#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
MTMR1	8776	genome.wustl.edu	37	X	149931163	149931163	+	Silent	SNP	G	G	A	rs143691344	byFrequency	TCGA-ZB-A96D-01A-11D-A428-09	TCGA-ZB-A96D-10A-01D-A42B-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	e5ab7dc0-9391-4515-8704-bea54cd0a647	64032bf9-77c9-4ca2-b1e0-2208c9a7e1bd	g.chrX:149931163G>A	ENST00000370390.3	+	15	2116	c.1959G>A	c.(1957-1959)tcG>tcA	p.S653S	MTMR1_ENST00000541925.1_Silent_p.S559S|MTMR1_ENST00000445323.2_Silent_p.S661S|MTMR1_ENST00000538506.1_Intron|MTMR1_ENST00000544228.1_Silent_p.S653S	NM_003828.2	NP_003819.1	Q13613	MTMR1_HUMAN	myotubularin related protein 1	653					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					GGGGCTCCTCGCCCTCCCACT	0.687																																							0											0										10,3825		0,9,1,1623,570	41.0	39.0	40.0		1959	-10.3	0.0	X	dbSNP_134	40	0,6726		0,0,0,2427,1872	no	coding-synonymous	MTMR1	NM_003828.2		0,9,1,4050,2442	AA,AG,A,GG,G		0.0,0.2608,0.0947		653/666	149931163	10,10551	2203	4299	6502	SO:0001819	synonymous_variant	0			U58032	CCDS14695.1	Xq28	2011-06-09			ENSG00000063601	ENSG00000063601		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7449	protein-coding gene	gene with protein product		300171				9828128	Standard	XM_005274765		Approved		uc004fei.3	Q13613	OTTHUMG00000024159	ENST00000370390.3:c.1959G>A	X.37:g.149931163G>A			A0A024RC07|Q9UBX6|Q9UEM0|Q9UQD5	Silent	SNP	pfam_Myotubularin-like_Pase_dom,pfam_GRAM,smart_GRAM,smart_Tyr_Pase_cat,pfscan_Tyr/Dual-sp_Pase	p.S661	ENST00000370390.3	37	c.1983	CCDS14695.1	X																																																																																			0	NULL		0.687	MTMR1-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	MTMR1	protein_coding	OTTHUMT00000060863.2	43	54	0	0.00	0	0	G	NM_003828, NM_176789	rs143691344	G->A		149931163	1	no_errors	ENST00000445323	ensembl	human	known	74_37	silent	22	34	15.38	8.11	4	3	SNP	0.002	A
HNRNPR	10236	genome.wustl.edu	37	1	23650155	23650155	+	Missense_Mutation	SNP	G	G	A			TCGA-ZB-A96D-01A-11D-A428-09	TCGA-ZB-A96D-10A-01D-A42B-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	e5ab7dc0-9391-4515-8704-bea54cd0a647	64032bf9-77c9-4ca2-b1e0-2208c9a7e1bd	g.chr1:23650155G>A	ENST00000374612.1	-	6	692	c.569C>T	c.(568-570)cCc>cTc	p.P190L	HNRNPR_ENST00000426846.2_Intron|HNRNPR_ENST00000374616.3_Missense_Mutation_p.P190L|HNRNPR_ENST00000302271.6_Missense_Mutation_p.P190L|HNRNPR_ENST00000478691.1_Missense_Mutation_p.P89L|HNRNPR_ENST00000606561.1_Missense_Mutation_p.P51L|HNRNPR_ENST00000427764.2_Missense_Mutation_p.P152L	NM_001102398.1|NM_005826.3	NP_001095868.1|NP_005817.1	O43390	HNRPR_HUMAN	heterogeneous nuclear ribonucleoprotein R	190	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00394)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;6.83e-27)|Colorectal(126;6.01e-08)|COAD - Colon adenocarcinoma(152;3.32e-06)|GBM - Glioblastoma multiforme(114;6.69e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00357)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0875)|LUSC - Lung squamous cell carcinoma(448;0.19)		ATCCCAAATGGGTCCGGCCTT	0.448																																							0											0													99.0	101.0	101.0					1																	23650155		2203	4300	6503	SO:0001583	missense	0			AF000364	CCDS232.1, CCDS44085.1, CCDS60020.1, CCDS72726.1, CCDS72727.1	1p36.12	2013-02-12		2007-08-16	ENSG00000125944	ENSG00000125944		"""RNA binding motif (RRM) containing"""	5047	protein-coding gene	gene with protein product		607201		HNRPR		9421497	Standard	XM_005245711		Approved	hnRNP-R	uc001bgp.4	O43390	OTTHUMG00000003224	ENST00000374612.1:c.569C>T	1.37:g.23650155G>A	ENSP00000363741:p.Pro190Leu		Q2L7G6|Q5TEH1|Q9BV64|S4R3J4	Missense_Mutation	SNP	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom,tigrfam_HnRNP_R/Q_splicing_fac	p.P190L	ENST00000374612.1	37	c.569	CCDS232.1	1	.	