#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_ ensembl_gene_id	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GMAF	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNP	i_default_gene_name	i_deletion_substructures	i_domain	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name	i_gene_name_source	i_gene_type	i_havana_transcript	i_n_alt_count	i_n_alt_count_full	i_n_alt_count_val	i_n_ref_count	i_n_ref_count_full	i_n_ref_count_val	i_normal_vaf	i_normal_vaf_val	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_t_alt_count_full	i_t_alt_count_val	i_t_ref_count_full	i_t_ref_count_val	i_tier	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_tumor_vaf	i_tumor_vaf_val	i_type	i_ucsc_cons	i_variant	t_alt_count	t_ref_count
NEDD8	4738	genome.wustl.edu	37	14	24701505	24701505	+	De_novo_Start_OutOfFrame	SNP	A	A	C			TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr14:24701505A>C	ENST00000250495.5	-	0	155				NEDD8_ENST00000524927.1_De_novo_Start_OutOfFrame|NEDD8-MDP1_ENST00000534348.1_De_novo_Start_OutOfFrame|GMPR2_ENST00000557854.1_5'Flank|GMPR2_ENST00000399440.2_5'Flank|GMPR2_ENST00000559836.1_5'Flank|GMPR2_ENST00000348719.7_5'Flank|GMPR2_ENST00000559104.1_5'Flank|GMPR2_ENST00000420554.2_5'Flank|GMPR2_ENST00000456667.3_5'Flank|NEDD8-MDP1_ENST00000604306.1_5'Flank|NEDD8_ENST00000533242.1_5'UTR|GMPR2_ENST00000355299.4_5'Flank|GMPR2_ENST00000559910.1_5'Flank	NM_006156.2	NP_006147.1	Q15843	NEDD8_HUMAN	neural precursor cell expressed, developmentally down-regulated 8						anatomical structure morphogenesis (GO:0009653)|cellular protein modification process (GO:0006464)|protein localization (GO:0008104)|protein neddylation (GO:0045116)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to organic cyclic compound (GO:0014070)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(2)	5				GBM - Glioblastoma multiforme(265;0.0186)		CACACGGATAAATTGCTGCTC	0.597													ENSG00000129559																																					0													91.0	83.0	86.0					14																	24701505		2203	4300	6503			0			-	D23662	CCDS9621.1	14q11.2	2008-08-13			ENSG00000129559	ENSG00000129559			7732	protein-coding gene	gene with protein product		603171				9353319	Standard	NM_006156		Approved	Nedd-8		Q15843	OTTHUMG00000029325	ENST00000250495.5:c.-32T>G	14.37:g.24701505A>C			Q3SXN8|Q6LES6	R	SNP	-	NULL	ENST00000250495.5	37	NULL	CCDS9621.1	14																																																																																			-	NEDD8	-	-		0.597	NEDD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NEDD8	HGNC	protein_coding	OTTHUMT00000073146.2	0	0		60	60		0.00		A	NM_006156		24701505	-1	38		14		tier1	no_errors	ENST00000526430	ensembl	human	known	74_37	rna	73.08		SNP	0.002	C	38	14
MARK4	57787	genome.wustl.edu	37	19	45783712	45783712	+	Missense_Mutation	SNP	A	A	G			TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr19:45783712A>G	ENST00000262891.4	+	11	1418	c.1087A>G	c.(1087-1089)Acc>Gcc	p.T363A	MARK4_ENST00000300843.4_Missense_Mutation_p.T363A	NM_001199867.1	NP_001186796.1	Q96L34	MARK4_HUMAN	MAP/microtubule affinity-regulating kinase 4	363	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nervous system development (GO:0007399)|positive regulation of programmed cell death (GO:0043068)|protein phosphorylation (GO:0006468)	centrosome (GO:0005813)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|microtubule binding (GO:0008017)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)|ubiquitin binding (GO:0043130)			NS(1)|biliary_tract(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	31		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)		AGTGACCGCCACCTACCTCCT	0.617													ENSG00000007047																																					0													112.0	110.0	111.0					19																	45783712		2203	4300	6503	SO:0001583	missense	0			-	AB049127	CCDS12658.1, CCDS56097.1	19q13.32	2014-04-07	2002-06-12	2002-06-14	ENSG00000007047	ENSG00000007047	2.7.11.1		13538	protein-coding gene	gene with protein product		606495	"""MAP/microtubule affinity-regulating kinase like 1"""	MARKL1		23400999, 11326310, 9108484	Standard	NM_001199867		Approved	Nbla00650, FLJ90097, KIAA1860, PAR-1D	uc002paz.2	Q96L34	OTTHUMG00000181769	ENST00000262891.4:c.1087A>G	19.37:g.45783712A>G	ENSP00000262891:p.Thr363Ala		Q8NG37|Q96JG7|Q96SQ2|Q9BYD8	Missense_Mutation	SNP	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_KA1_dom,pfam_UBA/Ts_N,superfamily_Kinase-like_dom,superfamily_KA1/Ssp2_C,superfamily_UBA-like,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_UBA/transl_elong_EF1B_N_euk,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_UBA/transl_elong_EF1B_N_euk,pfscan_Prot_kinase_dom	p.T363A	ENST00000262891.4	37	c.1087	CCDS56097.1	19	.	.	.	.	.	.	.	.	.	.	A	19.27	3.795223	0.70452	.	.	