#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_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_EVS_AA	i_EVS_All	i_EVS_EA	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_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	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_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	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_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
CATSPER2	117155	genome.wustl.edu	37	15	43939311	43939311	+	Missense_Mutation	SNP	G	G	C			TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr15:43939311G>C	ENST00000321596.5	-	4	524	c.325C>G	c.(325-327)Ctc>Gtc	p.L109V	CATSPER2_ENST00000464721.1_5'Flank|CATSPER2_ENST00000354127.4_Missense_Mutation_p.L109V|STRC_ENST00000541030.1_Intron|CATSPER2_ENST00000381761.1_Missense_Mutation_p.L115V|CATSPER2_ENST00000396879.1_Missense_Mutation_p.L109V|CATSPER2_ENST00000355438.2_Missense_Mutation_p.L109V			Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	109					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)	p.L109V(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		TTTTTGAAGAGAGGACCTGTT	0.373																																						dbGAP											1	Substitution - Missense(1)	breast(1)											113.0	106.0	109.0					15																	43939311		2199	4296	6495	-	-	-	SO:0001583	missense	0			AF411817	CCDS10099.1, CCDS32216.1, CCDS73714.1	15q15.3	2011-07-05			ENSG00000166762	ENSG00000166762		"""Voltage-gated ion channels / Cation channels, sperm associated"""	18810	protein-coding gene	gene with protein product		607249				11675491, 16382101	Standard	NM_172095		Approved		uc001zsh.3	Q96P56	OTTHUMG00000059902	ENST00000321596.5:c.325C>G	15.37:g.43939311G>C	ENSP00000321463:p.Leu109Val	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8NHT9|Q96P54|Q96P55	Missense_Mutation	SNP	pfam_Ion_trans_dom	p.L109V	ENST00000321596.5	37	c.325	CCDS10099.1	15	.	.	.	.	.	.	.	.	.	.	G	9.321	1.057968	0.19987	.	.	ENSG00000166762	ENST00000396879;ENST00000299989;ENST00000381761;ENST00000321596;ENST00000354127;ENST00000355438	D;D;D;D;D	0.97480	-4.4;-4.4;-4.4;-4.4;-4.4	3.29	-2.92	0.05615	.	2.227170	0.03142	N	0.166726	D	0.92244	0.7540	L	0.41824	1.3	0.22050	N	0.99939	B;B;B	0.22414	0.019;0.041;0.069	B;B;B	0.17979	0.011;0.019;0.02	T	0.83045	-0.0155	10	0.16420	T	0.52	.	0.3571	0.00358	0.2232:0.1639:0.279:0.3339	.	109;115;109	Q96P56-4;F8W9H2;Q96P56	.;.;CTSR2_HUMAN	V	109;109;115;109;109;109	ENSP00000380088:L109V;ENSP00000371180:L115V;ENSP00000321463:L109V;ENSP00000339137:L109V;ENSP00000347613:L109V	ENSP00000299989:L109V	L	-	1	0	CATSPER2	41726603	0.451000	0.25705	0.972000	0.41901	0.884000	0.51177	-0.725000	0.04942	-0.817000	0.04335	0.398000	0.26397	CTC	CATSPER2	-	NULL	ENSG00000166762		0.373	CATSPER2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CATSPER2	HGNC	protein_coding	OTTHUMT00000133151.2	181	0.00	0	G	NM_054020		43939311	43939311	-1	no_errors	ENST00000299989	ensembl	human	known	69_37n	missense	154	40.61	106	SNP	0.977	C
COQ9	57017	genome.wustl.edu	37	16	57493549	57493549	+	Frame_Shift_Del	DEL	T	T	-			TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr16:57493549delT	ENST00000262507.6	+	7	853	c.784delT	c.