.	.	.	.	.	.	.	.	.	G	18.24	3.579240	0.65878	.	.	ENSG00000125944	ENST00000374616;ENST00000374612;ENST00000302271;ENST00000427764	T;T;T;T	0.45276	0.9;0.9;0.9;1.21	5.14	5.14	0.70334	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.096580	0.64402	D	0.000001	T	0.65260	0.2674	M	0.82132	2.575	0.80722	D	1	D;B;B;B;B	0.56746	0.977;0.127;0.052;0.149;0.021	D;B;B;B;B	0.65233	0.933;0.173;0.115;0.122;0.039	T	0.65541	-0.6143	10	0.39692	T	0.17	-1.6103	17.5397	0.87843	0.0:0.0:1.0:0.0	.	152;51;167;190;190	Q2L7G6;B4DT28;Q6MZS5;O43390;O43390-2	.;.;.;HNRPR_HUMAN;.	L	190;190;190;152	ENSP00000363745:P190L;ENSP00000363741:P190L;ENSP00000304405:P190L;ENSP00000392799:P152L	ENSP00000304405:P190L	P	-	2	0	HNRNPR	23522742	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	9.695000	0.98691	2.567000	0.86603	0.561000	0.74099	CCC	0	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom,tigrfam_HnRNP_R/Q_splicing_fac		0.448	HNRNPR-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	HNRNPR	protein_coding	OTTHUMT00000008889.1	104	192	0	0.52	0	1	G	NM_005826	0	0		23650155	-1	no_errors	ENST00000374616	ensembl	human	known	74_37	missense	69	143	8	6.45	6	10	SNP	1	A
KCNT2	343450	genome.wustl.edu	37	1	196438174	196438174	+	Nonsense_Mutation	SNP	G	G	A			TCGA-ZB-A96D-01A-11D-A428-09	TCGA-ZB-A96D-10A-01D-A42B-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	e5ab7dc0-9391-4515-8704-bea54cd0a647	64032bf9-77c9-4ca2-b1e0-2208c9a7e1bd	g.chr1:196438174G>A	ENST00000294725.9	-	6	1324	c.409C>T	c.(409-411)Cga>Tga	p.R137*	KCNT2_ENST00000367431.4_Nonsense_Mutation_p.R137*|KCNT2_ENST00000609185.1_Nonsense_Mutation_p.R137*|KCNT2_ENST00000367433.5_Nonsense_Mutation_p.R137*|KCNT2_ENST00000451324.2_De_novo_Start_InFrame			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	137					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						AAGGGTATTCGTAAAATCTGT	0.333																																							0											0													43.0	44.0	43.0					1																	196438174		2199	4295	6494	SO:0001587	stop_gained	0			BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18866	protein-coding gene	gene with protein product	"""sodium and chloride activated ATP sensitive potassium channel"""	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.409C>T	1.37:g.196438174G>A	ENSP00000294725:p.Arg137*		Q3SY59|Q5VTN1|Q6ZMT3	Nonsense_Mutation	SNP	pfam_K_chnl_Ca-activ_BK_asu,pfam_2pore_dom_K_chnl_dom	p.R137*	ENST00000294725.9	37	c.409	CCDS1384.1	1	.	.	.	.	.	.	.	.	.	.	G	37	6.252061	0.97412	.	.	ENSG00000162687	ENST00000367433;ENST00000367431;ENST00000294725	.	.	.	5.41	4.49	0.54785	.	0.000000	0.46758	D	0.000268	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	-12.272	14.4884	0.67634	0.0:0.0:0.8516:0.1484	.	.	.	.	X	137	.	ENSP00000294725:R137X	R	-	1	2	KCNT2	194704797	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.754000	0.55189	1.490000	0.48466	0.557000	0.71058	CGA	0	NULL		0.333	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KCNT2	protein_coding	OTTHUMT00000086418.2	318	191	0.31	0.52	1	1	G	NM_198503	0	0		196438174	-1	no_errors	ENST00000294725	ensembl	human	known	74_37	nonsense	196	153	7.11	10.00	15	17	SNP	1	A