ENSG00000007047	ENST00000262893;ENST00000262891;ENST00000300843	T;T	0.19806	2.12;2.12	5.16	5.16	0.70880	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.41534	0.1163	M	0.66439	2.03	0.80722	D	1	P;B;B	0.38711	0.643;0.36;0.171	P;B;B	0.55455	0.776;0.329;0.119	T	0.27365	-1.0076	10	0.72032	D	0.01	.	12.9784	0.58549	1.0:0.0:0.0:0.0	.	229;363;363	Q8N2N5;Q96L34;Q96L34-2	.;MARK4_HUMAN;.	A	393;363;363	ENSP00000262891:T363A;ENSP00000300843:T363A	ENSP00000262891:T363A	T	+	1	0	MARK4	50475552	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.959000	0.93110	2.174000	0.68829	0.459000	0.35465	ACC	-	MARK4	-	pfam_UBA/Ts_N,superfamily_UBA-like,smart_UBA/transl_elong_EF1B_N_euk,pfscan_UBA/transl_elong_EF1B_N_euk		0.617	MARK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MARK4	HGNC	protein_coding	OTTHUMT00000457537.1	0	0		52	52		0.00		A	NM_031417		45783712	+1	45		45		tier1	no_errors	ENST00000262891	ensembl	human	known	74_37	missense	49.45		SNP	1.000	G	45	45
CLNK	116449	genome.wustl.edu	37	4	10560071	10560071	+	Missense_Mutation	SNP	G	G	T			TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr4:10560071G>T	ENST00000226951.6	-	8	644	c.405C>A	c.(403-405)gaC>gaA	p.D135E	CLNK_ENST00000442825.2_Missense_Mutation_p.D93E|CLNK_ENST00000507719.1_Missense_Mutation_p.D93E	NM_052964.2	NP_443196.2	Q7Z7G1	CLNK_HUMAN	cytokine-dependent hematopoietic cell linker	135					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	intracellular (GO:0005622)	SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)	17						AAATGGGTTTGTCCACCTGTA	0.373													ENSG00000109684																									GBM(87;402 1286 6949 13902 35851)												0													199.0	190.0	193.0					4																	10560071		1933	4137	6070	SO:0001583	missense	0			-	AB032369	CCDS47024.1	4p16.1	2013-02-14			ENSG00000109684	ENSG00000109684		"""SH2 domain containing"""	17438	protein-coding gene	gene with protein product	"""mast cell immunoreceptor signal transducer"""	611434				10562326, 10744659	Standard	NM_052964		Approved	MIST	uc003gmo.4	Q7Z7G1	OTTHUMG00000160062	ENST00000226951.6:c.405C>A	4.37:g.10560071G>T	ENSP00000226951:p.Asp135Glu		Q05C27|Q9P2U9	Missense_Mutation	SNP	pfam_SH2,smart_SH2,pfscan_SH2,prints_SH2	p.D135E	ENST00000226951.6	37	c.405	CCDS47024.1	4	.	.	.	.	.	.	.	.	.	.	G	7.302	0.613151	0.14066	.	.	ENSG00000109684	ENST00000226951;ENST00000429087;ENST00000442825;ENST00000507719	T;T;T	0.44881	1.97;0.91;0.91	4.53	-0.91	0.10511	.	3.191980	0.00664	N	0.000614	T	0.28001	0.0690	N	0.20986	0.625	0.09310	N	1	B;B	0.13594	0.008;0.001	B;B	0.19391	0.025;0.002	T	0.09997	-1.0649	10	0.30854	T	0.27	-5.734	2.9898	0.05980	0.0914:0.1427:0.2956:0.4702	.	93;135	Q7Z7G1-2;Q7Z7G1	.;CLNK_HUMAN	E	135;135;93;93	ENSP00000226951:D135E;ENSP00000390744:D93E;ENSP00000427208:D93E	ENSP00000226951:D135E	D	-	3	2	CLNK	10169169	0.000000	0.05858	0.001000	0.08648	0.338000	0.28826	0.128000	0.15810	-0.027000	0.13873	0.551000	0.68910	GAC	-	CLNK	-	NULL		0.373	CLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CLNK	HGNC	protein_coding	OTTHUMT00000359047.1	0	0		58	58		0.00		G	NM_052964		10560071	-1	18		43		tier1	no_errors	ENST00000226951	ensembl	human	known	74_37	missense	29.51		SNP	0.000	T	18	43
KBTBD7	84078	genome.wustl.edu	37	13	41767967	41767967	+	Missense_Mutation	SNP	G	G	A			TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr13:41767967G>A	ENST00000379483.3	-	1	735	c.427C>T	c.(427-429)Cgc>Tgc	p.R143C		NM_032138.4	NP_115514.2	Q8WVZ9	KBTB7_HUMAN	kelch repeat and BTB (POZ) domain containing 7	143										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(4)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Lung NSC(96;0.000105)|Breast(139;0.00715)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.21e-09)|Epithelial(112;6.99e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000196)|GBM - Glioblastoma multiforme(144;0.000857)|BRCA - Breast invasive adenocarcinoma(63;0.0669)		GCGTACAGGCGCTGCACATTG	0.602													ENSG00000120696																																					0													118.0	96.0	103.0					13																	41767967		2203	4300	6503	SO:0001583	missense	0			-	AL136782	CCDS9377.1	13q13.3	2013-01-08			ENSG00000120696	ENSG00000120696		"""BTB/POZ domain containing"""	25266	protein-coding gene	gene with protein product						11230166	Standard	NM_032138		Approved	DKFZP434E2318	uc001uxw.1	Q8WVZ9	OTTHUMG00000016789	ENST00000379483.3:c.427C>T	13.37:g.41767967G>A	ENSP00000368797:p.Arg143Cys		B5TZ86|Q5T6Y7|Q8NB99|Q9H0I6	Missense_Mutation	SNP	pfam_BTB_POZ,pfam_BACK,pfam_Kelch_1,superfamily_BTB/POZ_fold,smart_BTB/POZ-like,smart_BACK,smart_Kelch_1,pirsf_Kelch-like_gigaxonin,pfscan_BTB/POZ-like	p.R143C	ENST00000379483.3	37	c.427	CCDS9377.1	13	.	.	.	.	.	.	.	.	.	.	G	15.08	2.728555	0.48833	.	.	ENSG00000120696	ENST00000379483;ENST00000501885	T	0.71341	-0.56	4.79	4.79	0.61399	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.64402	U	0.000001	T	0.79581	0.4470	L	0.54323	1.7	0.54753	D	0.999982	D	0.89917	1.0	D	0.65773	0.938	T	0.79848	-0.1630	10	0.46703	T	0.11	.	15.6538	0.77118	0.0:0.0:1.0:0.0	.	143	Q8WVZ9	KBTB7_HUMAN	C	143;45	ENSP00000368797:R143C	ENSP00000368797:R143C	R	-	1	0	KBTBD7	40665967	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	1.324000	0.33712	2.343000	0.79666	0.563000	0.77884	CGC	-	KBTBD7	-	pfam_BTB_POZ,superfamily_BTB/POZ_fold,smart_BTB/POZ-like,pirsf_Kelch-like_gigaxonin		0.602	KBTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KBTBD7	HGNC	protein_coding	OTTHUMT00000044660.1	0	0		36	36		0.00		G	NM_032138		41767967	-1	23		24		tier1	no_errors	ENST00000379483	ensembl	human	known	74_37	missense	48.94		SNP	1.000	A	23	24
