_Missense_Mutation_p.P10T|PKMYT1_ENST00000574385.1_Missense_Mutation_p.P10T|PKMYT1_ENST00000440027.2_Missense_Mutation_p.P19T|PKMYT1_ENST00000431515.2_Missense_Mutation_p.P19T	NM_001258450.1|NM_004203.4|NM_182687.2	NP_001245379.1|NP_004194.3|NP_872629.1	Q99640	PMYT1_HUMAN	protein kinase, membrane associated tyrosine/threonine 1	19	Pro-rich.				G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						CTCAGAGGTGGCGGGGTGCCC	0.667																																																	0								ENSG00000127564						11.0	13.0	12.0					16																	3026988		2185	4273	6458	PKMYT1	SO:0001583	missense	0			-	HGNC	AK097642	CCDS10486.1, CCDS45391.1, CCDS58414.1, CCDS58415.1	16p13.3	2014-06-13			ENSG00000127564	ENSG00000127564			29650	protein-coding gene	gene with protein product	"""membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase"", ""protein phosphatase 1, regulatory subunit 126"""	602474				9001210, 12606722	Standard	NM_004203		Approved	MYT1, PPP1R126	uc002csn.3	Q99640	OTTHUMG00000128975	ENST00000262300.8:c.55C>A	16.37:g.3026988G>T	ENSP00000262300:p.Pro19Thr	Somatic	0	51	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	36	10.00	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pirsf_Tyr/Thr_kinase_Cdc2_inhib,pfscan_Prot_kinase_dom	p.P19T	ENST00000262300.8	37	c.55	CCDS10486.1	16	.	.	.	.	.	.	.	.	.	.	G	11.22	1.573717	0.28092	.	.	ENSG00000127564	ENST00000431515;ENST00000262300;ENST00000440027;ENST00000402679;ENST00000382240	T;T;T;T	0.61510	0.1;0.18;0.19;0.24	5.68	5.68	0.88126	.	0.067088	0.64402	D	0.000019	T	0.46718	0.1407	L	0.43152	1.355	0.35836	D	0.82566	B;P;P	0.43750	0.402;0.816;0.537	B;B;B	0.35470	0.1;0.152;0.203	T	0.56360	-0.7992	10	0.25106	T	0.35	-13.5316	15.2906	0.73862	0.0:0.0:1.0:0.0	.	10;19;19	A6NHV6;Q99640;F8W164	.;PMYT1_HUMAN;.	T	19;19;19;19;10	ENSP00000392855:P19T;ENSP00000262300:P19T;ENSP00000397739:P19T;ENSP00000371675:P10T	ENSP00000262300:P19T	P	-	1	0	PKMYT1	2966989	0.803000	0.28956	0.664000	0.29753	0.232000	0.25224	1.259000	0.32956	2.666000	0.90696	0.655000	0.94253	CCA	-	pirsf_Tyr/Thr_kinase_Cdc2_inhib		0.667	PKMYT1-001	KNOWN	basic|CCDS	protein_coding	PKMYT1	protein_coding	OTTHUMT00000250963.2	G	NM_004203	-		3026988	-1	no_errors	ENST00000262300	ensembl	human	known	74_37	missense	SNP	0.802	T
RGL3	57139	genome.wustl.edu	37	19	11526773	11526773	+	Silent	SNP	G	G	A			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr19:11526773G>A	ENST00000380456.3	-	5	540	c.477C>T	c.(475-477)ttC>ttT	p.F159F	RGL3_ENST00000393423.3_Silent_p.F159F	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	159	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(1)|skin(1)	18						GGGGGTCTCGGAAATCCTGAG	0.637																																					GBM(174;751 2067 17998 27979 33959)												0								ENSG00000205517						22.0	26.0	24.0					19																	11526773		2203	4300	6503	RGL3	SO:0001819	synonymous_variant	0			-	HGNC	BC014426	CCDS32910.1, CCDS54221.1	19p13.2	2008-02-05				ENSG00000205517			30282	protein-coding gene	gene with protein product						10869344	Standard	NM_001035223		Approved	FLJ32585	uc002mro.2	Q3MIN7		ENST00000380456.3:c.477C>T	19.37:g.11526773G>A		Somatic	0	19	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	9	17	34.62	B5ME84|B7ZL22|Q0P6G0	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	superfamily_Ras_GEF_dom,pfscan_Ras-like_Gua-exchang_fac_N	p.P158S	ENST00000380456.3	37	c.472	CCDS32910.1	19																																																																																			-	pfscan_Ras-like_Gua-exchang_fac_N		0.637	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RGL3	protein_coding	OTTHUMT00000421208.3	G	XM_290867	-		11526773	-1	no_errors	ENST00000563726	ensembl	human	known	74_37	missense	SNP	0.981	A
LRRC75A	388341	genome.wustl.edu	37	17	16344167	16344167	+	IGR	DEL	A	A	-	rs112317984|rs555182592	byFrequency	TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr17:16344167delA	ENST00000409083.3	-	0	2656				C17orf76-AS1_ENST00000487066.1_RNA|RP11-138I1.3_ENST00000585048.1_lincRNA|C17orf76-AS1_ENST00000580180.1_RNA|C17orf76-AS1_ENST00000365172.1_RNA|C17orf76-AS1_ENST00000581913.1_RNA|C17orf76-AS1_ENST00000478103.2_RNA|C17orf76-AS1_ENST00000484836.1_RNA|C17orf76-AS1_ENST00000391079.1_RNA|C17orf76-AS1_ENST00000477249.2_RNA|C17orf76-AS1_ENST00000492250.1_RNA|C17orf76-AS1_ENST00000583400.2_RNA|C17orf76-AS1_ENST00000475947.2_RNA|C17orf76-AS1_ENST00000475953.1_RNA|C17orf76-AS1_ENST00000581718.1_RNA|C17orf76-AS1_ENST00000384229.1_RNA|C17orf76-AS1_ENST00000584926.1_RNA|C17orf76-AS1_ENST00000472367.1_RNA|C17orf76-AS1_ENST00000481027.1_RNA|C17orf76-AS1_ENST00000460249.1_RNA|C17orf76-AS1_ENST00000580770.1_RNA|C17orf76-AS1_ENST00000480811.1_RNA|C17orf76-AS1_ENST00000584141.1_RNA|C17orf76-AS1_ENST00000584177.1_RNA|C17orf76-AS1_ENST00000579473.1_RNA|C17orf76-AS1_ENST00000470491.2_RNA|C17orf76-AS1_ENST00000481898.1_RNA|C17orf76-AS1_ENST00000582911.1_RNA|C17orf76-AS1_ENST00000578380.2_RNA|C17orf76-AS1_ENST00000483140.1_RNA|C17orf76-AS1_ENST00000491009.1_RNA	NM_207387.3	NP_997270.2														lung(1)	1						actccatctcaaaaaaaaaaa	0.413																																																	0								ENSG00000266651																																			RP11-138I1.3	SO:0001628	intergenic_variant	0				Clone_based_vega_gene																													17.37:g.16344167delA		Somatic	0	10	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	2	6	25.00		RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000409083.3	37	NULL	CCDS11178.2	17																																																																																			-	-		0.413	FAM211A-001	NOVEL	basic|exp_conf|CCDS	protein_coding	ENSG00000266651	protein_coding	OTTHUMT00000130461.2	A				16344167	-1	no_errors	ENST00000585048	ensembl	human	known	74_37	rna	DEL	0.000	-
SNORD3B-1	26851	genome.wustl.edu	37	17	18967152	18967152	+	lincRNA	SNP	C	C	T	rs560553456|rs62068862	byFrequency	TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr17:18967152C>T	ENST00000363359.1	+	0	432				SNORD3B-2_ENST00000364880.1_lincRNA					small nucleolar RNA, C/D box 3B-1																		TCTCGCTACACTGCCAAGCAG	0.542													-|||	2248	0.448882	0.6619	0.3444	5008	,	,		11923	0.4405		0.339	False		,,,				2504	0.3569																0								ENSG00000262074																																			SNORD3B-2			0			-	HGNC	AF020534, AF020533, AF020532		17p11.2	2013-09-05	2006-11-28	2006-11-28	ENSG00000200229	ENSG00000265185			10168	non-coding RNA	RNA, small nucleolar			"""RNA, U3A1 small nucleolar, RNA, U3A1 small nucleolar"""	RNU3A1		9365252	Standard	NR_003271		Approved	U3a, U3b1, U3b2					17.37:g.18967152C>T		Somatic	0	104	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	31	13.89		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000363359.1	37	NULL		17																																																																																			-	-		0.542	SNORD3B-1-201	KNOWN	basic	snoRNA	SNORD3B-2	lincRNA		C	NR_003271	rs116902881		18967152	-1	no_errors	ENST00000571722	ensembl	human	known	74_37	rna	SNP	0.000	T
PHACTR4	65979	genome.wustl.edu	37	1	28785730	28785730	+	Frame_Shift_Del	DEL	A	A	-	rs550399400		TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr1:28785730delA	ENST00000373839.3	+	3	412	c.151delA	c.(151-153)aaafs	p.K53fs	PHACTR4_ENST00000493669.1_3'UTR|PHACTR4_ENST00000373836.3_Frame_Shift_Del_p.K63fs	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	53					actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)	p.S64fs*12(3)		NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		GAAATGGAGGAAAAAAAAAAG	0.393																																																	3	Deletion - Frameshift(3)	ovary(2)|breast(1)						ENSG00000204138		,	74,3472		1,72,1700	69.0	66.0	67.0		,	4.4	1.0	1		71	172,7652		3,166,3743	no	frameshift,frameshift	PHACTR4	NM_023923.3,NM_001048183.1	,	4,238,5443	A1A1,A1R,RR		2.1984,2.0869,2.1636	,	,	28785730	246,11124	1842	4093	5935	PHACTR4	SO:0001589	frameshift_variant	0				HGNC	AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"""Phosphatase and actin regulators"""	25793	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 124"""	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.151delA	1.37:g.28785730delA	ENSP00000362945:p.Lys53fs	Somatic	0	21	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	29	9.38	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_RPEL_repeat,smart_RPEL_repeat,pfscan_RPEL_repeat	p.S64fs	ENST00000373839.3	37	c.181	CCDS41293.1	1																																																																																			-	NULL		0.393	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	PHACTR4	protein_coding	OTTHUMT00000009868.4	A	NM_023923			28785730	+1	no_errors	ENST00000373836	ensembl	human	known	74_37	frame_shift_del	DEL	1.000	-
C9	735	genome.wustl.edu	37	5	39288847	39288847	+	Silent	SNP	G	G	A			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr5:39288847G>A	ENST00000263408.4	-	10	1718	c.1623C>T	c.(1621-1623)atC>atT	p.I541I		NM_001737.3	NP_001728.1	P02748	CO9_HUMAN	complement component 9	541					complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|hemolysis by symbiont of host erythrocytes (GO:0019836)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane attack complex (GO:0005579)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	32	all_lung(31;0.000197)	all_neural(839;7.57e-10)|Lung NSC(810;2.62e-08)|Ovarian(839;0.00384)|Breast(839;0.0184)|Myeloproliferative disorder(839;0.0511)	Epithelial(62;0.158)			TTTGTTTACTGATTTCACAGG	0.358																																																	0								ENSG00000113600						116.0	111.0	113.0					5																	39288847		2203	4300	6503	C9	SO:0001819	synonymous_variant	0			-	HGNC		CCDS3929.1	5p14-p12	2014-09-17			ENSG00000113600	ENSG00000113600		"""Complement system"""	1358	protein-coding gene	gene with protein product		120940					Standard	NM_001737		Approved		uc003jlv.4	P02748	OTTHUMG00000094767	ENST00000263408.4:c.1623C>T	5.37:g.39288847G>A		Somatic	0	35	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	11	71	13.41		Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_MACPF,pfam_LDrepeatLR_classA_rpt,pfam_Thrombospondin_1_rpt,superfamily_Thrombospondin_1_rpt,superfamily_LDrepeatLR_classA_rpt,smart_Thrombospondin_1_rpt,smart_LDrepeatLR_classA_rpt,smart_MACPF,prints_MAC_perforin,pfscan_LDrepeatLR_classA_rpt,pfscan_Thrombospondin_1_rpt	p.I541	ENST00000263408.4	37	c.1623	CCDS3929.1	5																																																																																			-	NULL		0.358	C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C9	protein_coding	OTTHUMT00000211576.3	G		-		39288847	-1	no_errors	ENST00000263408	ensembl	human	known	74_37	silent	SNP	0.001	A
PLEKHG2	64857	genome.wustl.edu	37	19	39908220	39908220	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr19:39908220G>T	ENST00000409794.3	+	8	1620	c.770G>T	c.(769-771)gGc>gTc	p.G257V	PLEKHG2_ENST00000378550.1_Missense_Mutation_p.G257V|PLEKHG2_ENST00000458508.2_Missense_Mutation_p.G198V|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.G257V|PLEKHG2_ENST00000409797.2_Missense_Mutation_p.G257V	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	257	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.G257D(1)|p.G215D(1)		breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			TGGGCGGAGGGCCCAGGCACT	0.572																																																	2	Substitution - Missense(2)	skin(2)						ENSG00000090924						59.0	52.0	54.0					19																	39908220		2203	4300	6503	PLEKHG2	SO:0001583	missense	0			-	HGNC	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.770G>T	19.37:g.39908220G>T	ENSP00000386733:p.Gly257Val	Somatic	0	31	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	31	11.43	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_DH-domain,superfamily_DH-domain,smart_DH-domain,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology,pfscan_DH-domain	p.G257V	ENST00000409794.3	37	c.770	CCDS33022.2	19	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.53|12.53	1.965871|1.965871	0.34659|0.34659	.|.	.|.	ENSG00000090924|ENSG00000090924	ENST00000205135|ENST00000409794;ENST00000425673;ENST00000378550;ENST00000458508;ENST00000409797	.|T;T;T;T;T	.|0.72051	.|-0.31;-0.27;-0.62;-0.42;-0.62	4.68|4.68	4.68|4.68	0.58851|0.58851	.|Dbl homology (DH) domain (5);	.|0.000000	.|0.46442	.|D	.|0.000294	T|T	0.79358|0.79358	0.4432|0.4432	L|L	0.48877|0.48877	1.53|1.53	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D;D;B	.|0.89917	.|0.993;1.0;0.995;0.057	.|D;D;D;B	.|0.91635	.|0.97;0.999;0.976;0.113	T|T	0.80243|0.80243	-0.1463|-0.1463	5|10	.|0.59425	.|D	.|0.04	.|.	14.9813|14.9813	0.71313|0.71313	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|257;257;198;257	.|Q9H7P9-3;Q9H7P9;E7ESZ3;Q9H7P9-2	.|.;PKHG2_HUMAN;.;.	S|V	154|257;257;257;198;257	.|ENSP00000386733:G257V;ENSP00000392906:G257V;ENSP00000367812:G257V;ENSP00000408857:G198V;ENSP00000386492:G257V	.|ENSP00000367812:G257V	A|G	+|+	1|2	0|0	PLEKHG2|PLEKHG2	44600060|44600060	0.892000|0.892000	0.30473|0.30473	0.999000|0.999000	0.59377|0.59377	0.169000|0.169000	0.22640|0.22640	1.098000|1.098000	0.31000|0.31000	2.609000|2.609000	0.88269|0.88269	0.561000|0.561000	0.74099|0.74099	GCC|GGC	-	pfam_DH-domain,superfamily_DH-domain,smart_DH-domain,pfscan_DH-domain		0.572	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLEKHG2	protein_coding	OTTHUMT00000326802.1	G	NM_022835	-		39908220	+1	no_errors	ENST00000409794	ensembl	human	known	74_37	missense	SNP	0.998	T
NFATC2	4773	genome.wustl.edu	37	20	50049142	50049142	+	Missense_Mutation	SNP	G	G	C			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr20:50049142G>C	ENST00000396009.3	-	9	2403	c.2184C>G	c.(2182-2184)tgC>tgG	p.C728W	NFATC2_ENST00000609943.1_Missense_Mutation_p.C708W|NFATC2_ENST00000610033.1_Missense_Mutation_p.C509W|NFATC2_ENST00000371564.3_Missense_Mutation_p.C728W|NFATC2_ENST00000609507.1_Missense_Mutation_p.C509W|NFATC2_ENST00000414705.1_Missense_Mutation_p.C708W	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	728					B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					GGAACTGCTGGCAGGGAGCCA	0.692																																																	0								ENSG00000101096						22.0	27.0	26.0					20																	50049142		2201	4298	6499	NFATC2	SO:0001583	missense	0			-	HGNC	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"""Nuclear factor of activated T-cells"""	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.2184C>G	20.37:g.50049142G>C	ENSP00000379330:p.Cys728Trp	Somatic	0	136	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	16	111	12.60	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_RHD,pfam_IPT,superfamily_p53-like_TF_DNA-bd,superfamily_Ig_E-set,smart_IPT,pfscan_RHD,prints_NFAT	p.C728W	ENST00000396009.3	37	c.2184	CCDS13437.1	20	.	.	.	.	.	.	.	.	.	.	G	17.84	3.487428	0.63962	.	.	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000414705	T;T;T	0.22945	1.93;1.94;1.97	5.31	5.31	0.75309	.	0.096682	0.64402	D	0.000001	T	0.47116	0.1428	M	0.64170	1.965	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.85130	0.985;0.993;0.997;0.986	T	0.43750	-0.9372	10	0.72032	D	0.01	-20.9615	12.347	0.55126	0.0769:0.0:0.9231:0.0	.	708;708;728;728	B5B2N9;B5B2P2;Q13469;B5B2N8	.;.;NFAC2_HUMAN;.	W	728;728;708	ENSP00000360619:C728W;ENSP00000379330:C728W;ENSP00000396471:C708W	ENSP00000360619:C728W	C	-	3	2	NFATC2	49482549	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.619000	0.61218	2.494000	0.84150	0.555000	0.69702	TGC	-	NULL		0.692	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NFATC2	protein_coding	OTTHUMT00000079730.2	G	NM_012340	-		50049142	-1	no_errors	ENST00000396009	ensembl	human	known	74_37	missense	SNP	1.000	C