GTF2I	2969	genome.wustl.edu	37	7	74146970	74146970	+	Missense_Mutation	SNP	T	T	A			TCGA-ZB-A96D-01A-11D-A428-09	TCGA-ZB-A96D-10A-01D-A42B-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	e5ab7dc0-9391-4515-8704-bea54cd0a647	64032bf9-77c9-4ca2-b1e0-2208c9a7e1bd	g.chr7:74146970T>A	ENST00000324896.4	+	15	1660	c.1271T>A	c.(1270-1272)cTt>cAt	p.L424H	GTF2I_ENST00000346152.4_Missense_Mutation_p.L403H|GTF2I_ENST00000353920.4_Missense_Mutation_p.L404H|GTF2I_ENST00000416070.1_Missense_Mutation_p.L383H	NM_032999.2	NP_127492.1	P78347	GTF2I_HUMAN	general transcription factor IIi	424					negative regulation of angiogenesis (GO:0016525)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19						AGGATATTACTTGCAAAGGAA	0.378																																							0											0													13.0	13.0	13.0					7																	74146970		1741	3768	5509	SO:0001583	missense	0			U77948	CCDS5573.1, CCDS5574.1, CCDS5575.1, CCDS47614.1, CCDS64680.1	7q11.23	2011-05-25	2009-07-23			ENSG00000263001		"""General transcription factors"""	4659	protein-coding gene	gene with protein product		601679	"""general transcription factor II, i"""	WBSCR6		9334314, 9012831	Standard	NM_032999		Approved	TFII-I, BAP-135, SPIN, BTKAP1, DIWS, IB291	uc003uau.3	P78347		ENST00000324896.4:c.1271T>A	7.37:g.74146970T>A	ENSP00000322542:p.Leu424His		O14743|O15359|O43546|O43588|O43589|Q75M85|Q75M86|Q75M87|Q75M88|Q86U51|Q9BSZ4	Missense_Mutation	SNP	pfam_GTF2I,superfamily_GTF2I,pirsf_TF_II-I,pfscan_GTF2I	p.L424H	ENST00000324896.4	37	c.1271	CCDS5573.1	7	.	.	.	.	.	.	.	.	.	.	T	18.18	3.565904	0.65651	.	.	ENSG00000077809	ENST00000324896;ENST00000539339;ENST00000353920;ENST00000346152;ENST00000416070	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	4.72	4.72	0.59763	.	0.110120	0.39544	N	0.001322	T	0.37019	0.0988	N	0.14661	0.345	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.998;1.0;0.999	D;D;P;D;D	0.74348	0.983;0.979;0.874;0.971;0.963	T	0.36089	-0.9762	10	0.56958	D	0.05	-16.5588	13.3771	0.60745	0.0:0.0:0.0:1.0	.	402;383;404;403;424	Q499G6;P78347-2;P78347-3;P78347-4;P78347	.;.;.;.;GTF2I_HUMAN	H	424;419;404;403;383	ENSP00000322542:L424H;ENSP00000322671:L404H;ENSP00000322599:L403H;ENSP00000387651:L383H	ENSP00000322542:L424H	L	+	2	0	GTF2I	73784906	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	5.342000	0.65970	1.753000	0.51906	0.477000	0.44152	CTT	0	pfam_GTF2I,superfamily_GTF2I,pirsf_TF_II-I,pfscan_GTF2I		0.378	GTF2I-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GTF2I	protein_coding	OTTHUMT00000252708.1	531	153	0	0.00	0	0	T	NM_032999	0	0		74146970	1	no_errors	ENST00000324896	ensembl	human	known	74_37	missense	318	95	10.67	5.00	38	5	SNP	1	A
GPRC5C	55890	genome.wustl.edu	37	17	72428280	72428280	+	Splice_Site	SNP	G	G	A			TCGA-ZB-A96D-01A-11D-A428-09	TCGA-ZB-A96D-10A-01D-A42B-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	e5ab7dc0-9391-4515-8704-bea54cd0a647	64032bf9-77c9-4ca2-b1e0-2208c9a7e1bd	g.chr17:72428280G>A	ENST00000481232.1	+	1	614	c.103G>A	c.(103-105)Ggg>Agg	p.G35R	GPRC5C_ENST00000342648.5_Intron|GPRC5C_ENST00000392627.1_Splice_Site_p.G35R|GPRC5C_ENST00000392629.2_5'Flank			Q9NQ84	GPC5C_HUMAN	G protein-coupled receptor, class C, group 5, member C	0					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|vesicle (GO:0031982)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	17						TCAGCCTGGAGGTGAGTCGGG	0.672																																							0											0													31.0	27.0	28.0					17																	72428280		2192	4295	6487	SO:0001630	splice_region_variant	0			AF207989	CCDS11699.1, CCDS42378.1	17q25	2014-01-30	2014-01-30		ENSG00000170412	ENSG00000170412		"""GPCR / Class C : Orphans"""	13309	protein-coding gene	gene with protein product		605949	"""G protein-coupled receptor, family C, group 5, member C"""			10945465	Standard	NM_022036		Approved	RAIG-3	uc002jkr.3	Q9NQ84	OTTHUMG00000067613	ENST00000481232.1:c.103+1G>A	17.37:g.72428280G>A			B5BUN4|Q2NL85|Q9NZG5	Missense_Mutation	SNP	pfam_GPCR_3_C,pfscan_GPCR_3_C	p.G35R	ENST00000481232.1	37	c.103		17	.	