#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_CAF	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_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_normal_ref_reads	i_normal_ref_reads_val	i_normal_vaf	i_normal_vaf_val	i_normal_var_reads	i_normal_var_reads_val	i_reference	i_refseq_mrna_id	i_rsID	i_rsID_ref_var_alleles	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_tumor_ref_reads	i_tumor_ref_reads_val	i_tumor_vaf	i_tumor_vaf_val	i_tumor_var_reads	i_tumor_var_reads_val	i_type	i_ucsc_cons	i_variant
ATOH8	84913	genome.wustl.edu	37	2	85999798	85999798	+	Intron	SNP	A	A	G			TCGA-4V-A9QM-01A-11D-A423-09	TCGA-4V-A9QM-11A-11D-A426-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	660b7dac-fbdc-4ea6-b49d-dcc29088a5d4	cc42f8f7-c7cc-4bdc-adc5-250b99c4852b	g.chr2:85999798A>G	ENST00000306279.3	+	2	1256				ATOH8_ENST00000463422.1_3'UTR	NM_032827.6	NP_116216.2	Q96SQ7	ATOH8_HUMAN	atonal homolog 8 (Drosophila)						cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(1)|lung(2)	5						GGCAGCAGGGAAAACCGTGCA	0.517																																							0											0																																										SO:0001627	intron_variant	0			AK074681	CCDS1985.1	2p11.2	2013-05-21			ENSG00000168874	ENSG00000168874		"""Basic helix-loop-helix proteins"""	24126	protein-coding gene	gene with protein product	"""basic helix loop helix transcription factor 6"""					12419857	Standard	NM_032827		Approved	HATH6, FLJ14708, bHLHa21	uc002sqn.3	Q96SQ7	OTTHUMG00000130178	ENST00000306279.3:c.960+8493A>G	2.37:g.85999798A>G			Q504S2|Q659B0	RNA	SNP	0	NULL	ENST00000306279.3	37	NULL	CCDS1985.1	2																																																																																			0	0		0.517	ATOH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ATOH8	protein_coding	OTTHUMT00000252496.1	44	148	0	0.00	0	0	A	NM_032827	0	0		85999798	1	no_errors	ENST00000463422	ensembl	human	putative	74_37	rna	42	109	14.29	19.71	7	27	SNP	0.996	G
ECE2	9718	genome.wustl.edu	37	3	183976104	183976104	+	Intron	SNP	G	G	A			TCGA-4V-A9QM-01A-11D-A423-09	TCGA-4V-A9QM-11A-11D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	660b7dac-fbdc-4ea6-b49d-dcc29088a5d4	cc42f8f7-c7cc-4bdc-adc5-250b99c4852b	g.chr3:183976104G>A	ENST00000402825.3	+	2	480				EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000324557.4_Missense_Mutation_p.R170Q	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2						brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CCTGGAGGCCGGTTTATCTCA	0.552																																							0											0													146.0	139.0	141.0					3																	183976104		2203	4300	6503	SO:0001627	intron_variant	0			AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.480+560G>A	3.37:g.183976104G>A			A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Missense_Mutation	SNP	pfam_Methyltransf_11,pfam_Methyltransf_12	p.R170Q	ENST00000402825.3	37	c.509	CCDS3256.2	3	.	.	.	.	.	.	.	.	.	.	G	12.62	1.992438	0.35131	.	.	ENSG00000145194	ENST00000324557	T	0.64618	-0.11	4.97	3.19	0.36642	.	.	.	.	.	T	0.47507	0.1449	.	.	.	0.80722	D	1	B	0.20164	0.042	B	0.09377	0.004	T	0.30149	-0.9988	8	0.27785	T	0.31	.	10.4123	0.44301	0.1606:0.0:0.8394:0.0	.	170	O60344-4	.	Q	170	ENSP00000314295:R170Q	ENSP00000314295:R170Q	R	+	2	0	ECE2	185458798	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.675000	0.68123	0.698000	0.31739	0.655000	0.94253	CGG	0	pfam_Methyltransf_11,pfam_Methyltransf_12		0.552	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ECE2	protein_coding	OTTHUMT00000318874.3	46	179	0	0.56	0	1	G	NM_014693	0	0		183976104	1	no_errors	ENST00000324557	ensembl	human	known	74_37	missense	28	100	17.65	23.08	6	30	SNP	1	A