ABCA13	154664	genome.wustl.edu	37	7	48684278	48684278	+	Silent	SNP	C	C	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr7:48684278C>T	ENST00000435803.1	+	61	15033	c.15009C>T	c.(15007-15009)ttC>ttT	p.F5003F	ABCA13_ENST00000544596.1_Silent_p.F733F	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	5003					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CTGACTTGTTCAAAGTTATAG	0.323																																																	0								ENSG00000179869						69.0	71.0	70.0					7																	48684278		1832	4082	5914	ABCA13	SO:0001819	synonymous_variant	0			-	HGNC	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.15009C>T	7.37:g.48684278C>T		Somatic	0	27	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	18	14.29	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_ABC_transporter-like,superfamily_P-loop_NTPase,smart_AAA+_ATPase,pfscan_ABC_transporter-like	p.F5003	ENST00000435803.1	37	c.15009	CCDS47584.1	7																																																																																			-	NULL		0.323	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ABCA13	protein_coding	OTTHUMT00000341964.2	C	NM_152701	-		48684278	+1	no_errors	ENST00000435803	ensembl	human	known	74_37	silent	SNP	1.000	T
C1orf35	79169	genome.wustl.edu	37	1	228288708	228288709	+	3'UTR	INS	-	-	A			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr1:228288708_228288709insA	ENST00000272139.4	-	0	1149_1150				C1orf35_ENST00000472617.1_5'UTR	NM_024319.2	NP_077295.1	Q9BU76	MMTA2_HUMAN	chromosome 1 open reading frame 35								poly(A) RNA binding (GO:0044822)			large_intestine(1)|lung(1)|skin(1)	3		Prostate(94;0.0488)				GGCTGGTGCCCAGAGCCACTTC	0.614																																																	0								ENSG00000143793																																			C1orf35	SO:0001624	3_prime_UTR_variant	0				HGNC	AY137773	CCDS1566.1	1q42.13	2012-06-25			ENSG00000143793	ENSG00000143793			19032	protein-coding gene	gene with protein product	"""multiple myeloma tumor-associated protein 2"""					12545221	Standard	NM_024319		Approved	MGC4174, MMTAG2	uc001hrx.3	Q9BU76	OTTHUMG00000037793	ENST00000272139.4:c.*124->T	1.37:g.228288709_228288709dupA		Somatic	0	40	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	6	28	17.65	Q6P5Y0|Q6ZTZ6|Q6ZWA6|Q8IZH3	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000272139.4	37	NULL	CCDS1566.1	1																																																																																			-	-		0.614	C1orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C1orf35	protein_coding	OTTHUMT00000092245.1	-	NM_024319			228288709	-1	no_errors	ENST00000469781	ensembl	human	known	74_37	rna	INS	0.000:0.001	A
ACTR6	64431	genome.wustl.edu	37	12	100613903	100613903	+	Missense_Mutation	SNP	T	T	C			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr12:100613903T>C	ENST00000188312.2	+	10	1805	c.1040T>C	c.(1039-1041)gTt>gCt	p.V347A	ACTR6_ENST00000551617.1_Missense_Mutation_p.V245A|ACTR6_ENST00000546902.1_Missense_Mutation_p.V265A|ACTR6_ENST00000552376.1_Missense_Mutation_p.V327A	NM_022496.4	NP_071941.1	Q9GZN1	ARP6_HUMAN	ARP6 actin-related protein 6 homolog (yeast)	347						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	14						GATTATGATGTTTCTGTTGTG	0.383																																																	0								ENSG00000075089						145.0	133.0	137.0					12																	100613903		2203	4300	6503	ACTR6	SO:0001583	missense	0			-	HGNC	AF212251	CCDS9074.1	12q23.1	2012-07-09			ENSG00000075089	ENSG00000075089			24025	protein-coding gene	gene with protein product						11368909	Standard	NM_022496		Approved	ARP6, FLJ13433	uc001thb.2	Q9GZN1	OTTHUMG00000170245	ENST00000188312.2:c.1040T>C	12.37:g.100613903T>C	ENSP00000188312:p.Val347Ala	Somatic	0	33	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	22	23	48.89	B3KW37|B4DLG9|Q53GH2|Q9BY39|Q9H8H6	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Actin-related,smart_Actin-related	p.V347A	ENST00000188312.2	37	c.1040	CCDS9074.1	12	.	.	.	.	.	.	.	.	.	.	T	28.8	4.952410	0.92660	.	.	ENSG00000075089	ENST00000188312;ENST00000546902;ENST00000552376;ENST00000551617	D;D;T;T	0.95447	-3.71;-3.71;3.0;3.0	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	D	0.97660	0.9233	M	0.82323	2.585	0.80722	D	1	D;D;D;D	0.64830	0.992;0.992;0.992;0.994	P;P;D;D	0.67900	0.874;0.874;0.923;0.954	D	0.98344	1.0540	10	0.87932	D	0	.	16.4237	0.83790	0.0:0.0:0.0:1.0	.	265;245;327;347	G3V1Y1;F8VSD1;F8W057;Q9GZN1	.;.;.;ARP6_HUMAN	A	347;265;327;245	ENSP00000188312:V347A;ENSP00000448669:V265A;ENSP00000447237:V327A;ENSP00000448356:V245A	ENSP00000188312:V347A	V	+	2	0	ACTR6	99138034	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.417000	0.80156	2.279000	0.76181	0.533000	0.62120	GTT	-	pfam_Actin-related,smart_Actin-related		0.383	ACTR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ACTR6	protein_coding	OTTHUMT00000408159.1	T	NM_022496	-		100613903	+1	no_errors	ENST00000188312	ensembl	human	known	74_37	missense	SNP	1.000	C
NEK10	152110	genome.wustl.edu	37	3	27393955	27393955	+	Splice_Site	SNP	C	C	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr3:27393955C>T	ENST00000429845.2	-	4	495		c.e4+1		NEK10_ENST00000341435.5_Splice_Site			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10						positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						GAAAACGCTACCTGTTGTTTG	0.368																																																	0								ENSG00000163491						140.0	117.0	124.0					3																	27393955		1568	3582	5150	NEK10	SO:0001630	splice_region_variant	0			-	HGNC	AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)- related kinase 10"""			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.132+1G>A	3.37:g.27393955C>T		Somatic	0	25	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	12	7	63.16	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Splice_Site	SNP	NA	NA	NA	NA	NA	NA	-	e2+1	ENST00000429845.2	37	c.132+1		3	.	.	.	.	.	.	.	.	.	.	C	21.7	4.190036	0.78789	.	.	ENSG00000163491	ENST00000341435;ENST00000396636;ENST00000435750;ENST00000429845	.	.	.	5.95	5.95	0.96441	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1584	0.89701	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NEK10	27368959	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	4.829000	0.62737	2.825000	0.97269	0.655000	0.94253	.	-	-		0.368	NEK10-016	NOVEL	basic|appris_principal	protein_coding	NEK10	protein_coding	OTTHUMT00000438156.1	C	NM_152534	-	Intron	27393955	-1	no_errors	ENST00000341435	ensembl	human	known	74_37	splice_site	SNP	1.000	T
POLG	5428	genome.wustl.edu	37	15	89876827	89876828	+	In_Frame_Ins	INS	-	-	TGC	rs527965158|rs369920352|rs41550117|rs587781118|rs59510277	byFrequency	TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr15:89876827_89876828insTGC	ENST00000268124.5	-	2	491_492	c.158_159insGCA	c.(157-159)caa>caGCAa	p.53_53Q>QQ	POLG_ENST00000442287.2_In_Frame_Ins_p.53_53Q>QQ|POLG_ENST00000525806.1_5'Flank|RP11-217B1.2_ENST00000569473.1_RNA|RP11-217B1.2_ENST00000562356.1_RNA	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	53	Poly-Gln.				aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			gaggctgctgttgctgctgctg	0.693								DNA polymerases (catalytic subunits)																													Colon(73;648 1203 11348 18386 27782)												0								ENSG00000140521																																			POLG	SO:0001652	inframe_insertion	0				HGNC	X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"""DNA polymerases"""	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.156_158dupGCA	15.37:g.89876834_89876836dupTGC	ENSP00000268124:p.Gln55dup	Somatic	0	23	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	28	12.50	Q8NFM2|Q92515	In_Frame_Ins	INS	NA	NA	NA	NA	NA	NA	pirsf_DNA-dir_DNA_pol_A_mt_sub,pfam_DNA-dir_DNA_pol_A_palm_dom,superfamily_RNaseH-like_dom,smart_DNA-dir_DNA_pol_A_palm_dom,prints_DNA-dir_DNA_pol_A_mt	p.56in_frame_insQ	ENST00000268124.5	37	c.159_158	CCDS10350.1	15																																																																																			-	pirsf_DNA-dir_DNA_pol_A_mt_sub		0.693	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	POLG	protein_coding	OTTHUMT00000312854.2	-	NM_002693			89876828	-1	no_errors	ENST00000268124	ensembl	human	known	74_37	in_frame_ins	INS	0.004:0.005	TGC
GALNT5	11227	genome.wustl.edu	37	2	158155447	158155454	+	Intron	DEL	CGGAAGAC	CGGAAGAC	-	rs373019313|rs146351396	byFrequency	TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	CGGAAGAC	CGGAAGAC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr2:158155447_158155454delCGGAAGAC	ENST00000259056.4	+	6	2482				RN7SKP281_ENST00000410472.1_RNA	NM_014568.1	NP_055383.1	Q7Z7M9	GALT5_HUMAN	polypeptide N-acetylgalactosaminyltransferase 5						cellular protein metabolic process (GO:0044267)|glycosaminoglycan biosynthetic process (GO:0006024)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(4)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	56						atacccttgacggaagaccggaagaccg	0.558														4837	0.965855	0.9932	0.8631	5008	,	,		19880	0.999		0.9622	False		,,,				2504	0.9714																0								ENSG00000222404																																			RN7SKP281	SO:0001627	intron_variant	0				HGNC	AJ245539	CCDS2203.1	2q24.1	2014-03-13	2014-03-13		ENSG00000136542	ENSG00000136542	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4127	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 5"""	615129	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)"""			10545594	Standard	NM_014568		Approved	GalNAc-T5	uc002tzg.3	Q7Z7M9	OTTHUMG00000131965	ENST00000259056.4:c.1998-606CGGAAGAC>-	2.37:g.158155455_158155462delCGGAAGAC		Somatic	NA	NA	NA		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	A5PKZ1|Q9UGK7|Q9UHL6	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000259056.4	37	NULL	CCDS2203.1	2																																																																																			-	-		0.558	GALNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RN7SKP281	protein_coding	OTTHUMT00000254925.2	CGGAAGAC	NM_014568			158155454	-1	no_errors	ENST00000410472	ensembl	human	known	74_37	rna	DEL	0.150:0.154:0.158:0.162:0.165:0.167:0.170:0.172	-
ODF1	4956	genome.wustl.edu	37	8	103573011	103573037	+	In_Frame_Del	DEL	TGCAACCCCTGCAGCCCCTGCAACCCG	TGCAACCCCTGCAGCCCCTGCAACCCG	-	rs143802899|rs111689913|rs568456031|rs372688769|rs369192995|rs377699584|rs62523271|rs62523272|rs62523273|rs386728348|rs58232162|rs386728346|rs150771034	byFrequency	TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	TGCAACCCCTGCAGCCCCTGCAACCCG	TGCAACCCCTGCAGCCCCTGCAACCCG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr8:103573011_103573037delTGCAACCCCTGCAGCCCCTGCAACCCG	ENST00000285402.3	+	2	808_834	c.652_678delTGCAACCCCTGCAGCCCCTGCAACCCG	c.(652-678)tgcaacccctgcagcccctgcaacccgdel	p.CNPCSPCNP218del	ODF1_ENST00000518835.1_In_Frame_Del_p.CNPCSPCNP11del	NM_024410.3	NP_077721.2	Q14990	ODFP1_HUMAN	outer dense fiber of sperm tails 1	218	C-X-P repeat region.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|outer dense fiber (GO:0001520)		p.C218_P226delCNPCSPCNP(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(14;2.76e-05)|all_epithelial(15;4.54e-08)|Lung NSC(17;4.08e-05)|all_lung(17;9.15e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000125)|STAD - Stomach adenocarcinoma(118;0.0826)			ctgcagcccctgcaacccctgcagcccctgcaacccgtgcagcccAT	0.542														1567	0.312899	0.2731	0.4193	5008	,	,		21683	0.3244		0.2614	False		,,,				2504	0.3323																1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)						ENSG00000155087																																			ODF1	SO:0001651	inframe_deletion	0				HGNC	M93131	CCDS6293.1	8q22	2011-09-05	2002-10-21		ENSG00000155087	ENSG00000155087		"""Heat shock proteins / HSPB"""	8113	protein-coding gene	gene with protein product	"""cancer/testis antigen 133"""	182878	"""outer dense fibre of sperm tails 1"""			8305202	Standard	NM_024410		Approved	ODFPG, ODF27, RT7, HSPB10, CT133	uc003ykt.2	Q14990	OTTHUMG00000164719	ENST00000285402.3:c.652_678delTGCAACCCCTGCAGCCCCTGCAACCCG	8.37:g.103573011_103573037delTGCAACCCCTGCAGCCCCTGCAACCCG	ENSP00000285402:p.Cys218_Pro226del	Somatic	NA	NA	NA		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	Q3SX72	In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_a-crystallin/Hsp20_dom,superfamily_HSP20-like_chaperone,pfscan_a-crystallin/Hsp20_dom	p.NPCSPCNPC219in_frame_del	ENST00000285402.3	37	c.652_678	CCDS6293.1	8																																																																																			-	NULL		0.542	ODF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ODF1	protein_coding	OTTHUMT00000379884.1	TGCAACCCCTGCAGCCCCTGCAACCCG				103573037	+1	no_errors	ENST00000285402	ensembl	human	known	74_37	in_frame_del	DEL	0.995:0.998:0.993:0.606:0.498:0.829:0.957:0.993:0.985:0.985:0.958:0.001:0.001:0.001:0.728:0.987:0.994:0.989:0.990:0.972:0.003:0.001:0.000:0.002:0.891:0.887:0.486	-
TUBD1	51174	genome.wustl.edu	37	17	57968332	57968332	+	Missense_Mutation	SNP	C	C	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr17:57968332C>T	ENST00000592426.1	-	1	32	c.32G>A	c.(31-33)tGt>tAt	p.C11Y	TUBD1_ENST00000591611.1_5'UTR|TUBD1_ENST00000376094.4_Missense_Mutation_p.C11Y|RPS6KB1_ENST00000443572.2_5'Flank|TUBD1_ENST00000539018.1_Intron|RPS6KB1_ENST00000393021.3_5'Flank|RPS6KB1_ENST00000406116.3_5'Flank|RPS6KB1_ENST00000225577.4_5'Flank|TUBD1_ENST00000346141.6_Missense_Mutation_p.C11Y|TUBD1_ENST00000325752.3_Missense_Mutation_p.C11Y|TUBD1_ENST00000394239.3_Missense_Mutation_p.C11Y|TUBD1_ENST00000340993.6_Missense_Mutation_p.C11Y			Q9UJT1	TBD_HUMAN	tubulin, delta 1	11					cell differentiation (GO:0030154)|microtubule-based process (GO:0007017)|multicellular organismal development (GO:0007275)|protein polymerization (GO:0051258)|spermatogenesis (GO:0007283)	centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(2)	21	all_cancers(5;3.18e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;9.34e-13)|all cancers(12;1.91e-11)		Vinblastine(DB00570)	CTGATTGCCACACTGACCAAG	0.408																																																	0								ENSG00000108423						148.0	129.0	136.0					17																	57968332		2203	4300	6503	TUBD1	SO:0001583	missense	0			-	HGNC	AF201333	CCDS11620.1, CCDS54151.1, CCDS54152.1, CCDS54153.1, CCDS54154.1	17q23.1	2007-03-16						"""Tubulins"""	16811	protein-coding gene	gene with protein product		607344				10620804	Standard	NM_016261		Approved	FLJ12709, TUBD	uc002ixw.2	Q9UJT1		ENST00000592426.1:c.32G>A	17.37:g.57968332C>T	ENSP00000468518:p.Cys11Tyr	Somatic	0	8	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	6	11	35.29	B4DPT8|B4DW01|D3DU02|E9PCA7|E9PCQ8|Q5KU36|Q9BWG9|Q9H7Z8	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Tubulin_FtsZ_GTPase,superfamily_Tubulin_FtsZ_GTPase,superfamily_Tub_FtsZ_C,smart_Tubulin_FtsZ_GTPase,prints_Delta_tubulin,prints_Tubulin,prints_Epsilon_tubulin	p.C11Y	ENST00000592426.1	37	c.32	CCDS11620.1	17	.	.	.	.	.	.	.	.	.	.	C	20.7	4.039429	0.75617	.	.	ENSG00000108423	ENST00000325752;ENST00000340993;ENST00000346141;ENST00000394239;ENST00000376094	T;T;T;T;T	0.75260	-0.92;-0.92;-0.92;-0.92;-0.92	6.04	5.06	0.68205	Tubulin/FtsZ, GTPase domain (3);	0.043512	0.85682	N	0.000000	D	0.87593	0.6216	M	0.93854	3.465	0.80722	D	1	P;B;B;D;P	0.54964	0.931;0.082;0.008;0.969;0.931	P;B;B;P;P	0.56563	0.739;0.058;0.031;0.801;0.798	D	0.91049	0.4877	10	0.87932	D	0	-9.8784	15.7671	0.78135	0.0:0.9342:0.0:0.0658	.	11;11;11;11;11	E9PCA7;Q9UJT1-3;E9PCQ8;Q9UJT1-2;Q9UJT1	.;.;.;.;TBD_HUMAN	Y	11	ENSP00000320797:C11Y;ENSP00000342399:C11Y;ENSP00000342561:C11Y;ENSP00000377785:C11Y;ENSP00000365262:C11Y	ENSP00000320797:C11Y	C	-	2	0	TUBD1	55323114	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.206000	0.77891	1.554000	0.49487	0.650000	0.86243	TGT	-	pfam_Tubulin_FtsZ_GTPase,superfamily_Tubulin_FtsZ_GTPase,prints_Tubulin		0.408	TUBD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	TUBD1	protein_coding	OTTHUMT00000448815.1	C	NM_016261	-		57968332	-1	no_errors	ENST00000325752	ensembl	human	known	74_37	missense	SNP	1.000	T