.	.	.	.	.	.	.	.	.	G	12.69	2.014542	0.35511	.	.	ENSG00000170412	ENST00000342648	.	.	.	4.84	3.8	0.43715	.	0.430307	0.19232	N	0.119387	T	0.57198	0.2037	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54543	-0.8278	6	0.38643	T	0.18	.	7.2048	0.25901	0.1229:0.0:0.8771:0.0	.	.	.	.	R	35	.	ENSP00000340595:G35R	G	+	1	0	GPRC5C	69939875	0.995000	0.38212	1.000000	0.80357	0.684000	0.39900	0.943000	0.29030	2.506000	0.84524	0.462000	0.41574	GGG	0	NULL		0.672	GPRC5C-002	PUTATIVE	basic|exp_conf	protein_coding	GPRC5C	protein_coding	OTTHUMT00000145095.2	54	88	0	0.00	0	0	G		0	0	Missense_Mutation	72428280	1	no_errors	ENST00000392627	ensembl	human	known	74_37	missense	18	79	18.18	11.24	4	10	SNP	1	A
ZC3H4	23211	genome.wustl.edu	37	19	47569869	47569869	+	Missense_Mutation	SNP	T	T	C			TCGA-ZB-A96D-01A-11D-A428-09	TCGA-ZB-A96D-10A-01D-A42B-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	e5ab7dc0-9391-4515-8704-bea54cd0a647	64032bf9-77c9-4ca2-b1e0-2208c9a7e1bd	g.chr19:47569869T>C	ENST00000253048.5	-	15	3693	c.3656A>G	c.(3655-3657)aAc>aGc	p.N1219S	ZC3H4_ENST00000594019.1_5'UTR	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	1219							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		CCGGGGCCGGTTGTAGCTGTT	0.711																																							0											0													12.0	15.0	14.0					19																	47569869		1604	3522	5126	SO:0001583	missense	0			AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.3656A>G	19.37:g.47569869T>C	ENSP00000253048:p.Asn1219Ser		Q9Y420	Missense_Mutation	SNP	pfam_Znf_CCCH,smart_Znf_CCCH	p.N1219S	ENST00000253048.5	37	c.3656	CCDS42582.1	19	.	.	.	.	.	.	.	.	.	.	T	16.64	3.180630	0.57800	.	.	ENSG00000130749	ENST00000253048	T	0.18810	2.19	5.74	4.72	0.59763	.	0.000000	0.85682	D	0.000000	T	0.36468	0.0968	L	0.59436	1.845	0.51767	D	0.999937	D	0.69078	0.997	D	0.75020	0.985	T	0.18085	-1.0348	10	0.11182	T	0.66	.	11.3604	0.49640	0.1362:0.0:0.0:0.8638	.	1219	Q9UPT8	ZC3H4_HUMAN	S	1219	ENSP00000253048:N1219S	ENSP00000253048:N1219S	N	-	2	0	ZC3H4	52261709	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.257000	0.65473	0.988000	0.38734	0.460000	0.39030	AAC	0	NULL		0.711	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	ZC3H4	protein_coding	OTTHUMT00000466667.1	70	100	0	0.00	0	0	T		0	0		47569869	-1	no_errors	ENST00000253048	ensembl	human	known	74_37	missense	40	97	13.04	6.67	6	7	SNP	1	C
PLXNB2	23654	genome.wustl.edu	37	22	50715077	50715077	+	Missense_Mutation	SNP	T	T	A			TCGA-ZB-A96D-01A-11D-A428-09	TCGA-ZB-A96D-10A-01D-A42B-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	e5ab7dc0-9391-4515-8704-bea54cd0a647	64032bf9-77c9-4ca2-b1e0-2208c9a7e1bd	g.chr22:50715077T>A	ENST00000449103.1	-	35	5458	c.5318A>T	c.(5317-5319)cAc>cTc	p.H1773L	PLXNB2_ENST00000359337.4_Missense_Mutation_p.H1773L			O15031	PLXB2_HUMAN	plexin B2	1773					brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CTCTGCCAGGTGTGTGTTCAT	0.637											OREG0026679	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																											0											0													114.0	130.0	125.0					22																	50715077		2115	4231	6346	SO:0001583	missense	0				CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"""Plexins"""	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.5318A>T	22.37:g.50715077T>A	ENSP00000409171:p.His1773Leu	971	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	pfam_Plexin_cytoplasmic_RasGAP_dom,pfam_IPT,pfam_Semap_dom,pfam_Plexin_repeat,superfamily_Semap_dom,superfamily_Rho_GTPase_activation_prot,superfamily_Ig_E-set,superfamily_Plexin-like_fold,smart_Semap_dom,smart_Plexin-like_fold,smart_IPT,pfscan_Semap_dom	p.H1773L	ENST00000449103.1	37	c.5318	CCDS43035.1	22	.	