PLEKHO1	51177	genome.wustl.edu	37	1	150131221	150131222	+	Frame_Shift_Ins	INS	-	-	A			TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr1:150131221_150131222insA	ENST00000369124.4	+	6	1011_1012	c.733_734insA	c.(733-735)gaafs	p.E245fs	PLEKHO1_ENST00000479194.1_3'UTR|PLEKHO1_ENST00000369126.1_Frame_Shift_Ins_p.E62fs|PLEKHO1_ENST00000025469.6_Frame_Shift_Ins_p.E211fs	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	245	Interaction with ATM, CKIP, IFP35 and NMI.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	22	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCGACCTTGGGAAAAAACAGAC	0.639													ENSG00000023902																																					0																																										SO:0001589	frameshift_variant	0				AF073836	CCDS945.1	1q21.2	2013-01-10			ENSG00000023902	ENSG00000023902		"""Pleckstrin homology (PH) domain containing"""	24310	protein-coding gene	gene with protein product		608335				10799509	Standard	NM_016274		Approved	CKIP-1, OC120	uc001ett.3	Q53GL0	OTTHUMG00000012510	ENST00000369124.4:c.739dupA	1.37:g.150131227_150131227dupA	ENSP00000358120:p.Glu245fs		Q336K5|Q8IZ51|Q9NRV3|Q9UL48	Frame_Shift_Ins	INS	pfam_Pleckstrin_homology,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	p.T213fs	ENST00000369124.4	37	c.631_632	CCDS945.1	1																																																																																				PLEKHO1	-	NULL		0.639	PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	PLEKHO1	HGNC	protein_coding	OTTHUMT00000034962.1	0	0		36	36		0.00		-	NM_016274		150131222	+1	10		29		tier1	no_errors	ENST00000025469	ensembl	human	known	74_37	frame_shift_ins	25.64		INS	0.999:0.887	A	10	29
RNF123	63891	genome.wustl.edu	37	3	49749965	49749965	+	Missense_Mutation	SNP	G	G	T			TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr3:49749965G>T	ENST00000327697.6	+	27	2694	c.2550G>T	c.(2548-2550)gaG>gaT	p.E850D	RNF123_ENST00000432042.1_Missense_Mutation_p.E704D|RNF123_ENST00000433785.1_5'Flank	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	850					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		GGACCATTGAGCACGGTGATC	0.592													ENSG00000164068																																					0													144.0	109.0	121.0					3																	49749965		2203	4300	6503	SO:0001583	missense	0			-	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"""RING-type (C3HC4) zinc fingers"""	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.2550G>T	3.37:g.49749965G>T	ENSP00000328287:p.Glu850Asp		A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	pfam_SPRY_rcpt,superfamily_ConA-like_lec_gl_sf,smart_SPla/RYanodine_receptor_subgr,smart_Znf_RING,pfscan_B30.2/SPRY,pfscan_Znf_RING	p.E850D	ENST00000327697.6	37	c.2550	CCDS33758.1	3	.	.	.	.	.	.	.	.	.	.	G	17.89	3.498592	0.64298	.	.	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000432042	T;T	0.76839	-0.75;-1.05	5.91	5.03	0.67393	.	0.047408	0.85682	D	0.000000	D	0.82536	0.5058	L	0.47716	1.5	0.80722	D	1	D;D	0.64830	0.994;0.994	D;D	0.70716	0.97;0.97	T	0.83123	-0.0117	10	0.59425	D	0.04	-31.0211	10.3739	0.44071	0.148:0.0:0.852:0.0	.	704;850	C9J266;Q5XPI4	.;RN123_HUMAN	D	850;850;704	ENSP00000328287:E850D;ENSP00000392443:E704D	ENSP00000328287:E850D	E	+	3	2	RNF123	49724969	1.000000	0.71417	1.000000	0.80357	0.353000	0.29299	3.153000	0.50685	1.513000	0.48852	-0.145000	0.13849	GAG	-	RNF123	-	NULL		0.592	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RNF123	HGNC	protein_coding	OTTHUMT00000346475.2	0	0		37	37		0.00		G	NM_022064		49749965	+1	4		36		tier1	no_errors	ENST00000327697	ensembl	human	known	74_37	missense	10.00		SNP	1.000	T	4	36