SMAP1	60682	genome.wustl.edu	37	6	71508379	71508379	+	Missense_Mutation	SNP	A	A	C	rs138685504	byFrequency	TCGA-4V-A9QM-01A-11D-A423-09	TCGA-4V-A9QM-11A-11D-A426-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	660b7dac-fbdc-4ea6-b49d-dcc29088a5d4	cc42f8f7-c7cc-4bdc-adc5-250b99c4852b	g.chr6:71508379A>C	ENST00000370455.3	+	6	763	c.515A>C	c.(514-516)aAg>aCg	p.K172T	SMAP1_ENST00000370452.3_Missense_Mutation_p.K145T|SMAP1_ENST00000316999.5_Missense_Mutation_p.K145T	NM_001044305.1|NM_001281440.1	NP_001037770.1|NP_001268369.1	Q8IYB5	SMAP1_HUMAN	small ArfGAP 1	172					positive regulation of erythrocyte differentiation (GO:0045648)|regulation of ARF GTPase activity (GO:0032312)|regulation of clathrin-mediated endocytosis (GO:2000369)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.K145M(1)		breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(1)	15						gaaaaaaaaaaggaagagaaa	0.294																																							0											1	Substitution - Missense(1)	breast(1)											26.0	32.0	30.0					6																	71508379		2192	4273	6465	SO:0001583	missense	0			AK023221	CCDS4973.1, CCDS43478.1, CCDS64459.1, CCDS75478.1	6q12-q13	2009-11-30	2008-09-05		ENSG00000112305	ENSG00000112305		"""ADP-ribosylation factor GTPase activating proteins"""	19651	protein-coding gene	gene with protein product		611372	"""stromal membrane-associated protein 1"", ""stromal membrane-associated GTPase-activating protein 1"""			9644265, 12119110	Standard	NM_001044305		Approved	FLJ13159, SMAP-1	uc003pfr.3	Q8IYB5	OTTHUMG00000014996	ENST00000370455.3:c.515A>C	6.37:g.71508379A>C	ENSP00000359484:p.Lys172Thr		Q53H70|Q5SYQ2|Q6PK24|Q8NDH4|Q96L38|Q96L39|Q9H8X4	Missense_Mutation	SNP	pfam_ArfGAP,smart_ArfGAP,pfscan_ArfGAP,prints_ArfGAP	p.K172T	ENST00000370455.3	37	c.515	CCDS43478.1	6	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.17|16.17	3.048516|3.048516	0.55110|0.55110	.|.	.|.	ENSG00000112305|ENSG00000112305	ENST00000439432|ENST00000370452;ENST00000316999;ENST00000370455;ENST00000370442	T|T;T;T	0.63096|0.25414	-0.02|2.08;2.09;1.8	5.32|5.32	5.32|5.32	0.75619|0.75619	.|.	0.673120|0.673120	0.14847|0.14847	N|N	0.294925|0.294925	T|T	0.26738|0.26738	0.0654|0.0654	L|L	0.46157|0.46157	1.445|1.445	0.80722|0.80722	D|D	1|1	.|P;D;D;P	.|0.71674	.|0.704;0.998;0.99;0.704	.|B;D;P;B	.|0.63877	.|0.343;0.919;0.858;0.197	T|T	0.02632|0.02632	-1.1131|-1.1131	8|10	0.87932|0.15499	D|T	0|0.54	-6.764|-6.764	13.508|13.508	0.61495|0.61495	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|172;145;145;172	.|A8K333;Q8IYB5-3;Q8IYB5-2;Q8IYB5	.|.;.;.;SMAP1_HUMAN	N|T	46|145;145;172;84	ENSP00000398306:K46N|ENSP00000359481:K145T;ENSP00000313382:K145T;ENSP00000359484:K172T	ENSP00000398306:K46N|ENSP00000313382:K145T	K|K	+|+	3|2	2|0	SMAP1|SMAP1	71565100|71565100	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	4.929000|4.929000	0.63455|0.63455	2.130000|2.130000	0.65690|0.65690	0.533000|0.533000	0.62120|0.62120	AAA|AAG	0	NULL		0.294	SMAP1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	SMAP1	protein_coding	OTTHUMT00000041149.1	89	121	0	0.00	0	0	A	NM_001044305	0	0		71508379	1	no_errors	ENST00000370455	ensembl	human	known	74_37	missense	177	97	18.81	27.61	41	37	SNP	1	C
LMTK2	22853	genome.wustl.edu	37	7	97822349	97822349	+	Missense_Mutation	SNP	A	A	T			TCGA-4V-A9QM-01A-11D-A423-09	TCGA-4V-A9QM-11A-11D-A426-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	660b7dac-fbdc-4ea6-b49d-dcc29088a5d4	cc42f8f7-c7cc-4bdc-adc5-250b99c4852b	g.chr7:97822349A>T	ENST00000297293.5	+	11	2865	c.2572A>T	c.(2572-2574)Atc>Ttc	p.I858F		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	858					early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					CCACCAGGACATCAGTCCAGA	0.567																																							0											0													68.0	65.0	66.0					7																	97822349		2203	4300	6503	SO:0001583	missense	0			AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 100"""	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.2572A>T	7.37:g.97822349A>T	ENSP00000297293:p.Ile858Phe		A4D272|Q75MG7|Q9UPS3	Missense_Mutation	SNP	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,prints_Ser-Thr/Tyr_kinase_cat_dom	p.I858F	ENST00000297293.5	37	c.2572	CCDS5654.1	7	.	.	.	.	.	.	.	.	.	