.	.	.	.	.	.	.	.	.	T	16.47	3.132735	0.56828	.	.	ENSG00000196576	ENST00000449103;ENST00000359337	T;T	0.10763	2.84;2.84	3.98	3.98	0.46160	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.000000	0.64402	D	0.000002	T	0.20780	0.0500	L	0.42744	1.35	0.54753	D	0.999981	D	0.71674	0.998	D	0.74674	0.984	T	0.04781	-1.0927	10	0.12766	T	0.61	.	13.0403	0.58895	0.0:0.0:0.0:1.0	.	1773	O15031	PLXB2_HUMAN	L	1773	ENSP00000409171:H1773L;ENSP00000352288:H1773L	ENSP00000352288:H1773L	H	-	2	0	PLXNB2	49057204	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	4.405000	0.59741	1.663000	0.50791	0.379000	0.24179	CAC	0	pfam_Plexin_cytoplasmic_RasGAP_dom,superfamily_Rho_GTPase_activation_prot		0.637	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLXNB2	protein_coding	OTTHUMT00000316874.3	30	154	0	0.00	0	0	T	NM_012401	0	0		50715077	-1	no_errors	ENST00000359337	ensembl	human	known	74_37	missense	27	116	12.9	7.94	4	10	SNP	1	A
EOMES	8320	genome.wustl.edu	37	3	27763427	27763428	+	In_Frame_Ins	INS	-	-	CGGCGC	rs368178421|rs1874198|rs3062761	byFrequency	TCGA-ZB-A96D-01A-11D-A428-09	TCGA-ZB-A96D-10A-01D-A42B-09	-	-	-	CGGCGC	-	-	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	e5ab7dc0-9391-4515-8704-bea54cd0a647	64032bf9-77c9-4ca2-b1e0-2208c9a7e1bd	g.chr3:27763427_27763428insCGGCGC	ENST00000295743.4	-	1	561_562	c.358_359insGCGCCG	c.(358-360)gcc>gGCGCCGcc	p.119_120insGA	EOMES_ENST00000461503.1_Intron|EOMES_ENST00000537516.1_Intron|EOMES_ENST00000449599.1_In_Frame_Ins_p.119_120insGA			O95936	EOMES_HUMAN	eomesodermin	119	Ala-rich.		A -> G (in dbSNP:rs12715125).		brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell differentiation involved in embryonic placenta development (GO:0060706)|cerebral cortex neuron differentiation (GO:0021895)|cerebral cortex regionalization (GO:0021796)|endoderm formation (GO:0001706)|endodermal cell fate specification (GO:0001714)|interferon-gamma production (GO:0032609)|mesoderm formation (GO:0001707)|mesodermal to mesenchymal transition involved in gastrulation (GO:0060809)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|olfactory bulb development (GO:0021772)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|skeletal muscle cell differentiation (GO:0035914)|stem cell maintenance (GO:0019827)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)	21						ggcggcggcggctgcagcggcg	0.767														2685	0.536142	0.3147	0.5274	5008	,	,		7250	0.8363		0.3837	False		,,,				2504	0.6892						0.4635,.,0.5361,0.0003994											0										101,91,844		44,2,11,38,13,410						-0.4	0.1		dbSNP_102	1	316,357,1963		136,0,44,143,71,924	no	codingComplex	EOMES	NM_005442.2		180,2,55,181,84,1334	A1A1,A1A2,A1R,A2A2,A2R,RR		25.5311,18.5328,23.5566				417,448,2807				SO:0001652	inframe_insertion	0			BC025363	CCDS2646.1, CCDS63585.1	3p24.1	2011-06-13	2010-06-24		ENSG00000163508	ENSG00000163508		"""T-boxes"""	3372	protein-coding gene	gene with protein product	"""T-box brain2"""	604615	"""eomesodermin (Xenopus laevis) homolog"""			9888994, 9434949	Standard	NM_005442		Approved	TBR2	uc003cdy.4	O95936	OTTHUMG00000130570	ENST00000295743.4:c.358_359insGCGCCG	3.37:g.27763427_27763428insCGGCGC	ENSP00000295743:p.Ala119_Ala120insGlyAla		B7Z4I2|B7ZA51|G3XAI5|Q8TAZ2|Q9UPM7	In_Frame_Ins	INS	pfam_TF_T-box,superfamily_p53-like_TF_DNA-bd,smart_TF_T-box,pfscan_TF_T-box,prints_TF_T-box	p.120in_frame_insGA	ENST00000295743.4	37	c.359_358	CCDS2646.1	3																																																																																			0	NULL		0.767	EOMES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EOMES	protein_coding	OTTHUMT00000252995.1	11	2	0	0.00	0	0	0	NM_005442	rs368178421	G->GCGC,GCGGCGC,GCGGCGGCGC		27763428	-1	no_errors	ENST00000449599	ensembl	human	known	74_37	in_frame_ins	4	3	42.86	50.00	3	3	INS	0.116:0.075	CGGCGC