SPATC1	375686	genome.wustl.edu	37	8	145095574	145095574	+	Missense_Mutation	SNP	G	G	A			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr8:145095574G>A	ENST00000377470.3	+	3	974	c.872G>A	c.(871-873)gGc>gAc	p.G291D	SPATC1_ENST00000447830.2_Missense_Mutation_p.G291D	NM_198572.2	NP_940974.2	Q76KD6	SPERI_HUMAN	spermatogenesis and centriole associated 1	291						centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GGAGCCATGGGCACACCTGCT	0.647																																																	0								ENSG00000186583						227.0	111.0	151.0					8																	145095574		2203	4300	6503	SPATC1	SO:0001583	missense	0			-	HGNC	BC053547	CCDS6413.2, CCDS47937.1	8q24.3	2005-01-11			ENSG00000186583	ENSG00000186583			30510	protein-coding gene	gene with protein product		610874				15280373	Standard	NM_198572		Approved	MGC61633, SPATA15, SPERIOLIN	uc011lkw.2	Q76KD6	OTTHUMG00000156976	ENST00000377470.3:c.872G>A	8.37:g.145095574G>A	ENSP00000366690:p.Gly291Asp	Somatic	0	26	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	28	12.50	B4DWW9|Q5U5I8|Q7Z6L7	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.G291D	ENST00000377470.3	37	c.872	CCDS6413.2	8	.	.	.	.	.	.	.	.	.	.	G	10.89	1.479599	0.26511	.	.	ENSG00000186583	ENST00000377470;ENST00000447830	T	0.53640	0.61	3.88	2.99	0.34606	.	1.391060	0.05253	N	0.514240	T	0.51058	0.1652	L	0.54323	1.7	0.09310	N	1	P;P	0.51351	0.884;0.944	P;P	0.47470	0.484;0.548	T	0.33777	-0.9855	10	0.34782	T	0.22	.	9.0251	0.36224	0.0:0.3416:0.6584:0.0	.	291;291	B4DWW9;Q76KD6	.;SPERI_HUMAN	D	291	ENSP00000366690:G291D	ENSP00000366690:G291D	G	+	2	0	SPATC1	145167562	0.008000	0.16893	0.017000	0.16124	0.002000	0.02628	0.178000	0.16820	0.727000	0.32360	0.650000	0.86243	GGC	-	NULL		0.647	SPATC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SPATC1	protein_coding	OTTHUMT00000346926.1	G	NM_198572	-		145095574	+1	no_errors	ENST00000377470	ensembl	human	known	74_37	missense	SNP	0.022	A
THAP11	57215	genome.wustl.edu	37	16	67877046	67877060	+	In_Frame_Del	DEL	GCAGCCGCAGAGGGC	GCAGCCGCAGAGGGC	-			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	GCAGCCGCAGAGGGC	GCAGCCGCAGAGGGC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr16:67877046_67877060delGCAGCCGCAGAGGGC	ENST00000303596.1	+	1	834_848	c.589_603delGCAGCCGCAGAGGGC	c.(589-603)gcagccgcagagggcdel	p.AAAEG197del	CENPT_ENST00000562787.1_Intron	NM_020457.2	NP_065190.2	Q96EK4	THA11_HUMAN	THAP domain containing 11	197	Ala-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|urinary_tract(1)	8		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118)		AGTGGAGTTTGCAGCCGCAGAGGGCGCAGCCGCTG	0.656																																																	0								ENSG00000168286		,	1,4255		0,1,2127					,	-0.8	1.0			61	2,8244		0,2,4121	no	intron,coding	THAP11,CENPT	NM_025082.3,NM_020457.2	,	0,3,6248	A1A1,A1R,RR		0.0243,0.0235,0.024	,	,		3,12499				THAP11	SO:0001651	inframe_deletion	0				HGNC	AB015338	CCDS10847.1	16q22.1	2013-01-25			ENSG00000168286	ENSG00000168286		"""THAP (C2CH-type zinc finger) domain containing"""	23194	protein-coding gene	gene with protein product		609119				12575992, 8325628	Standard	NM_020457		Approved	HRIHFB2206, CTG-B45d, CTG-B43a	uc002euo.3	Q96EK4	OTTHUMG00000137546	ENST00000303596.1:c.589_603delGCAGCCGCAGAGGGC	16.37:g.67877046_67877060delGCAGCCGCAGAGGGC	ENSP00000304689:p.Ala197_Gly201del	Somatic	NA	NA	NA		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	A4UCT5|A8K002|O94795	In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Znf_C2CH,smart_Znf_C2CH,pfscan_Znf_C2CH	p.EGAAA200in_frame_del	ENST00000303596.1	37	c.589_603	CCDS10847.1	16																																																																																			-	NULL		0.656	THAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	THAP11	protein_coding	OTTHUMT00000268879.1	GCAGCCGCAGAGGGC	NM_020457			67877060	+1	no_errors	ENST00000303596	ensembl	human	known	74_37	in_frame_del	DEL	0.996:0.997:0.972:0.992:0.997:0.872:0.935:1.000:1.000:1.000:1.000:1.000:1.000:0.999:0.963	-
SLC9A1	6548	genome.wustl.edu	37	1	27432470	27432470	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr1:27432470G>T	ENST00000263980.3	-	5	1966	c.1391C>A	c.(1390-1392)tCt>tAt	p.S464Y	SLC9A1_ENST00000374086.3_Missense_Mutation_p.S464Y|SLC9A1_ENST00000545949.1_Missense_Mutation_p.S125Y	NM_003047.4	NP_003038.2	P19634	SL9A1_HUMAN	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	464					carbohydrate metabolic process (GO:0005975)|cardiac muscle cell differentiation (GO:0055007)|cell growth (GO:0016049)|cellular response to acidic pH (GO:0071468)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|hydrogen ion transmembrane transport (GO:1902600)|ion transport (GO:0006811)|negative regulation of apoptotic process (GO:0043066)|neuron death (GO:0070997)|positive regulation of action potential (GO:0045760)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial membrane permeability (GO:0035794)|protein oligomerization (GO:0051259)|regulation of intracellular pH (GO:0051453)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of the force of heart contraction (GO:0002026)|response to acidic pH (GO:0010447)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|sodium ion export (GO:0071436)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|sodium:proton antiporter activity (GO:0015385)|solute:proton antiporter activity (GO:0015299)			central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)	GTAGCCCAGAGAGAAGGCGAT	0.562																																																	0								ENSG00000090020						114.0	92.0	99.0					1																	27432470		2203	4300	6503	SLC9A1	SO:0001583	missense	0			-	HGNC	M81768	CCDS295.1	1p36.1-p35	2014-06-13	2012-03-22		ENSG00000090020	ENSG00000090020		"""Solute carriers"""	11071	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 143"""	107310	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive)"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 1"""	APNH, NHE1		8283968	Standard	NM_003047		Approved	PPP1R143	uc001bnm.4	P19634	OTTHUMG00000004271	ENST00000263980.3:c.1391C>A	1.37:g.27432470G>T	ENSP00000263980:p.Ser464Tyr	Somatic	0	23	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	22	15.38	B1ALD6|D3DPL4|Q96EM2	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Cation/H_exchanger,prints_Na/H_exchanger_1,prints_NaH_exchanger,tigrfam_NaH_exchanger	p.S464Y	ENST00000263980.3	37	c.1391	CCDS295.1	1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.941698	0.92526	.	.	ENSG00000090020	ENST00000263980;ENST00000545949;ENST00000374086	T;T;T	0.15139	2.45;2.45;2.45	5.11	5.11	0.69529	Cation/H+ exchanger (1);	0.102290	0.64402	D	0.000001	T	0.49012	0.1532	M	0.87038	2.855	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.78314	0.991;0.971	T	0.56402	-0.7985	10	0.87932	D	0	.	17.7526	0.88439	0.0:0.0:1.0:0.0	.	464;464	P19634-2;P19634	.;SL9A1_HUMAN	Y	464;125;464	ENSP00000263980:S464Y;ENSP00000445520:S125Y;ENSP00000363199:S464Y	ENSP00000263980:S464Y	S	-	2	0	SLC9A1	27305057	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	7.818000	0.86416	2.682000	0.91365	0.555000	0.69702	TCT	-	pfam_Cation/H_exchanger,tigrfam_NaH_exchanger		0.562	SLC9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC9A1	protein_coding	OTTHUMT00000012336.2	G	NM_003047	-		27432470	-1	no_errors	ENST00000263980	ensembl	human	known	74_37	missense	SNP	1.000	T
MAGED1	9500	genome.wustl.edu	37	X	51637744	51637744	+	Intron	SNP	G	G	C			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chrX:51637744G>C	ENST00000375722.1	+	2	297				MAGED1_ENST00000375772.3_Intron|MAGED1_ENST00000494718.1_Intron|MAGED1_ENST00000375695.2_Missense_Mutation_p.V23L|MAGED1_ENST00000326587.7_Intron			Q9Y5V3	MAGD1_HUMAN	melanoma antigen family D, 1						apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|circadian regulation of gene expression (GO:0032922)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of circadian rhythm (GO:0042752)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(4)|large_intestine(10)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	32	Ovarian(276;0.236)					TTGTAGAGCAGTCTGTCACCC	0.567										Multiple Myeloma(10;0.10)	OREG0019786	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					0								ENSG00000179222						35.0	32.0	33.0					X																	51637744		2203	4299	6502	MAGED1	SO:0001627	intron_variant	0			-	HGNC	AF124440	CCDS14337.1, CCDS35279.1	Xp11.23	2008-08-01			ENSG00000179222	ENSG00000179222			6813	protein-coding gene	gene with protein product		300224				10409427	Standard	NM_006986		Approved	NRAGE, DLXIN-1	uc004dpn.3	Q9Y5V3	OTTHUMG00000021540	ENST00000375722.1:c.45+299G>C	X.37:g.51637744G>C		Somatic	0	50	0.00	978	0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	50	12.28	Q5VSH6|Q8IZ84|Q8WY92|Q9H352|Q9HBT4|Q9UF36	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_MAGE,pfscan_MAGE	p.V23L	ENST00000375722.1	37	c.67	CCDS14337.1	X	.	.	.	.	.	.	.	.	.	.	G	0.233	-1.019692	0.02078	.	.	ENSG00000179222	ENST00000375695	T	0.02837	4.14	2.79	1.91	0.25777	.	.	.	.	.	T	0.02848	0.0085	.	.	.	0.09310	N	0.999996	B	0.02656	0.0	B	0.04013	0.001	T	0.40384	-0.9566	8	0.87932	D	0	.	6.8661	0.24094	0.0:0.3095:0.6905:0.0	.	23	Q9Y5V3-2	.	L	23	ENSP00000364847:V23L	ENSP00000364847:V23L	V	+	1	0	MAGED1	51654484	0.041000	0.20044	0.539000	0.28077	0.131000	0.20780	-0.037000	0.12164	0.586000	0.29626	0.425000	0.28330	GTC	-	NULL		0.567	MAGED1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	MAGED1	protein_coding	OTTHUMT00000056593.1	G	NM_001005332	-		51637744	+1	no_errors	ENST00000375695	ensembl	human	known	74_37	missense	SNP	0.484	C
ZHX3	23051	genome.wustl.edu	37	20	39831141	39831141	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr20:39831141G>T	ENST00000309060.3	-	4	2831	c.2416C>A	c.(2416-2418)Cca>Aca	p.P806T	ZHX3_ENST00000559234.1_Missense_Mutation_p.P806T|ZHX3_ENST00000540170.1_Missense_Mutation_p.P806T|ZHX3_ENST00000560361.1_Missense_Mutation_p.P806T|ZHX3_ENST00000558993.1_Intron|ZHX3_ENST00000432768.2_Missense_Mutation_p.P806T|ZHX3_ENST00000557816.1_Intron|ZHX3_ENST00000544979.2_Missense_Mutation_p.P806T			Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	806					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoblast differentiation (GO:0045669)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|kidney(5)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		Myeloproliferative disorder(115;0.00425)				ACCACCTCTGGCCGTGGCAGA	0.582																																																	0								ENSG00000174306						135.0	134.0	135.0					20																	39831141		2203	4300	6503	ZHX3	SO:0001583	missense	0			-	HGNC	AB007855	CCDS13315.1	20q12	2012-03-09	2004-01-29	2004-01-30	ENSG00000174306	ENSG00000174306		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	15935	protein-coding gene	gene with protein product		609598	"""triple homeobox 1"""	TIX1		9455477	Standard	XM_005260343		Approved	KIAA0395	uc002xjs.1	Q9H4I2	OTTHUMG00000032481	ENST00000309060.3:c.2416C>A	20.37:g.39831141G>T	ENSP00000312222:p.Pro806Thr	Somatic	0	58	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	57	8.06	E1P5W5|F5H820|O43145|Q6NUJ7	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Homeobox_dom,superfamily_Homeodomain-like,smart_Znf_C2H2-like,smart_Homeobox_dom,pfscan_Homeobox_dom	p.P806T	ENST00000309060.3	37	c.2416	CCDS13315.1	20	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.112|0.112	-1.137466|-1.137466	0.01742|0.01742	.|.	.|.	ENSG00000174306|ENSG00000174306	ENST00000421422|ENST00000309060;ENST00000373263;ENST00000540170;ENST00000544979;ENST00000373262	.|D;D;D	.|0.90955	.|-2.76;-2.76;-2.76	6.07|6.07	4.03|4.03	0.46877|0.46877	.|Homeodomain-related (1);Homeobox (2);Homeodomain-like (1);	.|0.284688	.|0.39615	.|N	.|0.001306	T|T	0.75258|0.75258	0.3825|0.3825	N|N	0.13043|0.13043	0.29|0.29	0.46061|0.46061	D|D	0.998844|0.998844	.|B;B;B	.|0.13145	.|0.0;0.0;0.007	.|B;B;B	.|0.14578	.|0.004;0.004;0.011	T|T	0.65417|0.65417	-0.6173|-0.6173	5|10	.|0.02654	.|T	.|1	-6.081|-6.081	3.4017|3.4017	0.07325|0.07325	0.1066:0.2961:0.4726:0.1248|0.1066:0.2961:0.4726:0.1248	.|.	.|806;806;806	.|A8K8Q0;Q9H4I2;F5H820	.|.;ZHX3_HUMAN;.	D|T	514|806;806;806;806;584	.|ENSP00000362360:P806T;ENSP00000442290:P806T;ENSP00000443783:P806T	.|ENSP00000312222:P806T	A|P	-|-	2|1	0|0	ZHX3|ZHX3	39264555|39264555	0.862000|0.862000	0.29867|0.29867	0.988000|0.988000	0.46212|0.46212	0.967000|0.967000	0.64934|0.64934	0.680000|0.680000	0.25306|0.25306	1.489000|1.489000	0.48450|0.48450	0.655000|0.655000	0.94253|0.94253	GCC|CCA	-	superfamily_Homeodomain-like,smart_Homeobox_dom,pfscan_Homeobox_dom		0.582	ZHX3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	ZHX3	protein_coding	OTTHUMT00000079262.3	G	NM_015035	-		39831141	-1	no_errors	ENST00000309060	ensembl	human	known	74_37	missense	SNP	1.000	T
LAMA4	3910	genome.wustl.edu	37	6	112521360	112521360	+	Intron	SNP	G	G	T	rs368840774		TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr6:112521360G>T	ENST00000230538.7	-	5	901				LAMA4_ENST00000424408.2_Intron|LAMA4_ENST00000524032.1_Intron|LAMA4_ENST00000522006.1_Intron|LAMA4_ENST00000389463.4_Intron	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4						blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		AAAGCCTCTCGTGCTCTGTGG	0.438																																																	0								ENSG00000112769						66.0	58.0	60.0					6																	112521360		876	1991	2867	LAMA4	SO:0001627	intron_variant	0			-	HGNC		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"""Laminins"""	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.503+1448C>A	6.37:g.112521360G>T		Somatic	0	26	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	33	10.81	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000230538.7	37	NULL	CCDS43491.1	6	.	.	.	.	.	.	.	.	.	.	G	0.718	-0.784507	0.02907	.	.	ENSG00000112769	ENST00000368639	.	.	.	3.33	-6.41	0.01938	.	.	.	.	.	T	0.12178	0.0296	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.33650	-0.9860	5	0.48119	T	0.1	.	3.0733	0.06237	0.3823:0.0:0.3081:0.3097	.	.	.	.	K	174	.	ENSP00000357628:T174K	T	-	2	0	LAMA4	112628053	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.141000	0.10327	-1.308000	0.02318	-0.657000	0.03884	ACG	-	-		0.438	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	LAMA4	protein_coding	OTTHUMT00000041876.2	G	NM_001105206	-		112521360	-1	no_errors	ENST00000423735	ensembl	human	known	74_37	rna	SNP	0.000	T
RTTN	25914	genome.wustl.edu	37	18	67836097	67836097	+	Silent	SNP	C	C	A			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr18:67836097C>A	ENST00000255674.6	-	12	1969	c.1683G>T	c.(1681-1683)ggG>ggT	p.G561G	RTTN_ENST00000454359.1_Silent_p.G561G|RTTN_ENST00000437017.1_Silent_p.G561G	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	561					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				TTACCTCTTTCCCAATATCAG	0.289																																																	0								ENSG00000176225						78.0	78.0	78.0					18																	67836097		1791	4063	5854	RTTN	SO:0001819	synonymous_variant	0			-	HGNC	AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.1683G>T	18.37:g.67836097C>A		Somatic	0	32	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	16	38	29.63	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Silent	SNP	NA	NA	NA	NA	NA	NA	superfamily_ARM-type_fold	p.G561	ENST00000255674.6	37	c.1683	CCDS42443.1	18																																																																																			-	superfamily_ARM-type_fold		0.289	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RTTN	protein_coding	OTTHUMT00000442988.1	C	NM_173630	-		67836097	-1	no_errors	ENST00000255674	ensembl	human	known	74_37	silent	SNP	0.061	A