.	A	9.336	1.061660	0.19987	.	.	ENSG00000164715	ENST00000297293	T	0.77750	-1.12	5.53	-11.1	0.00147	.	1.568470	0.03188	N	0.173030	T	0.56949	0.2020	L	0.29908	0.895	0.09310	N	1	B	0.18461	0.028	B	0.13407	0.009	T	0.46610	-0.9179	10	0.25751	T	0.34	.	2.5583	0.04765	0.2316:0.3696:0.246:0.1528	.	858	Q8IWU2	LMTK2_HUMAN	F	858	ENSP00000297293:I858F	ENSP00000297293:I858F	I	+	1	0	LMTK2	97660285	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.199000	0.09491	-3.975000	0.00085	-2.518000	0.00185	ATC	0	NULL		0.567	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LMTK2	protein_coding	OTTHUMT00000334560.1	30	141	0	0.00	0	0	A	NM_014916	0	0		97822349	1	no_errors	ENST00000297293	ensembl	human	known	74_37	missense	30	117	16.67	17.61	6	25	SNP	0	T
MTAP	4507	genome.wustl.edu	37	9	21815456	21815456	+	Missense_Mutation	SNP	C	C	G			TCGA-4V-A9QM-01A-11D-A423-09	TCGA-4V-A9QM-11A-11D-A426-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	660b7dac-fbdc-4ea6-b49d-dcc29088a5d4	cc42f8f7-c7cc-4bdc-adc5-250b99c4852b	g.chr9:21815456C>G	ENST00000460874.2	+	2	334	c.109C>G	c.(109-111)Ctg>Gtg	p.L37V	MTAP_ENST00000580900.1_Missense_Mutation_p.L20V|MTAP_ENST00000380172.4_Missense_Mutation_p.L20V|MTAP_ENST00000427788.2_3'UTR|RP11-145E5.5_ENST00000404796.2_Missense_Mutation_p.L20V					methylthioadenosine phosphorylase									p.0(1)|p.0?(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|lung(3)|pancreas(1)	10		all_cancers(5;0)|Hepatocellular(5;0.00162)|Colorectal(97;0.173)		GBM - Glioblastoma multiforme(3;0)|Lung(24;2.24e-57)|LUSC - Lung squamous cell carcinoma(38;1.97e-36)|STAD - Stomach adenocarcinoma(4;3.26e-05)|OV - Ovarian serous cystadenocarcinoma(39;0.00931)|COAD - Colon adenocarcinoma(8;0.15)		TGGAACAGGCCTGGATGATCC	0.308																																							0											2	Whole gene deletion(2)	lung(2)											66.0	70.0	69.0					9																	21815456		2203	4300	6503	SO:0001583	missense	0			AB062485	CCDS6509.1	9p21	2013-05-29			ENSG00000099810	ENSG00000099810	2.4.2.28		7413	protein-coding gene	gene with protein product	"""S-methyl-5'-thioadenosine phosphorylase"""	156540				11126361	Standard	NM_002451		Approved	MSAP, c86fus	uc003zph.3	Q13126	OTTHUMG00000019690	ENST00000460874.2:c.109C>G	9.37:g.21815456C>G	ENSP00000461932:p.Leu37Val			Missense_Mutation	SNP	pfam_Nucleoside_phosphorylase_d,tigrfam_MTAP	p.L20V	ENST00000460874.2	37	c.58		9	.	.	.	.	.	.	.	.	.	.	C	15.95	2.984495	0.53934	.	.	ENSG00000099810	ENST00000380172	T	0.53423	0.62	5.35	2.46	0.29980	Nucleoside phosphorylase domain (1);	0.000000	0.85682	D	0.000000	T	0.56381	0.1981	M	0.70595	2.14	0.80722	D	1	P;P;P	0.49635	0.519;0.836;0.926	B;P;P	0.56700	0.357;0.804;0.672	T	0.51020	-0.8758	10	0.34782	T	0.22	-12.6319	8.1314	0.31029	0.0:0.6698:0.0:0.3302	.	37;20;20	B4DUC8;F2Z2F3;Q13126	.;.;MTAP_HUMAN	V	20	ENSP00000369519:L20V	ENSP00000369519:L20V	L	+	1	2	MTAP	21805456	0.994000	0.37717	1.000000	0.80357	0.994000	0.84299	2.615000	0.46368	0.315000	0.23110	-0.251000	0.11542	CTG	0	pfam_Nucleoside_phosphorylase_d,tigrfam_MTAP		0.308	MTAP-003	PUTATIVE	basic|exp_conf	protein_coding	MTAP	protein_coding	OTTHUMT00000051929.2	45	127	0	0.00	0	0	C	NM_002451	0	0		21815456	1	no_errors	ENST00000380172	ensembl	human	known	74_37	missense	58	69	28.4	36.11	23	39	SNP	1	G
PLCE1	51196	genome.wustl.edu	37	10	96066442	96066442	+	Nonsense_Mutation	SNP	C	C	T			TCGA-4V-A9QM-01A-11D-A423-09	TCGA-4V-A9QM-11A-11D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	660b7dac-fbdc-4ea6-b49d-dcc29088a5d4	cc42f8f7-c7cc-4bdc-adc5-250b99c4852b	g.chr10:96066442C>T	ENST00000371380.3	+	25	6116	c.5881C>T	c.