WNT9A	7483	genome.wustl.edu	37	1	228112027	228112027	+	Missense_Mutation	SNP	C	C	T			TCGA-ZB-A96D-01A-11D-A428-09	TCGA-ZB-A96D-10A-01D-A42B-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	e5ab7dc0-9391-4515-8704-bea54cd0a647	64032bf9-77c9-4ca2-b1e0-2208c9a7e1bd	g.chr1:228112027C>T	ENST00000272164.5	-	3	437	c.427G>A	c.(427-429)Gcg>Acg	p.A143T		NM_003395.2	NP_003386.1	O14904	WNT9A_HUMAN	wingless-type MMTV integration site family, member 9A	143					canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cornea development in camera-type eye (GO:0061303)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal system morphogenesis (GO:0048704)|iris morphogenesis (GO:0061072)|mitotic cell cycle checkpoint (GO:0007093)|multicellular organismal development (GO:0007275)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of smoothened signaling pathway (GO:0045880)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Prostate(94;0.0405)				ATGCGGCCCGCGCTGCACGCC	0.652																																							0											0													72.0	72.0	72.0					1																	228112027		2203	4300	6503	SO:0001583	missense	0			AB060283	CCDS31045.1	1q42	2008-02-05	2003-03-11	2003-03-14	ENSG00000143816	ENSG00000143816		"""Wingless-type MMTV integration sites"""	12778	protein-coding gene	gene with protein product		602863	"""wingless-type MMTV integration site family, member 14"""	WNT14		9441749	Standard	NM_003395		Approved		uc001hri.2	O14904	OTTHUMG00000037592	ENST00000272164.5:c.427G>A	1.37:g.228112027C>T	ENSP00000272164:p.Ala143Thr		A6NLW2|Q2M2J3|Q5VWU0|Q96S50	Missense_Mutation	SNP	pfam_Wnt,smart_Wnt,prints_Wnt,prints_Wnt9a	p.A143T	ENST00000272164.5	37	c.427	CCDS31045.1	1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.344867	0.82022	.	.	ENSG00000143816	ENST00000272164	T	0.75704	-0.96	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	T	0.70185	0.3195	L	0.41492	1.28	0.51767	D	0.999937	P	0.52061	0.95	P	0.44732	0.459	T	0.71879	-0.4459	10	0.39692	T	0.17	.	17.0645	0.86556	0.0:1.0:0.0:0.0	.	143	O14904	WNT9A_HUMAN	T	143	ENSP00000272164:A143T	ENSP00000272164:A143T	A	-	1	0	WNT9A	226178650	1.000000	0.71417	0.115000	0.21578	0.904000	0.53231	4.861000	0.62969	2.267000	0.75376	0.491000	0.48974	GCG	0	pfam_Wnt,smart_Wnt,prints_Wnt		0.652	WNT9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WNT9A	protein_coding	OTTHUMT00000091646.1	49	22	0	0.00	0	0	C	NM_003395	0	0		228112027	-1	no_errors	ENST00000272164	ensembl	human	known	74_37	missense	45	10	8.16	0.00	4	0	SNP	0.947	T
CALCA	796	genome.wustl.edu	37	11	14991621	14991621	+	Splice_Site	SNP	C	C	T	rs556800566		TCGA-ZB-A96D-01A-11D-A428-09	TCGA-ZB-A96D-10A-01D-A42B-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	e5ab7dc0-9391-4515-8704-bea54cd0a647	64032bf9-77c9-4ca2-b1e0-2208c9a7e1bd	g.chr11:14991621C>T	ENST00000486207.1	-	2	95	c.87G>A	c.