PATE1	160065	genome.wustl.edu	37	11	125616250	125616250	+	Splice_Site	SNP	G	G	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr11:125616250G>T	ENST00000305738.5	+	1	63	c.51G>T	c.(49-51)agG>agT	p.R17S	PATE1_ENST00000437148.2_Splice_Site_p.R17S	NM_138294.2	NP_612151.1	Q8WXA2	PATE1_HUMAN	prostate and testis expressed 1	17						extracellular region (GO:0005576)				large_intestine(1)|lung(5)	6						gctgctttaggGGTGAGTCCC	0.542																																																	0								ENSG00000171053						143.0	127.0	133.0					11																	125616250		2201	4299	6500	PATE1	SO:0001630	splice_region_variant	0			-	HGNC	AF462605	CCDS8464.1	11q24.2	2008-12-17				ENSG00000171053		"""PATE family"""	24664	protein-coding gene	gene with protein product	"""expressed in prostate and testis"""	606861				11880645, 15798027	Standard	NM_138294		Approved	PATE	uc001qct.3	Q8WXA2		ENST00000305738.5:c.52+1G>T	11.37:g.125616250G>T		Somatic	0	53	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	45	8.16	Q3KNX2	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.R17S	ENST00000305738.5	37	c.51	CCDS8464.1	11	.	.	.	.	.	.	.	.	.	.	G	1.196	-0.633943	0.03584	.	.	ENSG00000171053	ENST00000305738;ENST00000437148	T;T	0.30182	1.54;1.54	3.94	-1.13	0.09775	.	0.494590	0.15333	N	0.267881	T	0.15955	0.0384	N	0.24115	0.695	0.09310	N	1	B;B	0.16396	0.017;0.017	B;B	0.21151	0.013;0.033	T	0.17623	-1.0363	10	0.87932	D	0	-23.2897	2.3595	0.04304	0.3083:0.0:0.2926:0.3991	.	17;17	Q8WXA2-2;Q8WXA2	.;PATE1_HUMAN	S	17	ENSP00000307164:R17S;ENSP00000396056:R17S	ENSP00000307164:R17S	R	+	3	2	PATE1	125121460	0.017000	0.18338	0.055000	0.19348	0.116000	0.19942	-0.248000	0.08854	-0.201000	0.10284	-1.087000	0.02190	AGG	-	NULL		0.542	PATE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PATE1	protein_coding	OTTHUMT00000386726.2	G	NM_138294	-	Missense_Mutation	125616250	+1	no_errors	ENST00000305738	ensembl	human	known	74_37	missense	SNP	0.107	T
TAT	6898	genome.wustl.edu	37	16	71610109	71610109	+	Frame_Shift_Del	DEL	G	G	-			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr16:71610109delG	ENST00000355962.4	-	2	343	c.210delC	c.(208-210)aacfs	p.N70fs	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	70			N -> D (in dbSNP:rs16973344).		2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|L-phenylalanine catabolic process (GO:0006559)|response to glucocorticoid (GO:0051384)|response to mercury ion (GO:0046689)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|L-tyrosine:2-oxoglutarate aminotransferase activity (GO:0004838)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(3)	29		Ovarian(137;0.125)		Kidney(780;0.0157)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)	TCATGGTTTTGTTTGGATTTG	0.498																																					Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)												0								ENSG00000198650						172.0	130.0	144.0					16																	71610109		2198	4300	6498	TAT	SO:0001589	frameshift_variant	0				HGNC		CCDS10903.1	16q22.1	2012-10-02			ENSG00000198650	ENSG00000198650	2.6.1.5		11573	protein-coding gene	gene with protein product		613018					Standard	NM_000353		Approved		uc002fap.2	P17735	OTTHUMG00000137590	ENST00000355962.4:c.210delC	16.37:g.71610109delG	ENSP00000348234:p.Asn70fs	Somatic	0	133	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	29	104	21.80	B2R8I1|D3DWS2	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Aminotransferase_I/II,pfam_Tyr_aminoTrfase_ubiquitination,pfam_ArAA_b-elim_lyase/Thr_aldolase,pfam_Aminotrans_V/Cys_dSase,pfam_DegT/StrS_aminotransferase,superfamily_PyrdxlP-dep_Trfase,pirsf_Tyrosine_transaminase,tigrfam_Tyrosine_aminoTrfase,tigrfam_TyrNic_aminoTrfase	p.N70fs	ENST00000355962.4	37	c.210	CCDS10903.1	16																																																																																			-	superfamily_PyrdxlP-dep_Trfase,pirsf_Tyrosine_transaminase,tigrfam_Tyrosine_aminoTrfase,tigrfam_TyrNic_aminoTrfase		0.498	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TAT	protein_coding	OTTHUMT00000268989.1	G				71610109	-1	no_errors	ENST00000355962	ensembl	human	known	74_37	frame_shift_del	DEL	0.983	-
TP53	7157	genome.wustl.edu	37	17	7577029	7577032	+	Frame_Shift_Del	DEL	GCTC	GCTC	-	rs587782391		TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	GCTC	GCTC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr17:7577029_7577032delGCTC	ENST00000269305.4	-	8	1095_1098	c.906_909delGAGC	c.(904-909)gggagcfs	p.GS302fs	TP53_ENST00000445888.2_Frame_Shift_Del_p.GS302fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Frame_Shift_Del_p.GS302fs|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Frame_Shift_Del_p.GS302fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.GS302fs	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	302	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.		G -> A (in a sporadic cancer; somatic mutation).|G -> E (in sporadic cancers; somatic mutation).|G -> R (in a sporadic cancer; somatic mutation).|G -> V (in a sporadic cancer; 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.0?(8)|p.?(3)|p.S303N(3)|p.S303T(3)|p.G302G(3)|p.S303C(2)|p.P301_S303delPGS(1)|p.L265_K305del41(1)|p.G302fs*2(1)|p.S303fs*42(1)|p.G293fs*1(1)|p.H296_S303delHHELPPGS(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)	CTCGCTTAGTGCTCCCTGGGGGCA	0.559		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)																											Pancreas(47;798 1329 9957 10801)		yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	28	Whole gene deletion(8)|Substitution - Missense(8)|Deletion - In frame(3)|Unknown(3)|Deletion - Frameshift(3)|Substitution - coding silent(3)	bone(5)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|lung(3)|stomach(2)|central_nervous_system(2)|urinary_tract(2)|oesophagus(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|prostate(1)						ENSG00000141510																																			TP53	SO:0001589	frameshift_variant	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;		HGNC	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.906_909delGAGC	17.37:g.7577029_7577032delGCTC	ENSP00000269305:p.Gly302fs	Somatic	0	62	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	30	26	53.57	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	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_p53_DNA-bd,pfam_p53_tetrameristn,pfam_p53_transactivation_domain,superfamily_p53-like_TF_DNA-bd,superfamily_p53_tetrameristn,prints_p53_tumour_suppressor	p.S303fs	ENST00000269305.4	37	c.909_906	CCDS11118.1	17																																																																																			-	NULL		0.559	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TP53	protein_coding	OTTHUMT00000367397.1	GCTC	NM_000546			7577032	-1	no_errors	ENST00000269305	ensembl	human	known	74_37	frame_shift_del	DEL	0.989:0.998:1.000:0.995	-
TRPM6	140803	genome.wustl.edu	37	9	77390934	77390934	+	Missense_Mutation	SNP	G	G	A			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr9:77390934G>A	ENST00000360774.1	-	24	3505	c.3268C>T	c.(3268-3270)Cgc>Tgc	p.R1090C	TRPM6_ENST00000451710.3_Missense_Mutation_p.R1090C|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376864.4_Missense_Mutation_p.R1090C|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000361255.3_Missense_Mutation_p.R1085C|TRPM6_ENST00000449912.2_Missense_Mutation_p.R1085C	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	1090					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						ATGATGTAGCGATAGCGGTTG	0.493																																																	0								ENSG00000119121						118.0	127.0	124.0					9																	77390934		2203	4300	6503	TRPM6	SO:0001583	missense	0			-	HGNC	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17995	protein-coding gene	gene with protein product		607009	"""hypomagnesemia, secondary hypocalcemia"""	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.3268C>T	9.37:g.77390934G>A	ENSP00000354006:p.Arg1090Cys	Somatic	0	58	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	41	15	73.21	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_MHCK_EF2_kinase,pfam_Ion_trans_dom,superfamily_Kinase-like_dom,smart_MHCK_EF2_kinase,pfscan_MHCK_EF2_kinase	p.R1090C	ENST00000360774.1	37	c.3268	CCDS6647.1	9	.	.	.	.	.	.	.	.	.	.	G	32	5.120843	0.94385	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T	0.55588	0.6;0.6;0.6;0.6;0.51	5.76	5.76	0.90799	.	0.046412	0.85682	D	0.000000	T	0.72779	0.3503	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.67900	0.932;0.931;0.954	T	0.74426	-0.3669	10	0.87932	D	0	.	19.9561	0.97218	0.0:0.0:1.0:0.0	.	1090;1085;1085	Q9BX84;Q9BX84-3;Q9BX84-2	TRPM6_HUMAN;.;.	C	1090;1090;1085;1085;1090;753;753	ENSP00000354006:R1090C;ENSP00000407341:R1090C;ENSP00000396672:R1085C;ENSP00000354962:R1085C;ENSP00000366060:R1090C	ENSP00000309693:R753C	R	-	1	0	TRPM6	76580754	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	7.827000	0.86722	2.725000	0.93324	0.591000	0.81541	CGC	-	NULL		0.493	TRPM6-001	KNOWN	basic|CCDS	protein_coding	TRPM6	protein_coding	OTTHUMT00000052693.1	G	NM_017662	-		77390934	-1	no_errors	ENST00000451710	ensembl	human	known	74_37	missense	SNP	1.000	A
FOXN4	121643	genome.wustl.edu	37	12	109725976	109725976	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr12:109725976G>T	ENST00000299162.5	-	4	346	c.242C>A	c.(241-243)gCt>gAt	p.A81D	FOXN4_ENST00000355216.1_Intron	NM_213596.2	NP_998761.2	Q96NZ1	FOXN4_HUMAN	forkhead box N4	81	Pro-rich.				amacrine cell differentiation (GO:0035881)|atrioventricular canal development (GO:0036302)|heart looping (GO:0001947)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of heart contraction (GO:0008016)|regulation of transcription, DNA-templated (GO:0006355)|retina layer formation (GO:0010842)|transcription, DNA-templated (GO:0006351)|ventral spinal cord interneuron fate commitment (GO:0060579)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(5)|lung(9)|ovary(2)	16						GGCCACCCCAGCCAAGGCACC	0.662																																																	0								ENSG00000139445						4.0	6.0	5.0					12																	109725976		659	1526	2185	FOXN4	SO:0001583	missense	0			-	HGNC	AF425596	CCDS9126.2	12q24.12	2008-02-05			ENSG00000139445	ENSG00000139445		"""Forkhead boxes"""	21399	protein-coding gene	gene with protein product		609429					Standard	NM_213596		Approved		uc001toe.4	Q96NZ1	OTTHUMG00000152868	ENST00000299162.5:c.242C>A	12.37:g.109725976G>T	ENSP00000299162:p.Ala81Asp	Somatic	0	57	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	27	12.90	Q6ZMR4|Q96NZ0	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_TF_fork_head,smart_TF_fork_head,pfscan_TF_fork_head,prints_TF_fork_head	p.A81D	ENST00000299162.5	37	c.242	CCDS9126.2	12	.	.	.	.	.	.	.	.	.	.	G	11.60	1.685564	0.29962	.	.	ENSG00000139445	ENST00000266856;ENST00000299162	D	0.93763	-3.28	4.64	2.74	0.32292	.	5.005580	0.04733	N	0.421475	D	0.90947	0.7154	L	0.50333	1.59	0.36133	D	0.846264	B	0.06786	0.001	B	0.04013	0.001	T	0.81250	-0.1018	10	0.72032	D	0.01	-24.3012	6.6685	0.23056	0.0942:0.0:0.7296:0.1762	.	81	Q96NZ1	FOXN4_HUMAN	D	81	ENSP00000299162:A81D	ENSP00000266856:A81D	A	-	2	0	FOXN4	108210359	0.973000	0.33851	0.462000	0.27118	0.575000	0.36095	1.810000	0.38932	0.457000	0.26962	0.561000	0.74099	GCT	-	NULL		0.662	FOXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FOXN4	protein_coding	OTTHUMT00000328306.1	G	XM_062735	-		109725976	-1	no_errors	ENST00000299162	ensembl	human	known	74_37	missense	SNP	0.808	T
RIMBP2	23504	genome.wustl.edu	37	12	130927134	130927134	+	Missense_Mutation	SNP	G	G	A	rs549158714		TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr12:130927134G>A	ENST00000261655.4	-	8	875	c.712C>T	c.(712-714)Cgg>Tgg	p.R238W	RIMBP2_ENST00000535703.1_Missense_Mutation_p.R146W|RIMBP2_ENST00000536002.1_Missense_Mutation_p.R146W	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	238					negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)				NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		CTTGCCAACCGCGACTCGTTG	0.587													G|||	1	0.000199681	0.0	0.0	5008	,	,		18516	0.0		0.0	False		,,,				2504	0.001																0								ENSG00000060709						130.0	129.0	129.0					12																	130927134		2203	4300	6503	RIMBP2	SO:0001583	missense	0			-	HGNC	AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 133"""	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.712C>T	12.37:g.130927134G>A	ENSP00000261655:p.Arg238Trp	Somatic	0	53	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	14	46	22.95	Q96ID2	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_SH3_2,pfam_SH3_domain,superfamily_SH3_domain,superfamily_Fibronectin_type3,smart_SH3_domain,smart_Fibronectin_type3,pfscan_Fibronectin_type3,pfscan_SH3_domain,prints_SH3_domain	p.R238W	ENST00000261655.4	37	c.712	CCDS31925.1	12	.	.	.	.	.	.	.	.	.	.	G	15.61	2.885658	0.51908	.	.	ENSG00000060709	ENST00000261655;ENST00000392375;ENST00000535703;ENST00000536002	T;T;T	0.30448	1.53;1.53;1.53	4.53	3.61	0.41365	Src homology-3 domain (1);	0.538961	0.20115	N	0.098937	T	0.52837	0.1759	M	0.68317	2.08	0.42057	D	0.991146	D;D	0.89917	0.998;1.0	D;D	0.83275	0.928;0.996	T	0.55611	-0.8114	10	0.66056	D	0.02	-24.1815	13.5684	0.61832	0.0:0.0:0.8432:0.1568	.	146;238	O15034-2;O15034	.;RIMB2_HUMAN	W	238;146;146;146	ENSP00000261655:R238W;ENSP00000440347:R146W;ENSP00000439159:R146W	ENSP00000261655:R238W	R	-	1	2	RIMBP2	129493087	1.000000	0.71417	0.020000	0.16555	0.317000	0.28152	5.216000	0.65246	0.840000	0.34995	0.561000	0.74099	CGG	-	superfamily_SH3_domain		0.587	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RIMBP2	protein_coding	OTTHUMT00000399520.1	G	NM_015347	-		130927134	-1	no_errors	ENST00000261655	ensembl	human	known	74_37	missense	SNP	0.780	A