(5881-5883)Cga>Tga	p.R1961*	PLCE1_ENST00000371385.3_Nonsense_Mutation_p.R1653*|PLCE1_ENST00000260766.3_Nonsense_Mutation_p.R1961*|PLCE1_ENST00000371375.1_Nonsense_Mutation_p.R1653*			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	1961					activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)			liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				AGCTTTAAAACGaggtagaat	0.358																																							0											0													48.0	42.0	44.0					10																	96066442		1841	4101	5942	SO:0001587	stop_gained	0				CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"""nephrosis type 3"""	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.5881C>T	10.37:g.96066442C>T	ENSP00000360431:p.Arg1961*		A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Nonsense_Mutation	SNP	pfam_PLipase_C_PInositol-sp_X_dom,pfam_PLipase_C_Pinositol-sp_Y,pfam_Ras-assoc,pfam_RasGRF_CDC25,pfam_PLipase_C_EF-hand-like,pfam_C2_dom,superfamily_PLC-like_Pdiesterase_TIM-brl,superfamily_Ras_GEF_dom,superfamily_C2_dom,smart_RasGRF_CDC25,smart_PLipase_C_PInositol-sp_X_dom,smart_PLipase_C_Pinositol-sp_Y,smart_C2_dom,smart_Ras-assoc,pfscan_C2_dom,pfscan_Ras-assoc,pfscan_PLipase_C_PInositol-sp_X_dom,pfscan_PLipase_C_Pinositol-sp_Y,pfscan_RasGRF_CDC25,prints_Pinositol_PLipase_C	p.R1961*	ENST00000371380.3	37	c.5881	CCDS41552.1	10	.	.	.	.	.	.	.	.	.	.	C	49	15.756234	0.99844	.	.	ENSG00000138193	ENST00000260766;ENST00000371380;ENST00000371385;ENST00000371375	.	.	.	5.43	-0.474	0.12108	.	0.150864	0.45361	D	0.000375	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	.	16.6404	0.85070	0.6921:0.3079:0.0:0.0	.	.	.	.	X	1961;1961;1653;1653	.	ENSP00000260766:R1961X	R	+	1	2	PLCE1	96056432	0.953000	0.32496	0.980000	0.43619	0.993000	0.82548	0.696000	0.25541	0.020000	0.15106	0.655000	0.94253	CGA	0	superfamily_C2_dom,smart_C2_dom,prints_Pinositol_PLipase_C		0.358	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PLCE1	protein_coding	OTTHUMT00000049469.3	42	215	0	0.00	0	0	C	NM_016341	0	0		96066442	1	no_errors	ENST00000260766	ensembl	human	known	74_37	nonsense	33	175	28.26	24.57	13	57	SNP	0.519	T
RBM23	55147	genome.wustl.edu	37	14	23375467	23375467	+	Missense_Mutation	SNP	G	G	A			TCGA-4V-A9QM-01A-11D-A423-09	TCGA-4V-A9QM-11A-11D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	660b7dac-fbdc-4ea6-b49d-dcc29088a5d4	cc42f8f7-c7cc-4bdc-adc5-250b99c4852b	g.chr14:23375467G>A	ENST00000359890.3	-	5	533	c.338C>T	c.(337-339)tCg>tTg	p.S113L	RBM23_ENST00000542016.2_5'UTR|RBM23_ENST00000346528.5_Missense_Mutation_p.S97L|RBM23_ENST00000556984.1_5'UTR|RBM23_ENST00000399922.2_Missense_Mutation_p.S97L|RBM23_ENST00000555209.1_5'UTR	NM_001077351.1	NP_001070819.1	Q86U06	RBM23_HUMAN	RNA binding motif protein 23	113	Arg-rich.				mRNA processing (GO:0006397)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.S113L(1)		endometrium(3)|kidney(2)|lung(3)|prostate(1)|skin(1)	10	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.0128)		CCGACTTCGCGACTCACTACC	0.517																																							0											1	Substitution - Missense(1)	lung(1)											82.0	86.0	85.0					14																	23375467		2097	4227	6324	SO:0001583	missense	0			AF275678	CCDS41919.1, CCDS41920.1, CCDS41921.1	14q11.1	2014-07-03	2004-04-23	2004-04-23		ENSG00000100461		"""RNA binding motif (RRM) containing"""	20155	protein-coding gene	gene with protein product	"""coactivator of activating protein-1 and estrogen recep- tors beta"""		"""RNA-binding region (RNP1, RRM) containing 4"""	RNPC4		15694343	Standard	NM_018107		Approved	FLJ10482, CAPERbeta	uc001whg.3	Q86U06		ENST00000359890.3:c.338C>T	14.37:g.23375467G>A	ENSP00000352956:p.Ser113Leu		D3DS32|Q8ND16|Q8TB88|Q8WY40|Q9BUJ1|Q9NVV7	Missense_Mutation	SNP	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom,tigrfam_CC1_SF	p.S113L	ENST00000359890.3	37	c.338	CCDS41921.1	14	.	.	.	.	.	.	.	.	.	.	G	7.688	0.690414	0.15039	.	.	ENSG00000100461	ENST00000359890;ENST00000338980;ENST00000399922;ENST00000346528;ENST00000554256;ENST00000557549;ENST00000555676	T;T;T	0.80033	-1.33;3.56;0.99	4.96	4.06	0.47325	.	0.248699	0.28016	N	0.016927	T	0.67107	0.2858	L	0.29908	0.895	0.80722	D	1	B;B;B;B	0.24483	0.104;0.104;0.104;0.063	B;B;B;B	0.21708	0.036;0.036;0.036;0.016	T	0.55897	-0.8068	10	0.10111	T	0.7	-1.3227	11.1765	0.48603	0.0774:0.1294:0.7932:0.0	.	113;97;97;113	Q86U06-3;Q86U06-4;Q86U06-2;Q86U06	.;.;.;RBM23_HUMAN	L	113;90;97;97;113;97;97	ENSP00000352956:S113L;ENSP00000382806:S97L;ENSP00000339220:S97L	ENSP00000305783:S113L	S	-	2	0	RBM23	22445307	0.879000	0.30193	0.998000	0.56505	0.635000	0.38103	1.454000	0.35178	0.623000	0.30267	-0.797000	0.03246	TCG	0	tigrfam_CC1_SF		0.517	RBM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RBM23	protein_coding	OTTHUMT00000413545.3	43	158	0	0.00	0	0	G		0	0		23375467	-1	no_errors	ENST00000359890	ensembl	human	known	74_37	missense	43	107	12.24	13.49	6	17	SNP	0.997	A