(85-87)agG>agA	p.R29R	CALCA_ENST00000331587.4_Splice_Site_p.R29R|CALCA_ENST00000359642.3_Splice_Site_p.R29R|CALCA_ENST00000396372.2_Splice_Site_p.R29R|CALCB_ENST00000523376.1_Intron|CALCA_ENST00000361010.3_Splice_Site_p.R29R			P06881	CALCA_HUMAN	calcitonin-related polypeptide alpha	29					activation of adenylate cyclase activity (GO:0007190)|cell-cell signaling (GO:0007267)|cytosolic calcium ion homeostasis (GO:0051480)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|G-protein coupled receptor internalization (GO:0002031)|leukocyte cell-cell adhesion (GO:0007159)|negative regulation of blood pressure (GO:0045776)|negative regulation of bone resorption (GO:0045779)|negative regulation of calcium ion transport into cytosol (GO:0010523)|negative regulation of osteoclast differentiation (GO:0045671)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of interleukin-1 alpha production (GO:0032730)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of vasodilation (GO:0045909)|protein phosphorylation (GO:0006468)|receptor internalization (GO:0031623)|regulation of blood pressure (GO:0008217)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	protein complex binding (GO:0032403)|receptor binding (GO:0005102)			central_nervous_system(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	8						CCAGGGCAGACCTGTGGAGGG	0.632																																							0											0													33.0	34.0	34.0					11																	14991621		2200	4294	6494	SO:0001630	splice_region_variant	0			X00356, M64486	CCDS7819.1, CCDS31432.1	11p15.2	2014-09-17	2008-02-20		ENSG00000110680	ENSG00000110680		"""Endogenous ligands"""	1437	protein-coding gene	gene with protein product	"""calcitonin"""	114130	"""calcitonin 1"""	CALC1		6546550	Standard	NM_001033953		Approved		uc001mlw.1	P01258	OTTHUMG00000159731	ENST00000486207.1:c.87-1G>A	11.37:g.14991621C>T			Q93048|Q9UCP0	Silent	SNP	pfam_Procalcitonin/adrenomedullin,smart_Calcitonin_peptide-like,prints_Calcitonin	p.R29	ENST00000486207.1	37	c.87	CCDS31432.1	11																																																																																			0	pfam_Procalcitonin/adrenomedullin		0.632	CALCA-004	KNOWN	basic|appris_principal|CCDS	protein_coding	CALCA	protein_coding	OTTHUMT00000357068.1	56	5	0	0.00	0	0	C	NM_001741	0	0	Silent	14991621	-1	no_errors	ENST00000331587	ensembl	human	known	74_37	silent	25	6	13.79	0.00	4	0	SNP	0.121	T
ARHGAP5	394	genome.wustl.edu	37	14	32546583	32546583	+	5'UTR	SNP	G	G	A			TCGA-ZB-A96D-01A-11D-A428-09	TCGA-ZB-A96D-10A-01D-A42B-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	e5ab7dc0-9391-4515-8704-bea54cd0a647	64032bf9-77c9-4ca2-b1e0-2208c9a7e1bd	g.chr14:32546583G>A	ENST00000345122.3	+	0	89				ARHGAP5_ENST00000396582.2_Silent_p.P4P|ARHGAP5_ENST00000556611.1_Intron|ARHGAP5-AS1_ENST00000553596.1_RNA|ARHGAP5_ENST00000432921.1_5'UTR|ARHGAP5_ENST00000539826.2_Intron|ARHGAP5_ENST00000433497.1_5'UTR	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5						cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		Tgtcgctgccgccgccaccgc	0.731																																					NSCLC(9;77 350 3443 29227 41353)		0											0													2.0	2.0	2.0					14																	32546583		650	1518	2168	SO:0001623	5_prime_UTR_variant	0			U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"""Rho GTPase activating proteins"""	675	protein-coding gene	gene with protein product		602680	"""growth factor independent 2"""	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.-227G>A	14.37:g.32546583G>A			A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Silent	SNP	pfam_RhoGAP_dom,superfamily_Rho_GTPase_activation_prot,smart_RhoGAP_dom,pfscan_RhoGAP_dom	p.P4	ENST00000345122.3	37	c.12	CCDS32062.1	14																																																																																			0	superfamily_Rho_GTPase_activation_prot,pfscan_RhoGAP_dom		0.731	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ARHGAP5	protein_coding	OTTHUMT00000409735.1	45	16	0	0.00	0	0	G	NM_001030055	0	0		32546583	1	no_errors	ENST00000396582	ensembl	human	known	74_37	silent	30	8	11.76	0.00	4	0	SNP	1	A