EXTL3	2137	genome.wustl.edu	37	8	28575380	28575380	+	Missense_Mutation	SNP	C	C	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr8:28575380C>T	ENST00000220562.4	+	3	2706	c.1804C>T	c.(1804-1806)Cgc>Tgc	p.R602C	EXTL3_ENST00000519886.1_Intron|EXTL3_ENST00000523149.1_Missense_Mutation_p.R218C	NM_001440.2	NP_001431.1	O43909	EXTL3_HUMAN	exostosin-like glycosyltransferase 3	602					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)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|positive regulation of cell growth (GO:0030307)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0001888)|metal ion binding (GO:0046872)			biliary_tract(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(8)|ovary(1)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(1)	36		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)		TGACTTTTACCGCAGCTGGAA	0.587																																																	0								ENSG00000012232						94.0	82.0	86.0					8																	28575380		2203	4300	6503	EXTL3	SO:0001583	missense	0			-	HGNC	U76188	CCDS6070.1	8p22-p12	2013-03-01	2013-03-01		ENSG00000012232	ENSG00000012232	2.4.1.223	"""Exostosin glycosyltransferase family"""	3518	protein-coding gene	gene with protein product	"""REG receptor"", ""glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase"""	605744	"""exostoses (multiple)-like 3"""			9479495, 9450183, 11257457	Standard	NM_001440		Approved	botv, REGR	uc003xgz.2	O43909	OTTHUMG00000102146	ENST00000220562.4:c.1804C>T	8.37:g.28575380C>T	ENSP00000220562:p.Arg602Cys	Somatic	0	39	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	11	46	19.30	D3DST8|O00225|Q53XT3	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_HexNAc_Trfase_a,pfam_Exostosin	p.R602C	ENST00000220562.4	37	c.1804	CCDS6070.1	8	.	.	.	.	.	.	.	.	.	.	C	15.05	2.719325	0.48728	.	.	ENSG00000012232	ENST00000523149;ENST00000220562	D;D	0.95482	-3.33;-3.72	6.04	5.16	0.70880	.	0.050594	0.85682	D	0.000000	D	0.95338	0.8487	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	P	0.58391	0.838	D	0.95595	0.8658	10	0.62326	D	0.03	-22.9675	14.5566	0.68103	0.318:0.682:0.0:0.0	.	602	O43909	EXTL3_HUMAN	C	218;602	ENSP00000428691:R218C;ENSP00000220562:R602C	ENSP00000220562:R602C	R	+	1	0	EXTL3	28631299	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.262000	0.51538	1.542000	0.49330	0.563000	0.77884	CGC	-	NULL		0.587	EXTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EXTL3	protein_coding	OTTHUMT00000219987.3	C	NM_001440	-		28575380	+1	no_errors	ENST00000220562	ensembl	human	known	74_37	missense	SNP	1.000	T
SRMS	6725	genome.wustl.edu	37	20	62172208	62172208	+	Missense_Mutation	SNP	C	C	T	rs368421364		TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr20:62172208C>T	ENST00000217188.1	-	8	1470	c.1430G>A	c.(1429-1431)cGg>cAg	p.R477Q		NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	477	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-tyrosine autophosphorylation (GO:0038083)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|stomach(1)	19	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			CAGCTTCTCCCGCAGCGTGGC	0.711													C|||	1	0.000199681	0.0	0.0	5008	,	,		16932	0.0		0.0	False		,,,				2504	0.001																0								ENSG00000125508	C	GLN/ARG	1,4403	2.1+/-5.4	0,1,2201	101.0	90.0	94.0		1430	-2.4	0.6	20		94	0,8600		0,0,4300	no	missense	SRMS	NM_080823.2	43	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	benign	477/489	62172208	1,13003	2202	4300	6502	SRMS	SO:0001583	missense	0			-	HGNC		CCDS13525.1	20q13.33	2013-02-14	2003-08-22		ENSG00000125508	ENSG00000125508		"""SH2 domain containing"""	11298	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 148"""	C20orf148		7935409	Standard	NM_080823		Approved	SRM, dJ697K14.1	uc002yfi.1	Q9H3Y6	OTTHUMG00000032977	ENST00000217188.1:c.1430G>A	20.37:g.62172208C>T	ENSP00000217188:p.Arg477Gln	Somatic	0	58	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	22	41	34.92		Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_dom,pfam_SH2,superfamily_Kinase-like_dom,superfamily_SH3_domain,smart_SH3_domain,smart_SH2,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_SH2,pfscan_SH3_domain,pfscan_Prot_kinase_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,prints_SH2	p.R477Q	ENST00000217188.1	37	c.1430	CCDS13525.1	20	.	.	.	.	.	.	.	.	.	.	C	0.542	-0.852984	0.02630	2.27E-4	0.0	ENSG00000125508	ENST00000217188	T	0.11495	2.77	5.17	-2.36	0.06663	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	1.024840	0.07842	N	0.963191	T	0.08846	0.0219	L	0.52573	1.65	0.19775	N	0.999953	B	0.19200	0.034	B	0.17098	0.017	T	0.47459	-0.9116	10	0.02654	T	1	.	10.2345	0.43275	0.0:0.7031:0.1318:0.1651	.	477	Q9H3Y6	SRMS_HUMAN	Q	477	ENSP00000217188:R477Q	ENSP00000217188:R477Q	R	-	2	0	SRMS	61642652	0.000000	0.05858	0.554000	0.28268	0.068000	0.16541	-0.025000	0.12413	-0.325000	0.08577	-0.345000	0.07892	CGG	-	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom		0.711	SRMS-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	SRMS	protein_coding	OTTHUMT00000080148.1	C	NM_080823	-		62172208	-1	no_errors	ENST00000217188	ensembl	human	known	74_37	missense	SNP	0.388	T
USP8	9101	genome.wustl.edu	37	15	50784950	50784950	+	Missense_Mutation	SNP	C	C	T	rs78143971	byFrequency	TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr15:50784950C>T	ENST00000396444.3	+	15	2625	c.2287C>T	c.(2287-2289)Cgg>Tgg	p.R763W	USP8_ENST00000433963.1_Missense_Mutation_p.R763W|USP8_ENST00000307179.4_Missense_Mutation_p.R763W|USP8_ENST00000425032.3_Missense_Mutation_p.R657W|RP11-562A8.5_ENST00000560159.1_lincRNA	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	763					cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		TTCTCAGATTCGGAACCTCAA	0.403																																																	0								ENSG00000138592						133.0	120.0	125.0					15																	50784950		2196	4294	6490	USP8	SO:0001583	missense	0			-	HGNC	D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"""Ubiquitin-specific peptidases"""	12631	protein-coding gene	gene with protein product		603158	"""ubiquitin specific protease 8"""			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.2287C>T	15.37:g.50784950C>T	ENSP00000379721:p.Arg763Trp	Somatic	0	31	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	8	33	19.51	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Peptidase_C19/C67,pfam_USP8_dimer,pfam_Rhodanese-like_dom,superfamily_Rhodanese-like_dom,superfamily_WW_dom,pfscan_Rhodanese-like_dom,pfscan_Peptidase_C19/C67	p.R763W	ENST00000396444.3	37	c.2287	CCDS10137.1	15	.	.	.	.	.	.	.	.	.	.	C	25.3	4.628030	0.87560	.	.	ENSG00000138592	ENST00000396444;ENST00000433963;ENST00000307179;ENST00000425032	T;T;T;T	0.21031	2.03;2.03;2.03;2.07	5.22	5.22	0.72569	.	0.556073	0.19308	N	0.117479	T	0.32255	0.0823	L	0.29908	0.895	0.80722	D	1	D;D	0.76494	0.995;0.999	P;P	0.61477	0.889;0.889	T	0.02320	-1.1177	10	0.56958	D	0.05	-12.0933	15.5388	0.76024	0.1385:0.8615:0.0:0.0	.	657;763	B4DKA8;P40818	.;UBP8_HUMAN	W	763;763;763;657	ENSP00000379721:R763W;ENSP00000405537:R763W;ENSP00000302239:R763W;ENSP00000412682:R657W	ENSP00000302239:R763W	R	+	1	2	USP8	48572242	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.586000	0.53950	2.593000	0.87608	0.650000	0.86243	CGG	-	NULL		0.403	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	USP8	protein_coding	OTTHUMT00000254541.1	C	NM_005154	rs78143971		50784950	+1	no_errors	ENST00000307179	ensembl	human	known	74_37	missense	SNP	1.000	T
MUC6	4588	genome.wustl.edu	37	11	1031025	1031025	+	Silent	SNP	G	G	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr11:1031025G>T	ENST00000421673.2	-	6	656	c.606C>A	c.(604-606)gcC>gcA	p.A202A		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	202	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GCTTCTGGAGGGCAGCAAACT	0.682																																																	0								ENSG00000184956						36.0	42.0	40.0					11																	1031025		1927	4109	6036	MUC6	SO:0001819	synonymous_variant	0			-	HGNC	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.606C>A	11.37:g.1031025G>T		Somatic	0	48	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	11	16	40.74	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_VWF_type-D,pfam_Unchr_dom_Cys-rich,pfam_TIL_dom,superfamily_TIL_dom,smart_VWF_type-D,smart_Unchr_dom_Cys-rich,smart_VWC_out,smart_Cys_knot_C,pfscan_Cys_knot_C	p.A202	ENST00000421673.2	37	c.606	CCDS44513.1	11																																																																																			-	NULL		0.682	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MUC6	protein_coding	OTTHUMT00000382120.2	G	XM_290540	-		1031025	-1	no_errors	ENST00000421673	ensembl	human	known	74_37	silent	SNP	0.015	T
POTEH	23784	genome.wustl.edu	37	22	16277955	16277955	+	Intron	SNP	A	A	G	rs4819442		TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr22:16277955A>G	ENST00000343518.6	-	5	1080				POTEH-AS1_ENST00000422014.1_RNA|RNU6-816P_ENST00000390914.1_RNA	NM_001136213.1	NP_001129685.1	Q6S545	POTEH_HUMAN	POTE ankyrin domain family, member H											NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(20)|ovary(1)|skin(7)|urinary_tract(2)	37						TTACCAATTTAACATCTTGCC	0.338																																																	0								ENSG00000236666																																			POTEH-AS1	SO:0001627	intron_variant	0			-	HGNC	AY462874	CCDS74808.1	22q11.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000198062	ENSG00000198062		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	133	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 7"""	608913	"""actin, beta-like 1"", ""ANKRD26-like family C, member 3"""	ACTBL1, A26C3		10591208, 15276201, 21439273	Standard	NM_001136213		Approved	POTE22, CT104.7	uc010gqp.2	Q6S545	OTTHUMG00000140314	ENST00000343518.6:c.1029-70T>C	22.37:g.16277955A>G		Somatic	0	20	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	15	25.00	A2CEK4|A6NCI1|A9Z1W0	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000343518.6	37	NULL	CCDS46658.1	22																																																																																			-	-		0.338	POTEH-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	POTEH-AS1	protein_coding	OTTHUMT00000276918.4	A	NM_001136213	-		16277955	+1	no_errors	ENST00000422014	ensembl	human	known	74_37	rna	SNP	0.004	G
NPC1	4864	genome.wustl.edu	37	18	21119815	21119815	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr18:21119815G>T	ENST00000269228.5	-	18	3309	c.2755C>A	c.(2755-2757)Ctg>Atg	p.L919M	NPC1_ENST00000412552.2_Missense_Mutation_p.L601M|NPC1_ENST00000540608.1_5'UTR	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	919					adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TGCTGCACCAGGGAATCATTG	0.567																																																	0								ENSG00000141458						83.0	77.0	79.0					18																	21119815		2203	4300	6503	NPC1	SO:0001583	missense	0			-	HGNC	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.2755C>A	18.37:g.21119815G>T	ENSP00000269228:p.Leu919Met	Somatic	0	34	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	41	10.87	B4DET3|Q9P130	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Patched,pfam_MMPL_dom,pfscan_SSD,tigrfam_NP_C_type	p.L919M	ENST00000269228.5	37	c.2755	CCDS11878.1	18	.	.	.	.	.	.	.	.	.	.	G	21.5	4.162771	0.78226	.	.	ENSG00000141458	ENST00000269228;ENST00000412552;ENST00000540608	D;D	0.95272	-3.66;-3.66	5.51	2.72	0.32119	.	0.068566	0.64402	D	0.000018	D	0.96571	0.8881	M	0.89904	3.07	0.54753	D	0.999986	D;D	0.56968	0.978;0.978	P;D	0.63192	0.883;0.912	D	0.94645	0.7834	10	0.56958	D	0.05	-11.8642	6.3668	0.21459	0.209:0.1319:0.6591:0.0	.	930;919	Q59GR1;O15118	.;NPC1_HUMAN	M	919;601;764	ENSP00000269228:L919M;ENSP00000408606:L601M	ENSP00000269228:L919M	L	-	1	2	NPC1	19373813	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	4.173000	0.58249	0.365000	0.24400	0.650000	0.86243	CTG	-	tigrfam_NP_C_type		0.567	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NPC1	protein_coding	OTTHUMT00000254823.2	G	NM_000271	-		21119815	-1	no_errors	ENST00000269228	ensembl	human	known	74_37	missense	SNP	0.992	T
USP8	9101	genome.wustl.edu	37	15	50784955	50784955	+	Missense_Mutation	SNP	C	C	A	rs74840283		TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr15:50784955C>A	ENST00000396444.3	+	15	2630	c.2292C>A	c.(2290-2292)aaC>aaA	p.N764K	USP8_ENST00000433963.1_Missense_Mutation_p.N764K|USP8_ENST00000307179.4_Missense_Mutation_p.N764K|USP8_ENST00000425032.3_Missense_Mutation_p.N658K|RP11-562A8.5_ENST00000560159.1_lincRNA	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	764					cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		AGATTCGGAACCTCAATCCTG	0.408																																																	0								ENSG00000138592						135.0	121.0	126.0					15																	50784955		2196	4294	6490	USP8	SO:0001583	missense	0			-	HGNC	D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"""Ubiquitin-specific peptidases"""	12631	protein-coding gene	gene with protein product		603158	"""ubiquitin specific protease 8"""			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.2292C>A	15.37:g.50784955C>A	ENSP00000379721:p.Asn764Lys	Somatic	0	29	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	9	34	20.93	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Peptidase_C19/C67,pfam_USP8_dimer,pfam_Rhodanese-like_dom,superfamily_Rhodanese-like_dom,superfamily_WW_dom,pfscan_Rhodanese-like_dom,pfscan_Peptidase_C19/C67	p.N764K	ENST00000396444.3	37	c.2292	CCDS10137.1	15	.	.	.	.	.	.	.	.	.	.	C	18.56	3.650128	0.67472	.	.	ENSG00000138592	ENST00000396444;ENST00000433963;ENST00000307179;ENST00000425032	T;T;T;T	0.18174	2.23;2.23;2.23;2.27	5.22	2.26	0.28386	.	0.395808	0.31859	N	0.006953	T	0.09069	0.0224	N	0.24115	0.695	0.48696	D	0.999694	B;B	0.26672	0.083;0.156	B;B	0.21546	0.035;0.03	T	0.19224	-1.0312	10	0.10902	T	0.67	-18.6446	9.071	0.36493	0.0:0.5813:0.0:0.4187	.	658;764	B4DKA8;P40818	.;UBP8_HUMAN	K	764;764;764;658	ENSP00000379721:N764K;ENSP00000405537:N764K;ENSP00000302239:N764K;ENSP00000412682:N658K	ENSP00000302239:N764K	N	+	3	2	USP8	48572247	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.755000	0.26405	0.695000	0.31675	0.650000	0.86243	AAC	-	NULL		0.408	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	USP8	protein_coding	OTTHUMT00000254541.1	C	NM_005154	rs74840283		50784955	+1	no_errors	ENST00000307179	ensembl	human	known	74_37	missense	SNP	1.000	A
GLRA1	2741	genome.wustl.edu	37	5	151235943	151235943	+	Splice_Site	SNP	T	T	C			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr5:151235943T>C	ENST00000455880.2	-	5	764	c.478A>G	c.(478-480)Atc>Gtc	p.I160V	GLRA1_ENST00000545569.1_Splice_Site_p.I77V|GLRA1_ENST00000471351.2_5'UTR|GLRA1_ENST00000274576.4_Splice_Site_p.I160V			P23415	GLRA1_HUMAN	glycine receptor, alpha 1	160					acrosome reaction (GO:0007340)|action potential (GO:0001508)|adult walking behavior (GO:0007628)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|muscle contraction (GO:0006936)|negative regulation of transmission of nerve impulse (GO:0051970)|neuromuscular process controlling posture (GO:0050884)|neuropeptide signaling pathway (GO:0007218)|positive regulation of acrosome reaction (GO:2000344)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|righting reflex (GO:0060013)|startle response (GO:0001964)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|external side of plasma membrane (GO:0009897)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|taurine binding (GO:0030977)|transmitter-gated ion channel activity (GO:0022824)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	23		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Ginkgo biloba(DB01381)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Lindane(DB00431)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	GTCAGGGTGATTCTGGGAAGA	0.473																																																	0								ENSG00000145888						97.0	89.0	92.0					5																	151235943		2203	4300	6503	GLRA1	SO:0001630	splice_region_variant	0			-	HGNC		CCDS4320.1, CCDS54942.1	5q33.1	2012-02-07	2008-01-24		ENSG00000145888	ENSG00000145888		"""Ligand-gated ion channels / Glycine receptors"""	4326	protein-coding gene	gene with protein product	"""startle disease/hyperekplexia"", ""stiff person syndrome"""	138491	"""glycine receptor, alpha 1 (startle disease/hyperekplexia)"""	STHE		1355335, 8298642	Standard	NM_000171		Approved		uc003lut.3	P23415	OTTHUMG00000130121	ENST00000455880.2:c.477-1A>G	5.37:g.151235943T>C		Somatic	0	25	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	8	45	15.09	B2R6T3|Q14C77|Q6DJV9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Neur_chan_lig-bd,pfam_Neurotrans-gated_channel_TM,superfamily_Neur_chan_lig-bd,superfamily_Neurotrans-gated_channel_TM,prints_GABAA_rcpt,prints_Glycine_rcpt_A,prints_Glycine_rcpt_A1,prints_Neur_channel,tigrfam_Neur_channel	p.I160V	ENST00000455880.2	37	c.478	CCDS54942.1	5	.	.	.	.	.	.	.	.	.	.	T	13.76	2.333919	0.41297	.	.	ENSG00000145888	ENST00000274576;ENST00000455880;ENST00000545569	T;T;T	0.79454	-1.27;-1.27;-1.27	4.78	4.78	0.61160	Neurotransmitter-gated ion-channel ligand-binding (3);	0.097831	0.64402	D	0.000002	T	0.72415	0.3457	L	0.43646	1.37	0.41149	D	0.986013	B;B;B	0.22480	0.067;0.07;0.055	B;B;B	0.33121	0.158;0.158;0.098	T	0.70252	-0.4923	10	0.42905	T	0.14	.	10.7437	0.46168	0.0:0.0:0.1593:0.8407	.	160;77;160	P23415;Q14C71;P23415-2	GLRA1_HUMAN;.;.	V	160;160;77	ENSP00000274576:I160V;ENSP00000411593:I160V;ENSP00000445913:I77V	ENSP00000274576:I160V	I	-	1	0	GLRA1	151216136	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	1.585000	0.36600	1.914000	0.55421	0.477000	0.44152	ATC	-	pfam_Neur_chan_lig-bd,superfamily_Neur_chan_lig-bd,tigrfam_Neur_channel		0.473	GLRA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GLRA1	protein_coding	OTTHUMT00000373959.1	T		-	Missense_Mutation	151235943	-1	no_errors	ENST00000455880	ensembl	human	known	74_37	missense	SNP	1.000	C