KIAA0556	23247	genome.wustl.edu	37	16	27763207	27763207	+	Missense_Mutation	SNP	C	C	T	rs558540912		TCGA-4V-A9QM-01A-11D-A423-09	TCGA-4V-A9QM-11A-11D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	660b7dac-fbdc-4ea6-b49d-dcc29088a5d4	cc42f8f7-c7cc-4bdc-adc5-250b99c4852b	g.chr16:27763207C>T	ENST00000261588.4	+	17	3533	c.3514C>T	c.(3514-3516)Cgg>Tgg	p.R1172W		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	1172						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						GGGGGATGAGCGGCCCTTCAC	0.627													C|||	1	0.000199681	0.0	0.0	5008	,	,		13963	0.0		0.0	False		,,,				2504	0.001						0.9998,0.0001997											0													40.0	42.0	41.0					16																	27763207		2197	4300	6497	SO:0001583	missense	0			AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.3514C>T	16.37:g.27763207C>T	ENSP00000261588:p.Arg1172Trp		A7E2C2	Missense_Mutation	SNP	superfamily_Thaumatin	p.R1172W	ENST00000261588.4	37	c.3514	CCDS32415.1	16	.	.	.	.	.	.	.	.	.	.	C	18.87	3.714770	0.68730	.	.	ENSG00000047578	ENST00000261588	T	0.13778	2.56	5.02	-0.0234	0.13943	.	0.000000	0.85682	D	0.000000	T	0.36441	0.0967	M	0.80028	2.48	0.44771	D	0.997778	D	0.89917	1.0	D	0.91635	0.999	T	0.27297	-1.0078	10	0.87932	D	0	.	13.846	0.63468	0.5455:0.4545:0.0:0.0	.	1172	O60303	K0556_HUMAN	W	1172	ENSP00000261588:R1172W	ENSP00000261588:R1172W	R	+	1	2	KIAA0556	27670708	0.924000	0.31332	0.908000	0.35775	0.734000	0.41952	0.826000	0.27407	-0.161000	0.10983	0.585000	0.79938	CGG	0	NULL		0.627	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KIAA0556	protein_coding	OTTHUMT00000433724.1	28	58	0	0.00	0	0	C	NM_015202	rs558540912	C->T		27763207	1	no_errors	ENST00000261588	ensembl	human	known	74_37	missense	18	41	21.74	21.15	5	11	SNP	1	T
C19orf57	79173	genome.wustl.edu	37	19	14001021	14001021	+	Silent	SNP	C	C	T			TCGA-4V-A9QM-01A-11D-A423-09	TCGA-4V-A9QM-11A-11D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	660b7dac-fbdc-4ea6-b49d-dcc29088a5d4	cc42f8f7-c7cc-4bdc-adc5-250b99c4852b	g.chr19:14001021C>T	ENST00000586783.1	-	5	647	c.648G>A	c.(646-648)ggG>ggA	p.G216G	C19orf57_ENST00000346736.2_Silent_p.G216G|C19orf57_ENST00000591586.1_Intron|C19orf57_ENST00000454313.1_Silent_p.G216G			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57	216					multicellular organismal development (GO:0007275)					breast(2)|kidney(1)|lung(3)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			TGTCATCGGCCCCTTGTTCTG	0.597																																							0											0													134.0	116.0	122.0					19																	14001021		2203	4300	6503	SO:0001819	synonymous_variant	0			BC012945	CCDS12299.1	19p13.12	2012-10-26			ENSG00000132016	ENSG00000132016			28153	protein-coding gene	gene with protein product						8228263	Standard	NM_024323		Approved	MGC11271	uc002mxl.1	Q0VDD7	OTTHUMG00000181851	ENST00000586783.1:c.648G>A	19.37:g.14001021C>T			Q13411|Q8N825|Q96D63|Q9BU49	Silent	SNP	NULL	p.G216	ENST00000586783.1	37	c.648		19																																																																																			0	NULL		0.597	C19orf57-003	NOVEL	basic	protein_coding	C19orf57	protein_coding	OTTHUMT00000457947.1	36	149	0	0.67	0	1	C	NM_024323	0	0		14001021	-1	no_errors	ENST00000454313	ensembl	human	known	74_37	silent	25	113	25.71	25.00	9	38	SNP	0.001	T