KCNC2	3747	genome.wustl.edu	37	12	75435987	75435987	+	3'UTR	DEL	T	T	-	rs537467144		TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr12:75435987delT	ENST00000549446.1	-	0	3495				KCNC2_ENST00000550433.1_Intron|KCNC2_ENST00000341669.3_Intron|RP11-81K13.1_ENST00000547040.1_RNA|KCNC2_ENST00000298972.1_Intron|RP11-81K13.1_ENST00000550049.1_RNA|KCNC2_ENST00000548513.1_Intron|RP11-81K13.1_ENST00000549762.1_RNA|KCNC2_ENST00000350228.2_Intron	NM_001260497.1|NM_139137.3	NP_001247426.1|NP_631875.1	Q96PR1	KCNC2_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 2						action potential (GO:0001508)|energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(28)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	54					Dalfampridine(DB06637)	ACCCTGGGTATTTTTTTTTTT	0.373													ENSG00000257434																																					0																																										SO:0001624	3_prime_UTR_variant	0				AF268896	CCDS9005.1, CCDS9006.1, CCDS9007.1, CCDS58255.1, CCDS58256.1, CCDS58257.1	12q14.1	2012-07-05						"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6234	protein-coding gene	gene with protein product		176256				8111118, 16382104	Standard	NM_139136		Approved	Kv3.2	uc001sxg.2	Q96PR1	OTTHUMG00000169717	ENST00000549446.1:c.*898A>-	12.37:g.75435987delT			B7Z231|F5H030|J3KPP5|Q4LE77|Q86W09|Q8N1V9|Q96PR0	R	DEL	-	NULL	ENST00000549446.1	37	NULL	CCDS9007.1	12																																																																																				RP11-81K13.1	-	-		0.373	KCNC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ENSG00000257434	Clone_based_vega_gene	protein_coding	OTTHUMT00000405581.2	0	0		20	20		0.00		T	NM_153748		75435987	+1	2		16		tier1	no_errors	ENST00000547040	ensembl	human	known	74_37	rna	11.11		DEL	0.005	-	2	16
SLC39A3	29985	genome.wustl.edu	37	19	2737421	2737421	+	Intron	DEL	T	T	-	rs567070163	byFrequency	TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr19:2737421delT	ENST00000269740.4	-	2	208				AC006538.4_ENST00000586572.1_Intron|SLC39A3_ENST00000455372.2_Intron|SLC39A3_ENST00000545664.1_Intron|SLC39A3_ENST00000590875.1_5'UTR	NM_144564.4	NP_653165.2	Q9BRY0	S39A3_HUMAN	solute carrier family 39 (zinc transporter), member 3						transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	10		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ttcttttttcttttttttttt	0.488													ENSG00000141873																																					0																																										SO:0001627	intron_variant	0				AF052125	CCDS12093.1, CCDS45909.1	19p13.3	2013-05-22			ENSG00000141873	ENSG00000141873		"""Solute carriers"""	17128	protein-coding gene	gene with protein product		612168				10681536	Standard	NM_144564		Approved	ZIP3	uc002lwg.3	Q9BRY0		ENST00000269740.4:c.122-44A>-	19.37:g.2737421delT			B3KMJ3|Q8WUG1	R	DEL	-	NULL	ENST00000269740.4	37	NULL	CCDS12093.1	19																																																																																				SLC39A3	-	-		0.488	SLC39A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC39A3	HGNC	protein_coding	OTTHUMT00000451354.2	0	0		25	25		0.00		T			2737421	-1	2		22		tier1	no_errors	ENST00000590875	ensembl	human	known	74_37	rna	8.33		DEL	0.018	-	2	22
C11orf30	56946	genome.wustl.edu	37	11	76237559	76237559	+	Silent	SNP	T	T	C			TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr11:76237559T>C	ENST00000529032.1	+	12	1875	c.1875T>C	c.(1873-1875)acT>acC	p.T625T	C11orf30_ENST00000524767.1_Silent_p.T640T|C11orf30_ENST00000343878.3_Silent_p.T625T|C11orf30_ENST00000334736.3_Silent_p.T625T|C11orf30_ENST00000525919.1_Silent_p.T626T|C11orf30_ENST00000533248.1_Silent_p.T639T|C11orf30_ENST00000524490.1_Silent_p.T541T|C11orf30_ENST00000525038.1_Silent_p.T640T			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	625	Thr-rich.				chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						CTATCCTTACTGCTACAAGAC	0.363													ENSG00000158636																																					0													122.0	107.0	112.0					11																	76237559		2200	4292	6492	SO:0001819	synonymous_variant	0			-	AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.1875T>C	11.37:g.76237559T>C			B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Silent	SNP	pfam_ENT_N,pfscan_ENT_N	p.T625	ENST00000529032.1	37	c.1875	CCDS8244.1	11																																																																																			-	C11orf30	-	NULL		0.363	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	C11orf30	HGNC	protein_coding	OTTHUMT00000383288.2	0	0		30	30		0.00		T	NM_020193		76237559	+1	4		24		tier1	no_errors	ENST00000334736	ensembl	human	known	74_37	silent	14.29		SNP	1.000	C	4	24
SIK3	23387	genome.wustl.edu	37	11	116728998	116728998	+	Frame_Shift_Del	DEL	T	T	-	rs536178660	byFrequency	TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr11:116728998delT	ENST00000292055.4	-	20	2900	c.2865delA	c.