THSD7B	80731	genome.wustl.edu	37	2	137814638	137814638	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr2:137814638G>T	ENST00000409968.1	+	3	966	c.788G>T	c.(787-789)gGa>gTa	p.G263V	THSD7B_ENST00000543459.1_Missense_Mutation_p.G122V|THSD7B_ENST00000272643.3_Missense_Mutation_p.G263V|THSD7B_ENST00000413152.2_Missense_Mutation_p.G232V			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	263						integral component of membrane (GO:0016021)				NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		AATCCAAGCGGAAGAACTGTT	0.393																																																	0								ENSG00000144229						120.0	118.0	119.0					2																	137814638		1870	4117	5987	THSD7B	SO:0001583	missense	0			-	HGNC			2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.788G>T	2.37:g.137814638G>T	ENSP00000387145:p.Gly263Val	Somatic	0	44	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	34	10.26		Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Thrombospondin_1_rpt,superfamily_Thrombospondin_1_rpt,smart_Thrombospondin_1_rpt,pfscan_Thrombospondin_1_rpt	p.G263V	ENST00000409968.1	37	c.788		2	.	.	.	.	.	.	.	.	.	.	G	11.61	1.688561	0.29962	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152;ENST00000543459	T;T;T;T	0.24723	2.41;2.28;1.89;1.84	5.45	0.41	0.16387	.	0.315850	0.38381	N	0.001718	T	0.38214	0.1032	M	0.72894	2.215	0.80722	D	1	P;D	0.54397	0.929;0.966	P;D	0.68943	0.862;0.961	T	0.34229	-0.9837	10	0.16420	T	0.52	.	5.8153	0.18490	0.3522:0.1258:0.522:0.0	.	263;232	Q9C0I4;C9JKN6	THS7B_HUMAN;.	V	263;263;232;122	ENSP00000387145:G263V;ENSP00000272643:G263V;ENSP00000413841:G232V;ENSP00000443370:G122V	ENSP00000272643:G263V	G	+	2	0	THSD7B	137531108	1.000000	0.71417	0.137000	0.22149	0.145000	0.21501	2.192000	0.42649	-0.126000	0.11682	0.585000	0.79938	GGA	-	NULL		0.393	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	THSD7B	protein_coding	OTTHUMT00000331769.2	G	XM_046570.9	-		137814638	+1	no_errors	ENST00000272643	ensembl	human	known	74_37	missense	SNP	0.910	T
SRSF5	6430	genome.wustl.edu	37	14	70234913	70234930	+	In_Frame_Del	DEL	GCGGCCAGGGAGAAGGAC	GCGGCCAGGGAGAAGGAC	-	rs149960633		TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	GCGGCCAGGGAGAAGGAC	GCGGCCAGGGAGAAGGAC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr14:70234913_70234930delGCGGCCAGGGAGAAGGAC	ENST00000553521.1	+	3	1493_1510	c.40_57delGCGGCCAGGGAGAAGGAC	c.(40-57)gcggccagggagaaggacdel	p.AAREKD14del	SRSF5_ENST00000557154.1_In_Frame_Del_p.AAREKD14del|SRSF5_ENST00000553548.1_In_Frame_Del_p.AAREKD14del|SRSF5_ENST00000554021.1_In_Frame_Del_p.AAREKD14del|SRSF5_ENST00000553635.1_In_Frame_Del_p.AAREKD14del|SRSF5_ENST00000394366.2_In_Frame_Del_p.AAREKD14del|SRSF5_ENST00000555349.1_In_Frame_Del_p.AAREKD14del|SRSF5_ENST00000556587.1_3'UTR|SRSF5_ENST00000451983.2_In_Frame_Del_p.AAREKD14del			Q13243	SRSF5_HUMAN	serine/arginine-rich splicing factor 5	14	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of cell cycle (GO:0051726)|response to wounding (GO:0009611)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			large_intestine(1)|liver(1)	2						ACTAAATCCAGCGGCCAGGGAGAAGGACGTGGAAAGAT	0.427																																																	0								ENSG00000100650																																			SRSF5	SO:0001651	inframe_deletion	0				HGNC	AF020307	CCDS32109.1	14q24	2013-02-12	2010-06-22	2010-06-22	ENSG00000100650	ENSG00000100650		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10787	protein-coding gene	gene with protein product	"""SR splicing factor 5"""	600914	"""splicing factor, arginine/serine-rich 5"""	SFRS5		7686911, 20516191	Standard	XM_005267998		Approved	SRP40, HRS	uc001xlp.3	Q13243		ENST00000553521.1:c.40_57delGCGGCCAGGGAGAAGGAC	14.37:g.70234913_70234930delGCGGCCAGGGAGAAGGAC	ENSP00000452123:p.Ala14_Asp19del	Somatic	NA	NA	NA		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	O14797|Q16662|Q49AD6|Q6FGE0	In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom	p.AAREKD14in_frame_del	ENST00000553521.1	37	c.40_57	CCDS32109.1	14																																																																																			-	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom		0.427	SRSF5-003	NOVEL	basic|appris_principal|CCDS	protein_coding	SRSF5	protein_coding	OTTHUMT00000412456.1	GCGGCCAGGGAGAAGGAC	NM_001039465			70234930	+1	no_errors	ENST00000451983	ensembl	human	known	74_37	in_frame_del	DEL	0.897:0.990:0.986:1.000:1.000:1.000:0.990:1.000:1.000:1.000:1.000:1.000:1.000:1.000:0.993:1.000:1.000:1.000	-
RYR1	6261	genome.wustl.edu	37	19	38951142	38951142	+	Missense_Mutation	SNP	C	C	T	rs142548565		TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr19:38951142C>T	ENST00000359596.3	+	20	2488	c.2488C>T	c.(2488-2490)Cgg>Tgg	p.R830W	RYR1_ENST00000355481.4_Missense_Mutation_p.R830W|RYR1_ENST00000360985.3_Missense_Mutation_p.R830W			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	830					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.R830W(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGAGTATCGACGGGAGGGGCC	0.632																																																	1	Substitution - Missense(1)	large_intestine(1)						ENSG00000196218	C	TRP/ARG,TRP/ARG	0,4406		0,0,2203	68.0	73.0	71.0		2488,2488	1.9	0.9	19	dbSNP_134	71	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	RYR1	NM_000540.2,NM_001042723.1	101,101	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	probably-damaging,probably-damaging	830/5039,830/5034	38951142	4,13002	2203	4300	6503	RYR1	SO:0001583	missense	0			-	HGNC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.2488C>T	19.37:g.38951142C>T	ENSP00000352608:p.Arg830Trp	Somatic	0	35	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	43	8.51	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Ca-rel_channel,pfam_Ryanodine_rcpt,pfam_Ryanrecept_TM4-6,pfam_SPRY_rcpt,pfam_Ins145_P3_rcpt,pfam_MIR_motif,pfam_RIH_assoc-dom,pfam_Ion_trans_dom,superfamily_MIR_motif,superfamily_ConA-like_lec_gl_sf,superfamily_MG_RAP_rcpt_1,smart_MIR_motif,smart_SPla/RYanodine_receptor_subgr,prints_Ryan_recept,pfscan_B30.2/SPRY,pfscan_MIR_motif	p.R830W	ENST00000359596.3	37	c.2488	CCDS33011.1	19	.	.	.	.	.	.	.	.	.	.	c	15.55	2.866632	0.51588	0.0	4.65E-4	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.96940	-4.17;-4.18;-4.17	4.13	1.89	0.25635	.	0.091594	0.43416	U	0.000573	D	0.96583	0.8885	L	0.57536	1.79	0.26910	N	0.966923	D;D	0.89917	1.0;0.999	D;D	0.70016	0.967;0.96	D	0.91398	0.5141	10	0.51188	T	0.08	.	8.8285	0.35069	0.3047:0.556:0.1393:0.0	.	830;830	P21817-2;P21817	.;RYR1_HUMAN	W	830	ENSP00000352608:R830W;ENSP00000347667:R830W;ENSP00000354254:R830W	ENSP00000347667:R830W	R	+	1	2	RYR1	43642982	0.468000	0.25839	0.892000	0.35008	0.972000	0.66771	1.165000	0.31822	0.447000	0.26695	0.299000	0.19835	CGG	-	NULL		0.632	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RYR1	protein_coding	OTTHUMT00000462137.1	C		rs142548565		38951142	+1	no_errors	ENST00000359596	ensembl	human	known	74_37	missense	SNP	0.739	T
ZNF19	7567	genome.wustl.edu	37	16	71509307	71509307	+	Missense_Mutation	SNP	C	C	A			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr16:71509307C>A	ENST00000288177.5	-	6	1398	c.1143G>T	c.(1141-1143)caG>caT	p.Q381H	AC010547.9_ENST00000561908.1_Intron|ZNF19_ENST00000565100.2_Missense_Mutation_p.Q311H|ZNF19_ENST00000564230.1_Missense_Mutation_p.Q381H|ZNF19_ENST00000565637.1_Missense_Mutation_p.Q339H|ZNF19_ENST00000567225.1_Intron	NM_006961.3	NP_008892.2	P17023	ZNF19_HUMAN	zinc finger protein 19	381					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|prostate(1)|stomach(1)	22		Ovarian(137;0.00965)		BRCA - Breast invasive adenocarcinoma(221;0.0161)|Kidney(780;0.0598)		AGGAAGACTCCTGAGTATGAA	0.403																																																	0								ENSG00000157429						89.0	87.0	87.0					16																	71509307		2198	4300	6498	ZNF19	SO:0001583	missense	0			-	HGNC	X52343	CCDS10901.1	16q22	2013-01-08	2006-05-10		ENSG00000157429	ENSG00000157429		"""Zinc fingers, C2H2-type"", ""-"""	12981	protein-coding gene	gene with protein product		194525	"""zinc finger protein 19 (KOX 12)"""			1505991, 1946370	Standard	NM_006961		Approved	KOX12, MGC51021	uc002fam.1	P17023	OTTHUMG00000137593	ENST00000288177.5:c.1143G>T	16.37:g.71509307C>A	ENSP00000288177:p.Gln381His	Somatic	0	67	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	14	60	18.92	A8K895|Q86Y66|Q8NDE2|Q96M79|Q96NE5	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.Q381H	ENST00000288177.5	37	c.1143	CCDS10901.1	16	.	.	.	.	.	.	.	.	.	.	C	8.104	0.777201	0.16120	.	.	ENSG00000157429	ENST00000288177	T	0.18810	2.19	3.27	-0.948	0.10379	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.539851	0.13974	N	0.349970	T	0.20981	0.0505	L	0.42632	1.34	0.23886	N	0.996561	P	0.40731	0.728	P	0.46110	0.504	T	0.15665	-1.0429	10	0.87932	D	0	.	7.5294	0.27674	0.0:0.5757:0.0:0.4243	.	381	P17023	ZNF19_HUMAN	H	381	ENSP00000288177:Q381H	ENSP00000288177:Q381H	Q	-	3	2	ZNF19	70066808	0.000000	0.05858	0.001000	0.08648	0.108000	0.19459	-3.209000	0.00557	-0.149000	0.11215	-0.150000	0.13652	CAG	-	pfscan_Znf_C2H2		0.403	ZNF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF19	protein_coding	OTTHUMT00000268993.2	C	NM_006961	-		71509307	-1	no_errors	ENST00000288177	ensembl	human	known	74_37	missense	SNP	0.938	A
EPPK1	83481	genome.wustl.edu	37	8	144940666	144940666	+	Silent	SNP	G	G	A	rs368004220		TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr8:144940666G>A	ENST00000525985.1	-	2	6827	c.6756C>T	c.(6754-6756)ggC>ggT	p.G2252G				P58107	EPIPL_HUMAN	epiplakin 1	2252						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GCCGCAGCACGCCCTTCCACA	0.711																																																	0								ENSG00000227184	G		1,4367		0,1,2183	55.0	52.0	53.0		6756	1.8	0.9	8		53	14,8508		0,14,4247	no	coding-synonymous	EPPK1	NM_031308.1		0,15,6430	AA,AG,GG		0.1643,0.0229,0.1164		2252/2420	144940666	15,12875	2184	4261	6445	EPPK1	SO:0001819	synonymous_variant	0			-	HGNC	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.6756C>T	8.37:g.144940666G>A		Somatic	0	40	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	32	13.51	Q76E58|Q9NSU9	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Plectin_repeat,smart_Plectin_repeat	p.G2252	ENST00000525985.1	37	c.6756		8																																																																																			-	pfam_Plectin_repeat,smart_Plectin_repeat		0.711	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	EPPK1	protein_coding	OTTHUMT00000382675.1	G	NM_031308	-		144940666	-1	no_errors	ENST00000525985	ensembl	human	known	74_37	silent	SNP	0.192	A
COL28A1	340267	genome.wustl.edu	37	7	7550731	7550731	+	Silent	SNP	T	T	C			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr7:7550731T>C	ENST00000399429.3	-	9	1058	c.918A>G	c.(916-918)aaA>aaG	p.K306K		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	306	Collagen-like 2.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		CCTTGTCACCTTTTATCCCTG	0.378																																																	0								ENSG00000215018						138.0	126.0	130.0					7																	7550731		1856	4103	5959	COL28A1	SO:0001819	synonymous_variant	0			-	HGNC	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.918A>G	7.37:g.7550731T>C		Somatic	0	49	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	9	23	28.12	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Collagen,pfam_VWF_A,pfam_Prot_inh_Kunz-m,superfamily_Prot_inh_Kunz-m,smart_VWF_A,smart_Prot_inh_Kunz-m,pfscan_VWF_A,pfscan_Prot_inh_Kunz-m	p.K306	ENST00000399429.3	37	c.918	CCDS43553.1	7																																																																																			-	NULL		0.378	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL28A1	protein_coding	OTTHUMT00000315899.1	T	NM_001037763	-		7550731	-1	no_errors	ENST00000399429	ensembl	human	known	74_37	silent	SNP	1.000	C
FBXO38	81545	genome.wustl.edu	37	5	147774413	147774413	+	Missense_Mutation	SNP	A	A	G			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr5:147774413A>G	ENST00000340253.5	+	2	242	c.74A>G	c.(73-75)gAa>gGa	p.E25G	FBXO38_ENST00000513826.1_Missense_Mutation_p.E25G|FBXO38_ENST00000394370.3_Missense_Mutation_p.E25G|FBXO38_ENST00000509699.2_3'UTR|FBXO38_ENST00000296701.6_Missense_Mutation_p.E25G			Q6PIJ6	FBX38_HUMAN	F-box protein 38	25					cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)			ATG4C/FBXO38(2)	NS(1)|breast(2)|endometrium(7)|kidney(5)|large_intestine(9)|lung(15)|ovary(5)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACAGCAGATGAAACAAAGGAC	0.383																																																	0								ENSG00000145868						178.0	165.0	170.0					5																	147774413		2203	4300	6503	FBXO38	SO:0001583	missense	0			-	HGNC	BC005873	CCDS43384.1, CCDS64285.1	5q33.1	2008-02-05			ENSG00000145868	ENSG00000145868		"""F-boxes /  ""other"""""	28844	protein-coding gene	gene with protein product		608533				12477932	Standard	NM_030793		Approved	MOKA, SP329, FLJ13962, Fbx38	uc003lpg.2	Q6PIJ6	OTTHUMG00000129929	ENST00000340253.5:c.74A>G	5.37:g.147774413A>G	ENSP00000342023:p.Glu25Gly	Somatic	0	64	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	26	102	20.31	Q6PK72|Q7Z2U0|Q86VN3|Q9BXY6|Q9H837|Q9HC40	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	superfamily_F-box_dom	p.E25G	ENST00000340253.5	37	c.74		5	.	.	.	.	.	.	.	.	.	.	A	20.9	4.062369	0.76187	.	.	ENSG00000145868	ENST00000340253;ENST00000296701;ENST00000394370;ENST00000513826	T;T;T;T	0.35236	1.32;1.34;1.32;1.34	5.56	5.56	0.83823	F-box domain, Skp2-like (1);	0.047993	0.85682	D	0.000000	T	0.29389	0.0732	L	0.27053	0.805	0.80722	D	1	P;P;B	0.50528	0.936;0.763;0.447	B;B;B	0.41917	0.37;0.311;0.075	T	0.10042	-1.0647	10	0.66056	D	0.02	-9.1294	14.8438	0.70246	1.0:0.0:0.0:0.0	.	25;25;25	Q6PIJ6-3;Q6PIJ6-2;Q6PIJ6	.;.;FBX38_HUMAN	G	25	ENSP00000342023:E25G;ENSP00000296701:E25G;ENSP00000377895:E25G;ENSP00000426410:E25G	ENSP00000296701:E25G	E	+	2	0	FBXO38	147754606	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	8.105000	0.89553	2.240000	0.73641	0.533000	0.62120	GAA	-	superfamily_F-box_dom		0.383	FBXO38-002	KNOWN	basic|appris_principal	protein_coding	FBXO38	protein_coding	OTTHUMT00000252185.2	A	NM_030793	-		147774413	+1	no_errors	ENST00000340253	ensembl	human	known	74_37	missense	SNP	1.000	G