ALDH16A1	126133	genome.wustl.edu	37	19	49967938	49967938	+	Missense_Mutation	SNP	G	G	T			TCGA-4V-A9QM-01A-11D-A423-09	TCGA-4V-A9QM-11A-11D-A426-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	660b7dac-fbdc-4ea6-b49d-dcc29088a5d4	cc42f8f7-c7cc-4bdc-adc5-250b99c4852b	g.chr19:49967938G>T	ENST00000293350.4	+	12	1650	c.1487G>T	c.(1486-1488)tGc>tTc	p.C496F	ALDH16A1_ENST00000455361.2_Missense_Mutation_p.C445F|CTD-3148I10.9_ENST00000599536.1_3'UTR|ALDH16A1_ENST00000540132.1_Missense_Mutation_p.C333F|ALDH16A1_ENST00000433981.2_Missense_Mutation_p.C331F	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	496						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		CGGCTGTCCTGCCTCTCCAAG	0.637																																							0											0													128.0	132.0	130.0					19																	49967938		2203	4300	6503	SO:0001583	missense	0			AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"""Aldehyde dehydrogenases"""	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.1487G>T	19.37:g.49967938G>T	ENSP00000293350:p.Cys496Phe		B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Missense_Mutation	SNP	pfam_Aldehyde_DH_dom,superfamily_Ald_DH/histidinol_DH,pirsf_Aldehyde_DH	p.C496F	ENST00000293350.4	37	c.1487	CCDS12766.1	19	.	.	.	.	.	.	.	.	.	.	G	2.170	-0.390192	0.04932	.	.	ENSG00000161618	ENST00000293350;ENST00000455361;ENST00000540132;ENST00000433981	T;T;T;T	0.72835	-0.69;-0.44;-0.61;-0.61	5.27	-6.93	0.01638	Aldehyde/histidinol dehydrogenase (1);	2.110200	0.02175	N	0.060023	T	0.39655	0.1086	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.36359	-0.9751	10	0.09843	T	0.71	-18.7822	1.2798	0.02038	0.1424:0.1911:0.2466:0.4198	.	333;445;496	F5H4B6;B4DLQ1;Q8IZ83	.;.;A16A1_HUMAN	F	496;445;333;331	ENSP00000293350:C496F;ENSP00000410142:C445F;ENSP00000445088:C333F;ENSP00000398675:C331F	ENSP00000293350:C496F	C	+	2	0	ALDH16A1	54659750	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-1.864000	0.01650	-1.026000	0.03330	-0.367000	0.07326	TGC	0	superfamily_Ald_DH/histidinol_DH,pirsf_Aldehyde_DH		0.637	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ALDH16A1	protein_coding	OTTHUMT00000465358.1	55	109	0	0.00	0	0	G	NM_153329	0	0		49967938	1	no_errors	ENST00000293350	ensembl	human	known	74_37	missense	43	73	27.12	23.96	16	23	SNP	0	T
EP300	2033	genome.wustl.edu	37	22	41521972	41521972	+	Silent	SNP	T	T	C	rs375358513		TCGA-4V-A9QM-01A-11D-A423-09	TCGA-4V-A9QM-11A-11D-A426-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	660b7dac-fbdc-4ea6-b49d-dcc29088a5d4	cc42f8f7-c7cc-4bdc-adc5-250b99c4852b	g.chr22:41521972T>C	ENST00000263253.7	+	3	2053	c.834T>C	c.(832-834)acT>acC	p.T278T		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	278					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						AGACAAAAACTGTACTATCAA	0.428			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome																														0		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	0													122.0	113.0	116.0					22																	41521972		2203	4300	6503	SO:0001819	synonymous_variant	0	Familial Cancer Database	Broad Thumb-Hallux syndrome	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"""Chromatin-modifying enzymes / K-acetyltransferases"""	3373	protein-coding gene	gene with protein product	"""histone acetyltransferase p300"""	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.834T>C	22.37:g.41521972T>C			B1AKC2	Silent	SNP	pfam_Histone_H3-K56_AcTrfase_RTT109,pfam_Nuc_rcpt_coact_CREBbp,pfam_KIX_dom,pfam_DUF902_CREBbp,pfam_Znf_TAZ,pfam_Bromodomain,pfam_Znf_ZZ,superfamily_Bromodomain,superfamily_Znf_TAZ,superfamily_KIX_dom,superfamily_Nuc_rcpt_coact,superfamily_Znf_FYVE_PHD,smart_Znf_TAZ,smart_Bromodomain,smart_Znf_ZZ,pfscan_KIX_dom,pfscan_Znf_TAZ,pfscan_Znf_ZZ,pfscan_Bromodomain,prints_Bromodomain	p.T278	ENST00000263253.7	37	c.834	CCDS14010.1	22																																																																																			0	NULL		0.428	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EP300	protein_coding	OTTHUMT00000320600.1	53	202	1.85	0.00	1	0	T	NM_001429	0	0		41521972	1	no_errors	ENST00000263253	ensembl	human	known	74_37	silent	54	146	18.18	26.26	12	52	SNP	0.988	C