(2863-2865)caafs	p.Q955fs	SIK3_ENST00000488337.1_5'UTR|AP006216.12_ENST00000444200.1_RNA|SIK3_ENST00000542607.1_Frame_Shift_Del_p.Q895fs|SIK3_ENST00000446921.2_Frame_Shift_Del_p.Q953fs|SIK3_ENST00000434315.2_Frame_Shift_Del_p.Q794fs|SIK3_ENST00000375288.1_Frame_Shift_Del_p.Q290fs|SIK3_ENST00000375300.1_Frame_Shift_Del_p.Q1013fs	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	955	Gln-rich.				protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	57						CCTGGTATTCTtgctgttgct	0.577													ENSG00000160584																																					0													47.0	45.0	46.0					11																	116728998		2201	4296	6497	SO:0001589	frameshift_variant	0				AB023216	CCDS8379.1, CCDS60974.1, CCDS8379.2	11q23.3	2010-02-17			ENSG00000160584	ENSG00000160584			29165	protein-coding gene	gene with protein product		614776				10231032, 8889548	Standard	NM_025164		Approved	FLJ12240, L19, KIAA0999, QSK	uc001ppy.3	Q9Y2K2	OTTHUMG00000066628	ENST00000292055.4:c.2865delA	11.37:g.116728998delT	ENSP00000292055:p.Gln955fs		A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Frame_Shift_Del	DEL	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_UBA/transl_elong_EF1B_N_euk,pfscan_Prot_kinase_dom	p.E1014fs	ENST00000292055.4	37	c.3039	CCDS8379.1	11																																																																																				SIK3	-	NULL		0.577	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	SIK3	HGNC	protein_coding		0	0		63	63		0.00		T	NM_025164		116728998	-1	22		39		tier1	no_errors	ENST00000375300	ensembl	human	known	74_37	frame_shift_del	36.07		DEL	0.195	-	22	39
RNF111	54778	genome.wustl.edu	37	15	59323560	59323560	+	Missense_Mutation	SNP	G	G	C			TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr15:59323560G>C	ENST00000557998.1	+	2	826	c.539G>C	c.(538-540)cGg>cCg	p.R180P	RNF111_ENST00000561186.1_Missense_Mutation_p.R180P|RNF111_ENST00000434298.1_Missense_Mutation_p.R180P|RNF111_ENST00000348370.4_Missense_Mutation_p.R180P|RNF111_ENST00000559209.1_Missense_Mutation_p.R180P	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	180					gene expression (GO:0010467)|pattern specification process (GO:0007389)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		CATAGTGCACGGTCTCATAAG	0.428													ENSG00000157450																									NSCLC(72;983 1365 10746 34387 47081)												0													96.0	91.0	93.0					15																	59323560		2192	4291	6483	SO:0001583	missense	0			-	AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"""RING-type (C3HC4) zinc fingers"""	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.539G>C	15.37:g.59323560G>C	ENSP00000452732:p.Arg180Pro		C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Missense_Mutation	SNP	pfam_Znf_C3HC4_RING-type,smart_Znf_RING,pfscan_Znf_RING	p.R180P	ENST00000557998.1	37	c.539	CCDS58366.1	15	.	.	.	.	.	.	.	.	.	.	G	25.0	4.592668	0.86953	.	.	ENSG00000157450	ENST00000348370;ENST00000434298	T;T	0.20200	2.09;2.09	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.47875	0.1469	M	0.65498	2.005	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.999	T	0.39522	-0.9610	10	0.66056	D	0.02	.	18.8745	0.92329	0.0:0.0:1.0:0.0	.	180;180;180	Q6ZNA4-3;Q6ZNA4;Q6ZNA4-2	.;RN111_HUMAN;.	P	180	ENSP00000288199:R180P;ENSP00000393641:R180P	ENSP00000288199:R180P	R	+	2	0	RNF111	57110852	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.910000	0.63321	2.688000	0.91661	0.650000	0.86243	CGG	-	RNF111	-	NULL		0.428	RNF111-003	KNOWN	basic|CCDS	protein_coding	RNF111	HGNC	protein_coding	OTTHUMT00000416012.1	0	0		35	35		0.00		G	NM_017610		59323560	+1	13		18		tier1	no_errors	ENST00000434298	ensembl	human	known	74_37	missense	41.94		SNP	1.000	C	13	18
SLC9A7P1	121456	genome.wustl.edu	37	12	98849591	98849591	+	RNA	SNP	C	C	T	rs555908551		TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr12:98849591C>T	ENST00000554295.1	-	0	1332					NR_033801.1				solute carrier family 9, subfamily A (NHE7, cation proton antiporter 7), member 7 pseudogene 1																		ATGATGAAAACAGGGCTGAAA	0.493													ENSG00000227825																																					0																																												0			-			12q23.1	2013-05-22	2012-03-22		ENSG00000227825	ENSG00000227825		"""Solute carriers"""	32679	pseudogene	pseudogene			"""solute carrier family 9 (sodium/hydrogen exchanger), member 7 pseudogene 1"""				Standard	NR_033801		Approved		uc009ztm.2		OTTHUMG00000170629		12.37:g.98849591C>T				R	SNP	-	NULL	ENST00000554295.1	37	NULL		12																																																																																			-	SLC9A7P1	-	-		0.493	SLC9A7P1-002	PUTATIVE	basic	processed_transcript	SLC9A7P1	HGNC	pseudogene	OTTHUMT00000409869.1	0	0		94	94		0.00		C			98849591	-1	24		52		tier1	no_errors	ENST00000554295	ensembl	human	putative	74_37	rna	31.58		SNP	0.996	T	24	52