TBX3	6926	genome.wustl.edu	37	12	115112627	115112627	+	Silent	SNP	G	G	A			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr12:115112627G>A	ENST00000257566.3	-	7	1502	c.1113C>T	c.(1111-1113)agC>agT	p.S371S	TBX3_ENST00000349155.2_Silent_p.S351S	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	371					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		TCTCACCCTCGCTGGGACATA	0.602																																																	0								ENSG00000135111						7.0	8.0	8.0					12																	115112627		2150	4185	6335	TBX3	SO:0001819	synonymous_variant	0			-	HGNC	BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"""T-boxes"""	11602	protein-coding gene	gene with protein product		601621	"""ulnar mammary syndrome"""	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.1113C>T	12.37:g.115112627G>A		Somatic	0	36	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	14	32	30.43	Q8TB20|Q9UKF8	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_TF_T-box,pfam_TBX,superfamily_p53-like_TF_DNA-bd,smart_TF_T-box,pfscan_TF_T-box,prints_TF_T-box	p.S371	ENST00000257566.3	37	c.1113	CCDS9176.1	12																																																																																			-	pfam_TBX		0.602	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TBX3	protein_coding	OTTHUMT00000404947.2	G	NM_016569, NM_005996	-		115112627	-1	no_errors	ENST00000257566	ensembl	human	known	74_37	silent	SNP	1.000	A
RP11-159F24.2	0	genome.wustl.edu	37	5	43348817	43348817	+	RNA	DEL	A	A	-	rs553054916	byFrequency	TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr5:43348817delA	ENST00000511991.1	+	0	431																											CCAAACTCTTAAAAAAAAAAA	0.338														4	0.000798722	0.0023	0.0014	5008	,	,		18773	0.0		0.0	False		,,,				2504	0.0																0								ENSG00000188850																																			RP11-159F24.2			0				Clone_based_vega_gene																													5.37:g.43348817delA		Somatic	0	15	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	21	12.50		RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000511991.1	37	NULL		5																																																																																			-	-		0.338	RP11-159F24.2-001	KNOWN	basic	processed_transcript	ENSG00000188850	pseudogene	OTTHUMT00000367972.1	A				43348817	+1	no_errors	ENST00000511991	ensembl	human	known	74_37	rna	DEL	0.000	-
CFP	5199	genome.wustl.edu	37	X	47487931	47487931	+	Intron	SNP	C	C	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chrX:47487931C>T	ENST00000396992.3	-	3	348				CFP_ENST00000247153.3_Intron|CFP_ENST00000480317.1_5'UTR|CFP_ENST00000377005.2_Intron	NM_001145252.1	NP_001138724.1	P27918	PROP_HUMAN	complement factor properdin						complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	18						AACACCAGGTCCGCAGTAAGC	0.453																																																	0								ENSG00000126759																																			CFP	SO:0001627	intron_variant	0			-	HGNC	M83652	CCDS14282.1	Xp11.4	2014-09-17	2006-03-02	2006-03-02	ENSG00000126759	ENSG00000126759		"""Complement system"""	8864	protein-coding gene	gene with protein product		300383	"""properdin P factor, complement"""	PFC		1783405	Standard	NM_001145252		Approved		uc004dih.3	P27918	OTTHUMG00000021451	ENST00000396992.3:c.228-255G>A	X.37:g.47487931C>T		Somatic	0	88	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	15	133	10.14	O15134|O15135|O15136|O75826	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000396992.3	37	NULL	CCDS14282.1	X																																																																																			-	-		0.453	CFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CFP	protein_coding	OTTHUMT00000056435.2	C	NM_002621	-		47487931	-1	no_errors	ENST00000480317	ensembl	human	known	74_37	rna	SNP	0.000	T
TP53	7157	genome.wustl.edu	37	17	7577033	7577033	+	Missense_Mutation	SNP	C	C	A			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr17:7577033C>A	ENST00000269305.4	-	8	1094	c.905G>T	c.(904-906)gGg>gTg	p.G302V	TP53_ENST00000445888.2_Missense_Mutation_p.G302V|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.G302V|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Missense_Mutation_p.G302V|TP53_ENST00000420246.2_Missense_Mutation_p.G302V	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	302	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.		G -> A (in a sporadic cancer; somatic mutation).|G -> E (in sporadic cancers; somatic mutation).|G -> R (in a sporadic cancer; somatic mutation).|G -> V (in a sporadic cancer; 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.0?(8)|p.?(3)|p.G302E(3)|p.P301_S303delPGS(1)|p.L299fs*2(1)|p.L265_K305del41(1)|p.G302fs*2(1)|p.G293fs*1(1)|p.H296_S303delHHELPPGS(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)	CTTAGTGCTCCCTGGGGGCAG	0.557		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)																											Pancreas(47;798 1329 9957 10801)		yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	20	Whole gene deletion(8)|Substitution - Missense(3)|Unknown(3)|Deletion - In frame(3)|Deletion - Frameshift(3)	bone(5)|breast(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|central_nervous_system(2)|stomach(1)|urinary_tract(1)|lung(1)|oesophagus(1)						ENSG00000141510						113.0	99.0	104.0					17																	7577033		2203	4300	6503	TP53	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;	-	HGNC	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.905G>T	17.37:g.7577033C>A	ENSP00000269305:p.Gly302Val	Somatic	0	60	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	31	24	56.36	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	NA	NA	NA	NA	NA	NA	pfam_p53_DNA-bd,pfam_p53_tetrameristn,pfam_p53_transactivation_domain,superfamily_p53-like_TF_DNA-bd,superfamily_p53_tetrameristn,prints_p53_tumour_suppressor	p.G302V	ENST00000269305.4	37	c.905	CCDS11118.1	17	.	.	.	.	.	.	.	.	.	.	C	17.35	3.367445	0.61513	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99760	-5.9;-5.62;-5.93;-5.92;-5.62;-6.66	5.26	2.06	0.26882	.	2.455680	0.01443	N	0.015197	D	0.99576	0.9847	M	0.85945	2.785	0.54753	D	0.999985	P;B;P;P	0.42556	0.745;0.355;0.783;0.751	P;B;P;B	0.48141	0.568;0.276;0.48;0.365	D	0.97727	1.0200	10	0.66056	D	0.02	-10.7674	6.155	0.20332	0.0:0.6957:0.0:0.3043	.	302;302;302;302	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	V	302;302;302;302;302;291;170	ENSP00000352610:G302V;ENSP00000269305:G302V;ENSP00000398846:G302V;ENSP00000391127:G302V;ENSP00000391478:G302V;ENSP00000425104:G170V	ENSP00000269305:G302V	G	-	2	0	TP53	7517758	0.000000	0.05858	0.095000	0.20976	0.224000	0.24922	0.496000	0.22499	0.804000	0.34136	0.561000	0.74099	GGG	-	NULL		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TP53	protein_coding	OTTHUMT00000367397.1	C	NM_000546	-		7577033	-1	no_errors	ENST00000269305	ensembl	human	known	74_37	missense	SNP	0.865	A
TADA3	10474	genome.wustl.edu	37	3	9833131	9833131	+	Missense_Mutation	SNP	C	C	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr3:9833131C>T	ENST00000301964.2	-	2	578	c.20G>A	c.(19-21)tGc>tAc	p.C7Y	TADA3_ENST00000440161.1_Missense_Mutation_p.C7Y|TADA3_ENST00000492635.1_Intron|ARPC4_ENST00000498623.2_5'Flank|ARPC4_ENST00000287613.7_5'Flank|ARPC4_ENST00000433034.1_5'Flank|ARPC4_ENST00000397261.3_5'Flank|TADA3_ENST00000343450.2_Missense_Mutation_p.C7Y|ARPC4-TTLL3_ENST00000397256.1_5'Flank	NM_006354.2	NP_006345.1	O75528	TADA3_HUMAN	transcriptional adaptor 3	7					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|intracellular estrogen receptor signaling pathway (GO:0030520)|mitotic nuclear division (GO:0007067)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of histone deacetylation (GO:0031063)|regulation of protein phosphorylation (GO:0001932)|regulation of protein stability (GO:0031647)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of tubulin deacetylation (GO:0090043)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|intracellular (GO:0005622)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	16						CTGCAAGGGGCAGTCTTTCAA	0.562																																																	0								ENSG00000171148						69.0	58.0	62.0					3																	9833131		2203	4300	6503	TADA3	SO:0001583	missense	0			-	HGNC	AF069733	CCDS2583.1, CCDS2584.1	3p25.3	2010-08-13	2009-10-02	2009-10-02	ENSG00000171148	ENSG00000171148			19422	protein-coding gene	gene with protein product		602945	"""transcriptional adaptor 3 (NGG1 homolog, yeast)-like"""	TADA3L		9674425, 11707411	Standard	NM_006354		Approved	FLJ20221, FLJ21329, ADA3, hADA3, NGG1	uc010hcn.2	O75528	OTTHUMG00000128440	ENST00000301964.2:c.20G>A	3.37:g.9833131C>T	ENSP00000307684:p.Cys7Tyr	Somatic	0	28	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	9	12	42.86	Q6FI83|Q9UFS2	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Histone_AcTrfase_su3	p.C7Y	ENST00000301964.2	37	c.20	CCDS2583.1	3	.	.	.	.	.	.	.	.	.	.	C	22.0	4.230430	0.79688	.	.	ENSG00000171148	ENST00000301964;ENST00000440161;ENST00000343450;ENST00000439043	.	.	.	4.77	3.88	0.44766	.	0.000000	0.85682	D	0.000000	T	0.44685	0.1305	L	0.50333	1.59	0.80722	D	1	D	0.56521	0.976	P	0.44359	0.447	T	0.49360	-0.8948	9	0.02654	T	1	-3.6403	14.1568	0.65422	0.1513:0.8487:0.0:0.0	.	7	O75528	TADA3_HUMAN	Y	7	.	ENSP00000307684:C7Y	C	-	2	0	TADA3	9808131	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.487000	0.81328	0.979000	0.38497	0.561000	0.74099	TGC	-	NULL		0.562	TADA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TADA3	protein_coding	OTTHUMT00000250236.1	C		-		9833131	-1	no_errors	ENST00000301964	ensembl	human	known	74_37	missense	SNP	1.000	T
GXYLT1	283464	genome.wustl.edu	37	12	42512805	42512805	+	Silent	SNP	G	G	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr12:42512805G>T	ENST00000398675.3	-	3	715	c.483C>A	c.(481-483)ggC>ggA	p.G161G	GXYLT1_ENST00000280876.6_Silent_p.G130G	NM_001099650.1|NM_173601.1	NP_001093120.1|NP_775872.1	Q4G148	GXLT1_HUMAN	glucoside xylosyltransferase 1	161					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|O-glycan processing (GO:0016266)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)			kidney(2)|large_intestine(4)|liver(3)|lung(8)	17						TACTTACTCTGCCTTTAAAGC	0.313																																																	0								ENSG00000151233						64.0	57.0	59.0					12																	42512805		1845	4085	5930	GXYLT1	SO:0001819	synonymous_variant	0			-	HGNC	BC015597	CCDS41771.1, CCDS41772.1	12q12	2013-10-11	2009-11-17	2009-11-17	ENSG00000151233	ENSG00000151233		"""Glycosyltransferase family 8 domain containing"""	27482	protein-coding gene	gene with protein product		613321	"""glycosyltransferase 8 domain containing 3"""	GLT8D3		19940119	Standard	NM_001099650		Approved	FLJ43151	uc001rms.4	Q4G148	OTTHUMG00000169379	ENST00000398675.3:c.483C>A	12.37:g.42512805G>T		Somatic	0	49	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	9	53	14.52	B3KWJ2|Q8IXV1|Q96BH4	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Glyco_trans_8	p.G161	ENST00000398675.3	37	c.483	CCDS41772.1	12																																																																																			-	NULL		0.313	GXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GXYLT1	protein_coding	OTTHUMT00000403778.1	G	XM_290597	-		42512805	-1	no_errors	ENST00000398675	ensembl	human	known	74_37	silent	SNP	0.962	T
KRTAP12-2	353323	genome.wustl.edu	37	21	46086641	46086641	+	Missense_Mutation	SNP	A	A	G			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr21:46086641A>G	ENST00000360770.3	-	1	203	c.163T>C	c.(163-165)Tgc>Cgc	p.C55R	TSPEAR_ENST00000323084.4_Intron	NM_181684.2	NP_859012.1	P59991	KR122_HUMAN	keratin associated protein 12-2	55	23 X 5 AA approximate repeats.					keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(1)|lung(3)	5						ACGGGCAGGCACACGGCTGGC	0.627																																																	0								ENSG00000221864						69.0	79.0	75.0					21																	46086641		2193	4282	6475	KRTAP12-2	SO:0001583	missense	0			-	HGNC	AJ566389	CCDS42965.1	21q22.3	2006-03-13			ENSG00000221864	ENSG00000221864		"""Keratin associated proteins"""	20530	protein-coding gene	gene with protein product							Standard	NM_181684		Approved	KRTAP12.2, KAP12.2	uc002zfu.3	P59991	OTTHUMG00000057636	ENST00000360770.3:c.163T>C	21.37:g.46086641A>G	ENSP00000354001:p.Cys55Arg	Somatic	0	62	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	19	30	38.78	A6NIS1|A6NMS9|Q0VAS4	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_KRTAP_PMG	p.C55R	ENST00000360770.3	37	c.163	CCDS42965.1	21	.	.	.	.	.	.	.	.	.	.	a	10.03	1.238613	0.22711	.	.	ENSG00000221864	ENST00000360770	T	0.06768	3.26	2.69	2.69	0.31865	.	.	.	.	.	T	0.14570	0.0352	M	0.85630	2.765	0.27643	N	0.947649	B	0.16396	0.017	B	0.10450	0.005	T	0.08743	-1.0707	9	0.87932	D	0	.	8.9666	0.35881	1.0:0.0:0.0:0.0	.	55	P59991	KR122_HUMAN	R	55	ENSP00000354001:C55R	ENSP00000354001:C55R	C	-	1	0	KRTAP12-2	44911069	0.001000	0.12720	0.011000	0.14972	0.017000	0.09413	0.358000	0.20216	1.280000	0.44463	0.321000	0.21382	TGC	-	pfam_KRTAP_PMG		0.627	KRTAP12-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KRTAP12-2	protein_coding	OTTHUMT00000128039.1	A	NM_181684	-		46086641	-1	no_errors	ENST00000360770	ensembl	human	known	74_37	missense	SNP	0.153	G
C17orf70	80233	genome.wustl.edu	37	17	79517588	79517588	+	Missense_Mutation	SNP	C	C	A			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr17:79517588C>A	ENST00000327787.8	-	3	978	c.932G>T	c.(931-933)tGc>tTc	p.C311F	C17orf70_ENST00000425898.2_5'Flank|C17orf70_ENST00000537152.1_Missense_Mutation_p.C160F			Q0VG06	FP100_HUMAN	chromosome 17 open reading frame 70	311					DNA repair (GO:0006281)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	19	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			GGCCACCAGGCAGTCACAGTG	0.612																																																	0								ENSG00000185504						46.0	48.0	47.0					17																	79517588		2202	4300	6502	C17orf70	SO:0001583	missense	0			-	HGNC	BC008883	CCDS32765.1, CCDS32765.2	17q25.3	2012-05-30			ENSG00000185504	ENSG00000185504			26171	protein-coding gene	gene with protein product	"""Fanconi anemia-associated protein, 100kDa"""	611301				17396147	Standard	NM_025161		Approved	FLJ22175, FAAP100	uc002kaq.3	Q0VG06	OTTHUMG00000167764	ENST00000327787.8:c.932G>T	17.37:g.79517588C>A	ENSP00000333283:p.Cys311Phe	Somatic	0	43	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	17	29.17	A6NNM1|Q8N3F7|Q9BV13|Q9H6K7|Q9H7E8	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.C311F	ENST00000327787.8	37	c.932	CCDS32765.2	17	.	.	.	.	.	.	.	.	.	.	C	17.61	3.433328	0.62844	.	.	ENSG00000185504	ENST00000327787;ENST00000537152;ENST00000541246;ENST00000544302	T;T	0.50001	0.76;0.79	3.91	2.89	0.33648	.	0.061261	0.64402	N	0.000003	T	0.64789	0.2630	M	0.72894	2.215	0.50039	D	0.999842	D	0.76494	0.999	D	0.87578	0.998	T	0.67094	-0.5757	10	0.87932	D	0	.	11.3157	0.49390	0.184:0.816:0.0:0.0	.	311	Q0VG06	FP100_HUMAN	F	311;160;160;160	ENSP00000333283:C311F;ENSP00000440151:C160F	ENSP00000333283:C311F	C	-	2	0	C17orf70	77128030	1.000000	0.71417	0.996000	0.52242	0.969000	0.65631	5.090000	0.64498	0.770000	0.33336	0.563000	0.77884	TGC	-	NULL		0.612	C17orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C17orf70	protein_coding	OTTHUMT00000396170.1	C	NM_025161	-		79517588	-1	no_errors	ENST00000327787	ensembl	human	known	74_37	missense	SNP	1.000	A