VCP	7415	genome.wustl.edu	37	9	35059646	35059647	+	Frame_Shift_Ins	INS	-	-	T			TCGA-4V-A9QM-01A-11D-A423-09	TCGA-4V-A9QM-11A-11D-A426-09	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	660b7dac-fbdc-4ea6-b49d-dcc29088a5d4	cc42f8f7-c7cc-4bdc-adc5-250b99c4852b	g.chr9:35059646_35059647insT	ENST00000358901.6	-	14	2742_2743	c.1847_1848insA	c.(1846-1848)aatfs	p.N616fs		NM_007126.3	NP_009057.1	P55072	TERA_HUMAN	valosin containing protein	616					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aggresome assembly (GO:0070842)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|positive regulation of Lys63-specific deubiquitinase activity (GO:1903007)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein K63-linked deubiquitination (GO:1903006)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|retrograde protein transport, ER to cytosol (GO:0030970)|translesion synthesis (GO:0019985)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Hrd1p ubiquitin ligase complex (GO:0000836)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|site of double-strand break (GO:0035861)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|deubiquitinase activator activity (GO:0035800)|lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|protein domain specific binding (GO:0019904)|protein phosphatase binding (GO:0019903)|ubiquitin-specific protease binding (GO:1990381)	p.N616fs*63(1)		breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			TGATGAACACATTTTTTTTTGT	0.515																																							0											1	Deletion - Frameshift(1)	large_intestine(1)																																								SO:0001589	frameshift_variant	0			AC004472	CCDS6573.1	9p13.3	2014-09-17	2011-01-25		ENSG00000165280	ENSG00000165280		"""ATPases / AAA-type"""	12666	protein-coding gene	gene with protein product		601023	"""valosin-containing protein"""			8595912, 7553851	Standard	NM_007126		Approved	IBMPFD, p97	uc003zvy.2	P55072	OTTHUMG00000019855	ENST00000358901.6:c.1848dupA	9.37:g.35059655_35059655dupT	ENSP00000351777:p.Asn616fs		B2R5T8|Q0V924|Q2TAI5|Q969G7|Q9UCD5	Frame_Shift_Ins	INS	pfam_ATPase_AAA_core,pfam_CDC4_N-term_subdom,pfam_DNA_helicase_Holl-junc_RuvB_N,pfam_Cdc48_dom2,pfam_ATPase_dyneun-rel_AAA,pfam_ATPase_AAA-2,pfam_Vps4_C,superfamily_P-loop_NTPase,superfamily_Asp_de-COase-like_dom,smart_AAA+_ATPase,tigrfam_AAA_ATPase_CDC48	p.N616fs	ENST00000358901.6	37	c.1848_1847	CCDS6573.1	9																																																																																			0	pfam_ATPase_AAA_core,superfamily_P-loop_NTPase,smart_AAA+_ATPase,tigrfam_AAA_ATPase_CDC48		0.515	VCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VCP	protein_coding	OTTHUMT00000052290.1	34	140	0	0.71	0	1	0	NM_007126	0	0		35059647	-1	no_errors	ENST00000358901	ensembl	human	known	74_37	frame_shift_ins	30	114	9.09	8.06	3	10	INS	1.000:1.000	T
SNX20	124460	genome.wustl.edu	37	16	50707489	50707489	+	Missense_Mutation	SNP	C	C	T			TCGA-4V-A9QM-01A-11D-A423-09	TCGA-4V-A9QM-11A-11D-A426-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	660b7dac-fbdc-4ea6-b49d-dcc29088a5d4	cc42f8f7-c7cc-4bdc-adc5-250b99c4852b	g.chr16:50707489C>T	ENST00000330943.4	-	4	950	c.779G>A	c.(778-780)cGg>cAg	p.R260Q	RP11-401P9.5_ENST00000570241.2_RNA|SNX20_ENST00000300590.3_Intron|RP11-401P9.5_ENST00000570167.1_RNA|SNX20_ENST00000423026.2_Intron	NM_182854.2	NP_878274.1	Q7Z614	SNX20_HUMAN	sorting nexin 20	260					protein transport (GO:0015031)	endosome (GO:0005768)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)			kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|skin(2)|stomach(1)	15						ATGGCCCTCCCGGGCCTGCAG	0.726																																							0											0													14.0	16.0	15.0					16																	50707489		2170	4249	6419	SO:0001583	missense	0			AK055837	CCDS10745.1, CCDS10744.1, CCDS45481.1	16q12.1	2008-03-25	2008-03-25		ENSG00000167208	ENSG00000167208		"""Sorting nexins"""	30390	protein-coding gene	gene with protein product	"""selectin ligand interactor cytoplasmic 1"""	613281				18196517, 16782399	Standard	NM_182854		Approved	SLIC-1, SLIC1	uc002egk.2	Q7Z614	OTTHUMG00000133173	ENST00000330943.4:c.779G>A	16.37:g.50707489C>T	ENSP00000332062:p.Arg260Gln		A8K9D5|Q08E98|Q6P4H2|Q8IV59	Missense_Mutation	SNP	pfam_Phox,superfamily_Phox,smart_Phox,pfscan_Phox	p.R260Q	ENST00000330943.4	37	c.779	CCDS10745.1	16	.	