ARRB1	408	genome.wustl.edu	37	11	74978736	74978736	+	Nonsense_Mutation	SNP	C	C	A	rs368013804		TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr11:74978736C>A	ENST00000420843.2	-	15	1202	c.1105G>T	c.(1105-1107)Gag>Tag	p.E369*	ARRB1_ENST00000360025.3_Nonsense_Mutation_p.E361*|CTD-2562J17.9_ENST00000529304.1_RNA|ARRB1_ENST00000393505.4_Nonsense_Mutation_p.E369*	NM_004041.4	NP_004032.2	P49407	ARRB1_HUMAN	arrestin, beta 1	369	Interaction with TRAF6.				activation of MAPK activity (GO:0000187)|apoptotic DNA fragmentation (GO:0006309)|blood coagulation (GO:0007596)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor internalization (GO:0002031)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of GTPase activity (GO:0034260)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein ubiquitination (GO:0031397)|Notch signaling pathway (GO:0007219)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of GTPase activity (GO:0043547)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H4 acetylation (GO:0090240)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-Golgi vesicle-mediated transport (GO:0006892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)|transcription from RNA polymerase II promoter (GO:0006366)	basolateral plasma membrane (GO:0016323)|chromatin (GO:0000785)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|pseudopodium (GO:0031143)	angiotensin receptor binding (GO:0031701)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|enzyme inhibitor activity (GO:0004857)|GTPase activator activity (GO:0005096)|insulin-like growth factor receptor binding (GO:0005159)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|large_intestine(2)|lung(4)|prostate(1)	11						ACTGGCGTCTCGTTCTCTGGA	0.602													ENSG00000137486																																					0													54.0	51.0	52.0					11																	74978736		2200	4293	6493	SO:0001587	stop_gained	0			-	BC003636	CCDS31640.1, CCDS44684.1	11q13	2008-12-11			ENSG00000137486	ENSG00000137486			711	protein-coding gene	gene with protein product	"""arrestin 2"""	107940		ARR1		8486659	Standard	NM_004041		Approved		uc001owe.2	P49407	OTTHUMG00000165444	ENST00000420843.2:c.1105G>T	11.37:g.74978736C>A	ENSP00000409581:p.Glu369*		B6V9G8|O75625|O75630|Q2PP20|Q9BTK8	Nonsense_Mutation	SNP	pfam_Arrestin-like_N,pfam_Arrestin_C-like,superfamily_Ig_E-set,prints_Arrestin	p.E369*	ENST00000420843.2	37	c.1105	CCDS44684.1	11	.	.	.	.	.	.	.	.	.	.	C	36	5.881324	0.97062	.	.	ENSG00000137486	ENST00000420843;ENST00000393505;ENST00000360025	.	.	.	5.15	4.24	0.50183	.	0.255939	0.28600	N	0.014774	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-27.4902	16.6933	0.85327	0.0:0.8672:0.1328:0.0	.	.	.	.	X	369;369;361	.	ENSP00000353124:E361X	E	-	1	0	ARRB1	74656384	1.000000	0.71417	0.962000	0.40283	0.899000	0.52679	4.240000	0.58701	0.690000	0.31570	-1.268000	0.01426	GAG	-	ARRB1	-	superfamily_Ig_E-set		0.602	ARRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ARRB1	HGNC	protein_coding	OTTHUMT00000384092.3	0	0		67	67		0.00		C	NM_004041		74978736	-1	20		34		tier1	no_errors	ENST00000393505	ensembl	human	known	74_37	nonsense	37.04		SNP	1.000	A	20	34
NLGN1	22871	genome.wustl.edu	37	3	173322871	173322871	+	Silent	SNP	G	G	T			TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr3:173322871G>T	ENST00000457714.1	+	3	912	c.483G>T	c.(481-483)ccG>ccT	p.P161P	NLGN1_ENST00000545397.1_Silent_p.P161P|NLGN1_ENST00000401917.3_Silent_p.P161P|NLGN1_ENST00000361589.4_Silent_p.P161P	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	161					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			TATATGTCCCGACTGAGGATG	0.338													ENSG00000169760																																					0													70.0	74.0	72.0					3																	173322871		2203	4300	6503	SO:0001819	synonymous_variant	0			-	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.483G>T	3.37:g.173322871G>T			Q9UPT2	Silent	SNP	pfam_CarbesteraseB,pfam_AB_hydrolase_3,prints_Neuroligin	p.P161	ENST00000457714.1	37	c.483	CCDS3222.1	3																																																																																			-	NLGN1	-	pfam_CarbesteraseB		0.338	NLGN1-001	KNOWN	basic|CCDS	protein_coding	NLGN1	HGNC	protein_coding	OTTHUMT00000347054.3	0	0		26	26		0.00		G	NM_014932		173322871	+1	4		18		tier1	no_errors	ENST00000401917	ensembl	human	known	74_37	silent	18.18		SNP	0.978	T	4	18
SARDH	1757	genome.wustl.edu	37	9	136584131	136584131	+	Missense_Mutation	SNP	C	C	A			TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr9:136584131C>A	ENST00000371872.4	-	7	1206	c.949G>T	c.(949-951)Gtc>Ttc	p.V317F	SARDH_ENST00000439388.1_Missense_Mutation_p.V317F|SARDH_ENST00000371867.1_Missense_Mutation_p.V228F|SARDH_ENST00000422262.2_Missense_Mutation_p.V149F	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	317					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		CGGAGGTAGACAGAGGCATCA	0.582													ENSG00000123453																																					0													145.0	121.0	129.0					9																	136584131		2203	4300	6503	SO:0001583	missense	0			-		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.949G>T	9.37:g.136584131C>A	ENSP00000360938:p.Val317Phe		B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Missense_Mutation	SNP	pfam_FAD-dep_OxRdtase,pfam_GCV_T_N,pfam_GCV_T_C	p.V317F	ENST00000371872.4	37	c.949	CCDS6978.1	9	.	.	.	.	.	.	.	.	.	.	C	19.12	3.766615	0.69878	.	.	