NKX2-2	4821	genome.wustl.edu	37	20	21494277	21494277	+	Missense_Mutation	SNP	A	A	C			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr20:21494277A>C	ENST00000377142.4	-	1	387	c.31T>G	c.(31-33)Tcg>Gcg	p.S11A	NKX2-2-AS1_ENST00000549659.1_RNA	NM_002509.3	NP_002500.1	O95096	NKX22_HUMAN	NK2 homeobox 2	11					astrocyte differentiation (GO:0048708)|brain development (GO:0007420)|digestive tract development (GO:0048565)|endocrine pancreas development (GO:0031018)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|oligodendrocyte development (GO:0014003)|optic nerve development (GO:0021554)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell fate commitment (GO:0003327)|ventral spinal cord interneuron fate determination (GO:0060580)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|core promoter proximal region DNA binding (GO:0001159)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21						TCCTTGACCGAAAACCCCGTC	0.567																																																	0								ENSG00000125820						65.0	65.0	65.0					20																	21494277		2203	4300	6503	NKX2-2	SO:0001583	missense	0			-	HGNC	AF019415	CCDS13145.1	20p11.22	2012-03-09	2007-07-09	2002-10-04	ENSG00000125820	ENSG00000125820		"""Homeoboxes / ANTP class : NKL subclass"""	7835	protein-coding gene	gene with protein product		604612	"""NK-2 (Drosophila) homolog B"", ""NK2 transcription factor related, locus 2 (Drosophila)"""	NKX2B		9703340, 1346742	Standard	NM_002509		Approved	NKX2.2	uc002wsi.3	O95096	OTTHUMG00000170524	ENST00000377142.4:c.31T>G	20.37:g.21494277A>C	ENSP00000366347:p.Ser11Ala	Somatic	0	50	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	35	35	50.00		Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Homeobox_dom,superfamily_Homeodomain-like,smart_Homeobox_dom,pfscan_Homeobox_dom,prints_Homeobox_metazoa	p.S11A	ENST00000377142.4	37	c.31	CCDS13145.1	20	.	.	.	.	.	.	.	.	.	.	A	18.61	3.662115	0.67700	.	.	ENSG00000125820	ENST00000377142	D	0.91011	-2.77	4.75	4.75	0.60458	.	0.071666	0.64402	D	0.000017	D	0.86577	0.5966	L	0.47716	1.5	0.46222	D	0.998938	P	0.34864	0.473	B	0.30105	0.111	D	0.87069	0.2158	10	0.66056	D	0.02	.	13.9483	0.64099	1.0:0.0:0.0:0.0	.	11	O95096	NKX22_HUMAN	A	11	ENSP00000366347:S11A	ENSP00000366347:S11A	S	-	1	0	NKX2-2	21442277	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.854000	0.75440	1.774000	0.52232	0.460000	0.39030	TCG	-	NULL		0.567	NKX2-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NKX2-2	protein_coding	OTTHUMT00000078278.9	A		-		21494277	-1	no_errors	ENST00000377142	ensembl	human	known	74_37	missense	SNP	1.000	C
ATRX	546	genome.wustl.edu	37	X	76888683	76888697	+	Splice_Site	DEL	TTAATACCTTACCTG	TTAATACCTTACCTG	-			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	TTAATACCTTACCTG	TTAATACCTTACCTG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chrX:76888683_76888697delTTAATACCTTACCTG	ENST00000373344.5	-	19	5346_5349	c.5132_5135delCAGGTAAGGTATTAA	c.(5131-5136)ccaggt>ct	p.PG1711del	ATRX_ENST00000395603.3_Splice_Site_p.PG1673del|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1711	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						TCACTGTCTATTAATACCTTACCTGGATCAACCAA	0.316			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																																	Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	1	Unknown(1)	bone(1)						ENSG00000085224																																			ATRX	SO:0001630	splice_region_variant	0				HGNC	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.5134+1CAGGTAAGGTATTAA>-	X.37:g.76888683_76888697delTTAATACCTTACCTG		Somatic	NA	NA	NA		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Splice_Site	DEL	NA	NA	NA	NA	NA	NA	-	e20-1	ENST00000373344.5	37	c.5134+4_5134+1	CCDS14434.1	X																																																																																			-	-		0.316	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ATRX	protein_coding	OTTHUMT00000058860.2	TTAATACCTTACCTG	NM_000489		In_Frame_Del	76888697	-1	no_errors	ENST00000373344	ensembl	human	known	74_37	splice_site_del	DEL	0.000:0.000:0.001:0.001:0.060:0.078:0.018:0.028:0.138:0.969:1.000:1.000:1.000:1.000:1.000	-
GOLGA6L4	643707	genome.wustl.edu	37	15	84909385	84909385	+	Missense_Mutation	SNP	G	G	A	rs77228815	byFrequency	TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr15:84909385G>A	ENST00000510439.2	+	6	1341	c.1279G>A	c.(1279-1281)Gat>Aat	p.D427N	GOLGA6L4_ENST00000424966.1_Missense_Mutation_p.D8N|GOLGA6L4_ENST00000422563.2_Missense_Mutation_p.D103N	NM_001267536.1	NP_001254465.1	A6NEF3	GG6L4_HUMAN	golgin A6 family-like 4	427																	TCGGCAACAGGATGAGAGGCT	0.657													g|||	1748	0.349042	0.4652	0.1729	5008	,	,		18779	0.4563		0.175	False		,,,				2504	0.3855																0								ENSG00000184206																																			GOLGA6L4	SO:0001583	missense	0			-	HGNC	BC101294	CCDS73774.1	15q25.2	2012-11-16	2010-02-12		ENSG00000184206	ENSG00000184206			27256	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 4"""			12477932	Standard	NG_006151		Approved		uc021stn.2	A6NEF3	OTTHUMG00000163050	ENST00000510439.2:c.1279G>A	15.37:g.84909385G>A	ENSP00000421586:p.Asp427Asn	Somatic	0	91	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	12	118	9.23	D6REZ9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.D103N	ENST00000510439.2	37	c.307		15	.	.	.	.	.	.	.	.	.	.	.	6.987	0.552282	0.13374	.	.	ENSG00000184206	ENST00000510439;ENST00000424966;ENST00000422563	T	0.15139	2.45	0.613	0.613	0.17597	.	.	.	.	.	T	0.21227	0.0511	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.31998	-0.9923	5	0.72032	D	0.01	.	7.3831	0.26868	1.0E-4:0.0:0.9999:0.0	.	.	.	.	N	427;8;103	ENSP00000421586:D427N	ENSP00000389305:D103N	D	+	1	0	GOLGA6L4	82700389	0.000000	0.05858	0.010000	0.14722	0.008000	0.06430	-0.956000	0.03865	0.701000	0.31803	0.504000	0.49776	GAT	-	NULL		0.657	GOLGA6L4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate_longest	protein_coding	GOLGA6L4	protein_coding	OTTHUMT00000371478.2	G	NM_001267536	rs77228815		84909385	+1	no_errors	ENST00000422563	ensembl	human	known	74_37	missense	SNP	0.004	A
SHROOM4	57477	genome.wustl.edu	37	X	50350758	50350759	+	In_Frame_Ins	INS	-	-	TGCTGCTGCTGT	rs201922875|rs553160982		TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chrX:50350758_50350759insTGCTGCTGCTGT	ENST00000289292.7	-	6	3666_3667	c.3383_3384insACAGCAGCAGCA	c.(3382-3384)cag>caACAGCAGCAGCAg	p.1128_1128Q>QQQQQ	SHROOM4_ENST00000376020.2_In_Frame_Ins_p.1128_1128Q>QQQQQ|SHROOM4_ENST00000460112.3_In_Frame_Ins_p.1012_1012Q>QQQQQ			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1128	Gln-rich.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					cctgttgcttctgctgctgctg	0.589																																																	0								ENSG00000158352			12,1892,1813		0,4,5,3,450,721,267,412,263						-6.4	0.0			16	21,2147,4298		1,7,3,9,306,942,586,1095,1163	no	codingComplex	SHROOM4	NM_020717.3		1,11,8,12,756,1663,853,1507,1426	A1A1,A1A2,A1R,A1,A2A2,A2R,A2,RR,R		33.5292,49.0987,39.9882				33,4039,6111				SHROOM4	SO:0001652	inframe_insertion	0				HGNC	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3372_3383dupACAGCAGCAGCA	X.37:g.50350758_50350759insTGCTGCTGCTGT	ENSP00000289292:p.GlnGlnGlnGln1128dup	Somatic	NA	NA	NA		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	A7E2X9|D6RFW0|Q96LA0	In_Frame_Ins	INS	NA	NA	NA	NA	NA	NA	pfam_ASD2,pfam_PDZ,superfamily_PDZ,smart_PDZ,pfscan_PDZ	p.1129in_frame_insQQQQ	ENST00000289292.7	37	c.3384_3383	CCDS35277.1	X																																																																																			-	NULL		0.589	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	SHROOM4	protein_coding	OTTHUMT00000056564.4	-	NM_020717			50350759	-1	no_errors	ENST00000289292	ensembl	human	known	74_37	in_frame_ins	INS	0.000:0.000	TGCTGCTGCTGT
ZNF573	126231	genome.wustl.edu	37	19	38231024	38231024	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr19:38231024G>T	ENST00000590414.2	-	4	388	c.367C>A	c.(367-369)Caa>Aaa	p.Q123K	ZNF573_ENST00000536220.1_Missense_Mutation_p.Q35K|ZNF573_ENST00000339503.4_Missense_Mutation_p.Q65K|ZNF573_ENST00000392138.1_Missense_Mutation_p.Q36K|ZNF573_ENST00000357309.3_Missense_Mutation_p.Q35K|ZNF573_ENST00000585724.1_3'UTR			Q86YE8	ZN573_HUMAN	zinc finger protein 573	123					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(3)|endometrium(2)|large_intestine(8)|liver(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)|Lung(45;0.0813)|LUSC - Lung squamous cell carcinoma(53;0.146)			CTCTGAAGTTGTGTAGAGGAT	0.318																																																	0								ENSG00000189144						69.0	76.0	73.0					19																	38231024		2202	4300	6502	ZNF573	SO:0001583	missense	0			-	HGNC	AK074539	CCDS12508.1, CCDS54260.1, CCDS59381.1	19q13.12	2013-09-20			ENSG00000189144	ENSG00000189144		"""Zinc fingers, C2H2-type"", ""-"""	26420	protein-coding gene	gene with protein product						12477932	Standard	NM_152360		Approved	FLJ30921	uc002ohe.3	Q86YE8	OTTHUMG00000048183	ENST00000590414.2:c.367C>A	19.37:g.38231024G>T	ENSP00000465020:p.Gln123Lys	Somatic	0	28	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	37	9.30	B7WPE1|K7EJ45|Q6P1P1|Q7Z7Q3|Q8N2Q1|Q96BM3|Q96NH0	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.Q123K	ENST00000590414.2	37	c.367	CCDS59381.1	19	.	.	.	.	.	.	.	.	.	.	g	0.009	-1.830088	0.00584	.	.	ENSG00000189144	ENST00000392138;ENST00000536220;ENST00000357309;ENST00000339503;ENST00000427026	T;T;T;T	0.06768	3.31;3.26;3.26;3.29	1.79	-0.543	0.11851	.	.	.	.	.	T	0.03520	0.0101	N	0.16233	0.39	0.09310	N	1	B;B;B;B	0.23185	0.081;0.081;0.049;0.081	B;B;B;B	0.15052	0.005;0.012;0.003;0.007	T	0.45131	-0.9282	9	0.05959	T	0.93	.	4.8145	0.13360	0.1357:0.0:0.6536:0.2107	.	36;65;103;35	Q86YE8-4;Q86YE8-3;Q86YE8;Q86YE8-2	.;.;ZN573_HUMAN;.	K	36;35;35;65;35	ENSP00000375983:Q36K;ENSP00000440464:Q35K;ENSP00000349861:Q35K;ENSP00000340171:Q65K	ENSP00000340171:Q65K	Q	-	1	0	ZNF573	42922864	.	.	0.001000	0.08648	0.027000	0.11550	.	.	-0.064000	0.13043	-0.194000	0.12790	CAA	-	NULL		0.318	ZNF573-007	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF573	protein_coding	OTTHUMT00000459773.2	G	NM_152360	-		38231024	-1	no_errors	ENST00000590414	ensembl	human	known	74_37	missense	SNP	0.001	T
COL4A2	1284	genome.wustl.edu	37	13	111114516	111114516	+	Missense_Mutation	SNP	G	G	A			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr13:111114516G>A	ENST00000360467.5	+	23	1958	c.1652G>A	c.(1651-1653)aGa>aAa	p.R551K	COL4A2-AS2_ENST00000458403.2_RNA	NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	551	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			GGAGATTCCAGAACAATCACA	0.532																																																	0								ENSG00000134871						75.0	80.0	78.0					13																	111114516		1968	4157	6125	COL4A2	SO:0001583	missense	0			-	HGNC	AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"""Collagens"""	2203	protein-coding gene	gene with protein product	"""canstatin"", ""collagen type IV alpha 2"""	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.1652G>A	13.37:g.111114516G>A	ENSP00000353654:p.Arg551Lys	Somatic	0	59	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	8	23	25.81	Q14052|Q548C3|Q5VZA9|Q66K23	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Collagen,pfam_Collagen_VI_NC,superfamily_C-type_lectin_fold,smart_Collagen_VI_NC	p.R551K	ENST00000360467.5	37	c.1652	CCDS41907.1	13	.	.	.	.	.	.	.	.	.	.	G	7.925	0.739414	0.15642	.	.	ENSG00000134871	ENST00000360467;ENST00000257309	D	0.93189	-3.18	5.48	4.62	0.57501	.	0.243677	0.29707	N	0.011408	D	0.84920	0.5579	N	0.08118	0	0.09310	N	1	P	0.40144	0.704	B	0.42462	0.388	T	0.77373	-0.2612	10	0.51188	T	0.08	.	6.3305	0.21266	0.0904:0.0:0.726:0.1836	.	551	P08572	CO4A2_HUMAN	K	551	ENSP00000353654:R551K	ENSP00000257309:R551K	R	+	2	0	COL4A2	109912517	0.007000	0.16637	0.016000	0.15963	0.535000	0.34838	1.159000	0.31749	2.576000	0.86940	0.655000	0.94253	AGA	-	NULL		0.532	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL4A2	protein_coding	OTTHUMT00000045761.2	G	NM_001846	-		111114516	+1	no_errors	ENST00000360467	ensembl	human	known	74_37	missense	SNP	0.003	A
UPK1B	7348	genome.wustl.edu	37	3	118909894	118909894	+	Silent	SNP	T	T	C			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr3:118909894T>C	ENST00000264234.3	+	5	560	c.411T>C	c.(409-411)aaT>aaC	p.N137N	UPK1B_ENST00000497685.1_Silent_p.N57N|UPK1B_ENST00000460625.1_Silent_p.N129N	NM_006952.3	NP_008883.2	O75841	UPK1B_HUMAN	uroplakin 1B	137				N -> D (in Ref. 1; BAA33724). {ECO:0000305}.	epithelial cell differentiation (GO:0030855)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	structural molecule activity (GO:0005198)			breast(1)|endometrium(3)|large_intestine(2)|lung(6)|pancreas(1)|skin(1)	14				GBM - Glioblastoma multiforme(114;0.222)		CTCCAAACAATGATGACCAGT	0.478																																																	0								ENSG00000114638						269.0	266.0	267.0					3																	118909894		2203	4300	6503	UPK1B	SO:0001819	synonymous_variant	0			-	HGNC	AF082888	CCDS2985.1	3q13.32	2013-02-14			ENSG00000114638	ENSG00000114638		"""Tetraspanins"""	12578	protein-coding gene	gene with protein product		602380		UPK1		9935153, 9846985	Standard	NM_006952		Approved	TSPAN20	uc003ecc.3	O75841	OTTHUMG00000159354	ENST00000264234.3:c.411T>C	3.37:g.118909894T>C		Somatic	0	54	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	9	34	20.93	O60753|Q9UIM2|Q9UNX6	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Tetraspanin/Peripherin,superfamily_Tetraspanin_EC2,prints_Tetraspanin	p.N137	ENST00000264234.3	37	c.411	CCDS2985.1	3																																																																																			-	pfam_Tetraspanin/Peripherin,superfamily_Tetraspanin_EC2		0.478	UPK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	UPK1B	protein_coding	OTTHUMT00000354883.2	T		-		118909894	+1	no_errors	ENST00000264234	ensembl	human	known	74_37	silent	SNP	0.941	C
TCP11L2	255394	genome.wustl.edu	37	12	106729591	106729591	+	Missense_Mutation	SNP	A	A	C			TCGA-K1-A42W-01A-11D-A24N-09	TCGA-K1-A42W-10A-01D-A24N-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd93f952-2796-426f-add8-9a7ab441c794	39fd2203-42c8-4284-98bc-ff7ca45239ac	g.chr12:106729591A>C	ENST00000299045.3	+	7	1121	c.947A>C	c.(946-948)aAa>aCa	p.K316T		NM_152772.1	NP_689985.1	Q8N4U5	T11L2_HUMAN	t-complex 11, testis-specific-like 2	316										endometrium(2)|kidney(2)|large_intestine(5)|ovary(3)|prostate(1)|urinary_tract(2)	15						TATCAGAAAAAAGAATTACCA	0.388																																																	0								ENSG00000166046						69.0	74.0	72.0					12																	106729591		2203	4300	6503	TCP11L2	SO:0001583	missense	0			-	HGNC	BC033617	CCDS9104.1, CCDS66456.1	12q23.3	2014-08-12	2012-09-20		ENSG00000166046	ENSG00000166046			28627	protein-coding gene	gene with protein product			"""t-complex 11 (mouse) like 2"", ""t-complex 11 (mouse)-like 2"""				Standard	XM_005268769		Approved	MGC40368	uc001tln.3	Q8N4U5	OTTHUMG00000170087	ENST00000299045.3:c.947A>C	12.37:g.106729591A>C	ENSP00000299045:p.Lys316Thr	Somatic	0	25	0.00		0.7355201918986322	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	11	10	52.38	B2RA65|G3V1Y9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Tcp11	p.K316T	ENST00000299045.3	37	c.947	CCDS9104.1	12	.	.	.	.	.	.	.	.	.	.	A	13.17	2.155780	0.38021	.	.	ENSG00000166046	ENST00000299045	T	0.11712	2.75	5.9	3.54	0.40534	.	0.436773	0.28889	N	0.013805	T	0.10208	0.0250	N	0.24115	0.695	0.80722	D	1	B	0.34399	0.452	B	0.43155	0.41	T	0.32613	-0.9900	10	0.25751	T	0.34	-1.7492	10.3366	0.43854	0.8659:0.0:0.1341:0.0	.	316	Q8N4U5	T11L2_HUMAN	T	316	ENSP00000299045:K316T	ENSP00000299045:K316T	K	+	2	0	TCP11L2	105253721	0.998000	0.40836	0.991000	0.47740	0.996000	0.88848	2.989000	0.49393	1.067000	0.40740	0.460000	0.39030	AAA	-	pfam_Tcp11		0.388	TCP11L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TCP11L2	protein_coding	OTTHUMT00000407206.1	A	NM_152772	-		106729591	+1	no_errors	ENST00000299045	ensembl	human	known	74_37	missense	SNP	0.993	C