.	.	.	.	.	.	.	.	.	C	16.07	3.018604	0.54576	.	.	ENSG00000167208	ENST00000330943	T	0.30448	1.53	5.78	4.82	0.62117	.	0.266794	0.39544	N	0.001336	T	0.29882	0.0747	M	0.68317	2.08	0.09310	N	1	D	0.55385	0.971	B	0.42087	0.375	T	0.30880	-0.9963	10	0.36615	T	0.2	-31.6085	7.5476	0.27777	0.1474:0.7325:0.0:0.12	.	260	Q7Z614	SNX20_HUMAN	Q	260	ENSP00000332062:R260Q	ENSP00000332062:R260Q	R	-	2	0	SNX20	49264990	0.013000	0.17824	0.974000	0.42286	0.955000	0.61496	0.618000	0.24373	1.424000	0.47217	0.561000	0.74099	CGG	0	NULL		0.726	SNX20-002	KNOWN	basic|appris_principal|CCDS	protein_coding	SNX20	protein_coding	OTTHUMT00000256879.2	48	12	0	0.00	0	0	C	NM_153337	0	0		50707489	-1	no_errors	ENST00000330943	ensembl	human	known	74_37	missense	41	9	8.89	0.00	4	0	SNP	0.001	T
SRPX	8406	genome.wustl.edu	37	X	38080003	38080005	+	In_Frame_Del	DEL	GCA	GCA	-			TCGA-4V-A9QM-01A-11D-A423-09	TCGA-4V-A9QM-11A-11D-A426-09	GCA	GCA					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	660b7dac-fbdc-4ea6-b49d-dcc29088a5d4	cc42f8f7-c7cc-4bdc-adc5-250b99c4852b	g.chrX:38080003_38080005delGCA	ENST00000378533.3	-	1	147_149	c.41_43delTGC	c.(40-45)ctgccg>ccg	p.L14del	TM4SF2_ENST00000465127.1_Intron|SRPX_ENST00000544439.1_In_Frame_Del_p.L14del|RP13-43E11.1_ENST00000423919.1_RNA|SRPX_ENST00000343800.6_Intron|SRPX_ENST00000538295.1_In_Frame_Del_p.L14del|SRPX_ENST00000432886.2_In_Frame_Del_p.L14del	NM_006307.4	NP_006298.1	P78539	SRPX_HUMAN	sushi-repeat containing protein, X-linked	14					autophagy (GO:0006914)|cell adhesion (GO:0007155)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|phagolysosome assembly (GO:0001845)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|response to endoplasmic reticulum stress (GO:0034976)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				autonomic_ganglia(1)|breast(2)|endometrium(5)|large_intestine(5)|lung(10)|prostate(2)	25						agcagaggcggcagcagcagcag	0.734											OREG0019726	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																											0											0									,,,	60,1977		11,31,7,847,252					,,,	-4.7	0.0		dbSNP_126	3	148,3919		6,91,45,1486,856	no	coding,coding,coding,coding	SRPX	NM_006307.4,NM_001170752.1,NM_001170751.1,NM_001170750.1	,,,	17,122,52,2333,1108	A1A1,A1R,A1,RR,R		3.639,2.9455,3.4076	,,,	,,,		208,5896				SO:0001651	inframe_deletion	0			U78093	CCDS14245.1, CCDS55400.1, CCDS55401.1, CCDS55402.1	Xp21.1	2011-01-25	2011-01-25		ENSG00000101955	ENSG00000101955			11309	protein-coding gene	gene with protein product		300187	"""sushi-repeat-containing protein, X chromosome"", ""sushi-repeat-containing protein, X-linked"""			8634708, 8634709	Standard	NM_006307		Approved	ETX1	uc004ddy.2	P78539	OTTHUMG00000021362	ENST00000378533.3:c.41_43delTGC	X.37:g.38080012_38080014delGCA	ENSP00000367794:p.Leu14del	875	A8K065|B3KWP8|B4DDB8|B4DQH5|F5H4D7|G3V1L0|Q4VX66|Q99652|Q99913	In_Frame_Del	DEL	pfam_Hyalin,pfam_Sushi_SCR_CCP,superfamily_Sushi_SCR_CCP,smart_Sushi_SCR_CCP,pfscan_Hyalin,pfscan_Sushi_SCR_CCP	p.L14in_frame_del	ENST00000378533.3	37	c.43_41	CCDS14245.1	X																																																																																			0	NULL		0.734	SRPX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	SRPX	protein_coding	OTTHUMT00000056243.1	15	1	6.25	0.00	1	0	GCA	NM_006307	0	0		38080005	-1	no_errors	ENST00000378533	ensembl	human	known	74_37	in_frame_del	16	3	15.79	0.00	3	0	DEL	0.001:0.001:0.001	0