ENSG00000123453	ENST00000371872;ENST00000439388;ENST00000422262;ENST00000427237;ENST00000539227;ENST00000535281;ENST00000371867;ENST00000393050	T;T;T;T	0.78364	-1.17;-1.17;-1.17;-1.17	4.43	2.56	0.30785	FAD dependent oxidoreductase (1);	0.071516	0.56097	D	0.000036	T	0.75867	0.3908	L	0.28115	0.83	0.80722	D	1	P	0.49447	0.924	P	0.57468	0.821	T	0.74734	-0.3565	10	0.62326	D	0.03	-29.3741	10.4602	0.44575	0.0:0.8368:0.0:0.1632	.	317	Q9UL12	SARDH_HUMAN	F	317;317;149;317;317;317;228;295	ENSP00000360938:V317F;ENSP00000403084:V317F;ENSP00000415537:V149F;ENSP00000360933:V228F	ENSP00000360933:V228F	V	-	1	0	SARDH	135573952	1.000000	0.71417	0.421000	0.26609	0.961000	0.63080	4.661000	0.61518	0.324000	0.23333	0.462000	0.41574	GTC	-	SARDH	-	pfam_FAD-dep_OxRdtase		0.582	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SARDH	HGNC	protein_coding	OTTHUMT00000054931.1	0	0		56	56		0.00		C			136584131	-1	28		48		tier1	no_errors	ENST00000371872	ensembl	human	known	74_37	missense	36.84		SNP	0.992	A	28	48
HRNR	388697	genome.wustl.edu	37	1	152189237	152189237	+	Missense_Mutation	SNP	C	C	G	rs200543988	byFrequency	TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr1:152189237C>G	ENST00000368801.2	-	3	4943	c.4868G>C	c.(4867-4869)aGc>aCc	p.S1623T	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1623					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTGGCCACTGCTGGAAGACCG	0.617													ENSG00000197915																																					0													5.0	1.0	3.0					1																	152189237		494	616	1110	SO:0001583	missense	0			-	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.4868G>C	1.37:g.152189237C>G	ENSP00000357791:p.Ser1623Thr		Q5DT20|Q5U1F4	Missense_Mutation	SNP	pfam_S100_Ca-bd_sub,pfscan_EF_hand_dom	p.S1623T	ENST00000368801.2	37	c.4868	CCDS30859.1	1	.	.	.	.	.	.	.	.	.	.	C	7.019	0.558245	0.13436	.	.	ENSG00000197915	ENST00000368801	T	0.05199	3.48	4.35	-1.7	0.08159	.	.	.	.	.	T	0.01254	0.0041	L	0.48642	1.525	0.09310	N	1	B	0.30281	0.275	B	0.18263	0.021	T	0.46965	-0.9153	9	0.12766	T	0.61	.	6.3832	0.21546	0.0:0.3868:0.4467:0.1665	.	1623	Q86YZ3	HORN_HUMAN	T	1623	ENSP00000357791:S1623T	ENSP00000357791:S1623T	S	-	2	0	HRNR	150455861	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.035000	0.12205	-0.146000	0.11274	-0.241000	0.12123	AGC	rs200543988	HRNR	-	NULL		0.617	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HRNR	HGNC	protein_coding	OTTHUMT00000034016.1	0	0		16	16		0.00		C	XM_373868		152189237	-1	3		8		tier1	no_errors	ENST00000368801	ensembl	human	known	74_37	missense	27.27		SNP	0.000	G	3	8
LCE6A	448835	genome.wustl.edu	37	1	152816119	152816119	+	Silent	SNP	T	T	C			TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr1:152816119T>C	ENST00000431011.2	+	2	288	c.123T>C	c.(121-123)ggT>ggC	p.G41G		NM_001128600.1	NP_001122072.1	A0A183	LCE6A_HUMAN	late cornified envelope 6A	41					keratinization (GO:0031424)												ATTCAGAAGGTTGTCATTCCA	0.547													ENSG00000235942																																					0													127.0	118.0	120.0					1																	152816119		692	1591	2283	SO:0001819	synonymous_variant	0			-	DQ991251	CCDS44227.1	1q21.3	2011-05-24	2006-09-18	2006-09-18	ENSG00000235942	ENSG00000235942		"""Late cornified envelopes"""	31824	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 44"""	C1orf44			Standard	NM_001128600		Approved		uc001fas.4	A0A183	OTTHUMG00000012448	ENST00000431011.2:c.123T>C	1.37:g.152816119T>C				Silent	SNP	NULL	p.G41	ENST00000431011.2	37	c.123	CCDS44227.1	1																																																																																			-	LCE6A	-	NULL		0.547	LCE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LCE6A	HGNC	protein_coding	OTTHUMT00000034661.2	0	0		54	54		0.00		T			152816119	+1	15		47		tier1	no_errors	ENST00000431011	ensembl	human	known	74_37	silent	24.19		SNP	0.001	C	15	47
GTF2F2	2963	genome.wustl.edu	37	13	45781540	45781540	+	Intron	DEL	T	T	-	rs560126070|rs75710948	byFrequency	TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr13:45781540delT	ENST00000340473.6	+	5	445				GTF2F2_ENST00000494087.1_3'UTR	NM_004128.2	NP_004119.1	P13984	T2FB_HUMAN	general transcription factor IIF, polypeptide 2, 30kDa						7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|prostate(1)|upper_aerodigestive_tract(1)	10		Lung NSC(96;0.00115)|Prostate(109;0.00578)|Breast(139;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.133)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000647)		CTCTGAATCCTTTTTTTTTTC	0.313													ENSG00000188342	|||unknown(HR)	104	0.0207668	0.0295	0.0144	5008	,	,		18900	0.0079		0.0129	False		,,,				2504	0.0348																0													38.0	41.0	40.0					13																	45781540		2203	4300	6503	SO:0001627	intron_variant	0				X16901	CCDS9395.1	13q14	2012-01-23	2002-08-29		ENSG00000188342	ENSG00000188342		"""General transcription factors"""	4653	protein-coding gene	gene with protein product		189969	"""general transcription factor IIF, polypeptide 1 (74kD subunit)"""			8162052	Standard	NM_004128		Approved	TFIIF, BTF4, RAP30	uc001uzw.3	P13984	OTTHUMG00000016849	ENST00000340473.6:c.305-19T>-	13.37:g.45781540delT			A6NNS5|Q5W0H3	R	DEL	-	NULL	ENST00000340473.6	37	NULL	CCDS9395.1	13																																																																																				GTF2F2	-	-		0.313	GTF2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GTF2F2	HGNC	protein_coding	OTTHUMT00000044767.2	0	0		36	36		0.00		T	NM_004128		45781540	+1	3		30		tier1	no_errors	ENST00000494087	ensembl	human	known	74_37	rna	9.09		DEL	0.001	-	3	30