NPIPA2	642799	genome.wustl.edu	37	16	14859247	14859247	+	Missense_Mutation	SNP	C	C	T			TCGA-ZB-A96D-01A-11D-A428-09	TCGA-ZB-A96D-10A-01D-A42B-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	e5ab7dc0-9391-4515-8704-bea54cd0a647	64032bf9-77c9-4ca2-b1e0-2208c9a7e1bd	g.chr16:14859247C>T	ENST00000529166.1	+	8	1087	c.1087C>T	c.(1087-1089)Cgg>Tgg	p.R363W	NPIPA2_ENST00000553201.1_Missense_Mutation_p.R344W			E9PIF3	NPIA2_HUMAN	nuclear pore complex interacting protein family, member A2	363																	CCACCCTCAGCGGATGATAAT	0.418																																							0											0																																										SO:0001583	missense	0				CCDS59263.1	16p13.11	2013-06-11			ENSG00000254852	ENSG00000254852			41979	protein-coding gene	gene with protein product							Standard	NM_001277324		Approved			E9PIF3	OTTHUMG00000166264	ENST00000529166.1:c.1087C>T	16.37:g.14859247C>T	ENSP00000432029:p.Arg363Trp			Missense_Mutation	SNP	NULL	p.R363W	ENST00000529166.1	37	c.1087		16	.	.	.	.	.	.	.	.	.	.	.	9.766	1.171381	0.21621	.	.	ENSG00000254852	ENST00000529166;ENST00000553201	T;T	0.52526	1.97;0.66	.	.	.	.	.	.	.	.	T	0.36608	0.0973	N	0.19112	0.55	0.09310	N	1	D	0.58620	0.983	P	0.49637	0.617	T	0.23119	-1.0197	7	0.87932	D	0	.	.	.	.	.	363	E9PJI5	.	W	363;344	ENSP00000432029:R363W;ENSP00000446882:R344W	ENSP00000432029:R363W	R	+	1	2	RP11-719K4.2	14766748	.	.	0.064000	0.19789	0.064000	0.16182	.	.	0.073000	0.16731	0.074000	0.15403	CGG	0	NULL		0.418	NPIPA2-002	NOVEL	basic|appris_candidate_longest	protein_coding	NPIPA2	protein_coding	OTTHUMT00000389062.1	99	0	1	0.00	1	0	C		0	0		14859247	1	no_errors	ENST00000529166	ensembl	human	novel	74_37	missense	56	0	8.2	0.00	5	0	SNP	0.065	T
PSMD2	5708	genome.wustl.edu	37	3	184017113	184017113	+	Frame_Shift_Del	DEL	C	C	-			TCGA-ZB-A96D-01A-11D-A428-09	TCGA-ZB-A96D-10A-01D-A42B-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	e5ab7dc0-9391-4515-8704-bea54cd0a647	64032bf9-77c9-4ca2-b1e0-2208c9a7e1bd	g.chr3:184017113delC	ENST00000310118.4	+	1	617	c.59delC	c.(58-60)gccfs	p.A20fs	PSMD2_ENST00000459910.1_3'UTR|PSMD2_ENST00000435761.1_5'Flank|EIF2B5_ENST00000444495.1_Intron|PSMD2_ENST00000439383.1_5'Flank	NM_002808.3	NP_002799.3	Q13200	PSMD2_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 2	20					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|liver(1)|lung(12)|prostate(3)|upper_aerodigestive_tract(2)	27	all_cancers(143;1.54e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Bortezomib(DB00188)	CCAGCGGCGGCCCCCGGCGGC	0.751																																					Colon(24;313 636 6917 9932 15554)		0											0													3.0	7.0	6.0					3																	184017113		1418	2791	4209	SO:0001589	frameshift_variant	0			AK095245	CCDS3258.1, CCDS63853.1, CCDS63854.1	3q27.3	2008-05-22			ENSG00000175166	ENSG00000175166		"""Proteasome (prosome, macropain) subunits"""	9559	protein-coding gene	gene with protein product		606223				8774743	Standard	NM_002808		Approved	S2, P97, TRAP2, MGC14274, Rpn1	uc003fnn.1	Q13200	OTTHUMG00000156796	ENST00000310118.4:c.59delC	3.37:g.184017113delC	ENSP00000310129:p.Ala20fs		B4DX07|B4DXY1|E7EW34|E9PCS3|Q12932|Q15321|Q53XQ4|Q96I12	Frame_Shift_Del	DEL	pfam_Proteasome/cyclosome_rpt,superfamily_ARM-type_fold,pirsf_26S_Psome_Rpn1	p.G22fs	ENST00000310118.4	37	c.59	CCDS3258.1	3																																																																																			0	pirsf_26S_Psome_Rpn1		0.751	PSMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PSMD2	protein_coding	OTTHUMT00000345843.1	10	23	0	0.00	0	0	C	NM_002808	0	0		184017113	1	no_errors	ENST00000310118	ensembl	human	known	74_37	frame_shift_del	4	10	33.33	0.00	2	0	DEL	0.002	0