FPGS	2356	genome.wustl.edu	37	9	130573242	130573242	+	Missense_Mutation	SNP	G	G	T			TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr9:130573242G>T	ENST00000373247.2	+	14	1356	c.1306G>T	c.(1306-1308)Gcc>Tcc	p.A436S	FPGS_ENST00000373245.1_3'UTR|FPGS_ENST00000460181.1_3'UTR|FPGS_ENST00000393706.2_Missense_Mutation_p.A410S|FPGS_ENST00000373225.3_Missense_Mutation_p.A386S	NM_004957.4	NP_004948.4	Q05932	FOLC_HUMAN	folylpolyglutamate synthase	436					brain development (GO:0007420)|folic acid metabolic process (GO:0046655)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|one-carbon metabolic process (GO:0006730)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|tetrahydrofolylpolyglutamate synthase activity (GO:0004326)			endometrium(2)|kidney(1)|lung(3)|ovary(1)	7					Methotrexate(DB00563)|Pralatrexate(DB06813)|Raltitrexed(DB00293)	GTTTGACTATGCCGTCTTCTG	0.592													ENSG00000136877																																					0													58.0	41.0	47.0					9																	130573242		2200	4299	6499	SO:0001583	missense	0			-		CCDS35148.1, CCDS35149.1, CCDS75905.1	9q34.11	2013-09-19			ENSG00000136877	ENSG00000136877	6.3.2.17		3824	protein-coding gene	gene with protein product		136510					Standard	NM_004957		Approved		uc004bsg.1	Q05932	OTTHUMG00000020716	ENST00000373247.2:c.1306G>T	9.37:g.130573242G>T	ENSP00000362344:p.Ala436Ser		B3KPW4|B7Z2Z3|F5H0K6|Q5JU19|Q5JU22|Q6P2P6	Missense_Mutation	SNP	superfamily_Mur_ligase_cen,superfamily_Mur_ligase_C,tigrfam_Folylpolyglutamate_synth	p.A436S	ENST00000373247.2	37	c.1306	CCDS35148.1	9	.	.	.	.	.	.	.	.	.	.	G	19.21	3.784500	0.70222	.	.	ENSG00000136877	ENST00000373247;ENST00000393706;ENST00000373225	T;T;T	0.43688	0.94;0.94;0.94	5.27	4.38	0.52667	Mur ligase, C-terminal (1);	0.164005	0.53938	D	0.000051	T	0.60586	0.2280	M	0.90019	3.08	0.80722	D	1	P;P	0.45428	0.858;0.55	P;B	0.49999	0.628;0.389	T	0.68062	-0.5508	10	0.52906	T	0.07	-24.6971	12.9822	0.58570	0.0785:0.0:0.9215:0.0	.	410;436	Q05932-4;Q05932	.;FOLC_HUMAN	S	436;410;386	ENSP00000362344:A436S;ENSP00000377309:A410S;ENSP00000362322:A386S	ENSP00000362322:A386S	A	+	1	0	FPGS	129613063	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.185000	0.65076	1.250000	0.43966	0.555000	0.69702	GCC	-	FPGS	-	superfamily_Mur_ligase_C,tigrfam_Folylpolyglutamate_synth		0.592	FPGS-011	KNOWN	basic|appris_principal|CCDS	protein_coding	FPGS	HGNC	protein_coding	OTTHUMT00000054251.1	0	0		31	31		0.00		G			130573242	+1	5		33		tier1	no_errors	ENST00000373247	ensembl	human	known	74_37	missense	13.16		SNP	1.000	T	5	33
GPCPD1	56261	genome.wustl.edu	37	20	5527435	5527435	+	3'UTR	DEL	T	T	-	rs61493788	byFrequency	TCGA-IS-A3K8-01A-11D-A21Q-09	TCGA-IS-A3K8-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq 2500	6561d745-a655-499e-b74b-4f471d9899b7	b123395c-9192-4f50-a4c5-2f9fe3706427	g.chr20:5527435delT	ENST00000379019.4	-	0	3103				GPCPD1_ENST00000481038.1_5'UTR	NM_019593.3	NP_062539.1	Q9NPB8	GPCP1_HUMAN	glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)						glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)	glycerophosphocholine phosphodiesterase activity (GO:0047389)|starch binding (GO:2001070)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)	16						ACAAACAGCCTTTTTTTTTTA	0.383													ENSG00000125772	|||unknown(HR)	607	0.121206	0.2753	0.072	5008	,	,		17791	0.1091		0.0328	False		,,,				2504	0.0511																0																																										SO:0001624	3_prime_UTR_variant	0					CCDS13090.1	20p12.3	2011-01-25			ENSG00000125772	ENSG00000125772			26957	protein-coding gene	gene with protein product		614124				10718198, 20576599	Standard	NM_019593		Approved	KIAA1434, GDE5, GDPD6	uc002wme.4	Q9NPB8	OTTHUMG00000031806	ENST00000379019.4:c.*872A>-	20.37:g.5527435delT			D3DW06|Q9BQL8|Q9NUX0	R	DEL	-	NULL	ENST00000379019.4	37	NULL	CCDS13090.1	20																																																																																				GPCPD1	-	-		0.383	GPCPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPCPD1	HGNC	protein_coding	OTTHUMT00000077869.1	0	0		25	25		0.00		T	NM_019593		5527435	-1	2		21		tier1	no_errors	ENST00000481038	ensembl	human	known	74_37	rna	8.70		DEL	0.008	-	2	21