(784-786)tccfs	p.S263fs	POLR2C_ENST00000219252.5_5'Flank|COQ9_ENST00000567072.1_Frame_Shift_Del_p.S228fs|AC009052.12_ENST00000567090.1_RNA|COQ9_ENST00000567933.1_Frame_Shift_Del_p.S152fs	NM_020312.3	NP_064708.1	O75208	COQ9_HUMAN	coenzyme Q9	263					mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)	16						GATGCAGGACTCCTCTCCAGA	0.537																																						dbGAP											0													140.0	131.0	134.0					16																	57493549		2198	4300	6498	-	-	-	SO:0001589	frameshift_variant	0			BC064946	CCDS32459.1	16q13	2013-10-18	2013-10-18	2006-01-13	ENSG00000088682	ENSG00000088682			25302	protein-coding gene	gene with protein product		612837	"""chromosome 16 open reading frame 49"", ""coenzyme Q9 homolog (yeast)"", ""coenzyme Q9 homolog (S. cerevisiae)"""	C16orf49		19375058	Standard	NM_020312		Approved	DKFZP434K046	uc002elq.3	O75208		ENST00000262507.6:c.784delT	16.37:g.57493549delT	ENSP00000262507:p.Ser263fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K3L2|Q7L5V7|Q7Z5T6|Q8NBL4|Q9NTJ2|Q9P056	Frame_Shift_Del	DEL	pfam_COQ9,superfamily_Homeodomain-like,tigrfam_Ubiq_biosynth_COQ9	p.S262fs	ENST00000262507.6	37	c.784	CCDS32459.1	16																																																																																			COQ9	-	pfam_COQ9,tigrfam_Ubiq_biosynth_COQ9	ENSG00000088682		0.537	COQ9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COQ9	HGNC	protein_coding	OTTHUMT00000432598.3	179	0.00	0	T	NM_020312		57493549	57493549	+1	no_errors	ENST00000262507	ensembl	human	known	69_37n	frame_shift_del	15	11.76	2	DEL	1.000	-
CP	1356	genome.wustl.edu	37	3	148930395	148930395	+	Silent	SNP	G	G	A			TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr3:148930395G>A	ENST00000264613.6	-	2	499	c.237C>T	c.(235-237)acC>acT	p.T79T		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	79	F5/8 type A 1.|Plastocyanin-like 1.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)	p.T79T(1)		breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	TTGTCCTAAAGGTTTCATCTG	0.373																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											96.0	93.0	94.0					3																	148930395		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.237C>T	3.37:g.148930395G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q14063|Q2PP18|Q9UKS4	Silent	SNP	pfam_Cu-oxidase_2,pfam_Cu-oxidase_3,pfam_Cu-oxidase,superfamily_Cupredoxin	p.T79	ENST00000264613.6	37	c.237	CCDS3141.1	3																																																																																			CP	-	superfamily_Cupredoxin	ENSG00000047457		0.373	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CP	HGNC	protein_coding	OTTHUMT00000317498.1	131	0.00	0	G	NM_000096		148930395	148930395	-1	no_errors	ENST00000264613	ensembl	human	known	69_37n	silent	138	45.70	117	SNP	0.298	A
ELAC2	60528	genome.wustl.edu	37	17	12901771	12901771	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr17:12901771G>A	ENST00000338034.4	-	16	1717	c.1478C>T	c.(1477-1479)cCg>cTg	p.P493L	ELAC2_ENST00000395962.2_Missense_Mutation_p.P474L|ELAC2_ENST00000426905.3_Missense_Mutation_p.P453L	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	493					mitochondrial tRNA 3'-trailer cleavage, endonucleolytic (GO:0072684)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.P493L(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|skin(1)	23						AATCTTCATCGGGATGGCAGA	0.423																																						dbGAP											1	Substitution - Missense(1)	breast(1)											181.0	154.0	163.0					17																	12901771		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF304370	CCDS11164.1, CCDS54093.1	17p11.2	2013-05-24	2013-05-24		ENSG00000006744	ENSG00000006744	3.1.26.11		14198	protein-coding gene	gene with protein product	"""tRNase Z (long form)"""	605367	"""elaC (E. coli) homolog 2"", ""elaC homolog 2 (E. coli)"""			10986046, 16636667, 21559454	Standard	NM_018127		Approved	FLJ10530, HPC2	uc010vvr.2	Q9BQ52	OTTHUMG00000058764	ENST00000338034.4:c.1478C>T	17.37:g.12901771G>A	ENSP00000337445:p.Pro493Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Nonsense_Mutation	SNP	pfam_Beta-lactamas-like	p.R293*	ENST00000338034.4	37	c.877	CCDS11164.1	17	.	.	.	.	.	.	.	.	.	.	G	17.10	3.303234	0.60195	.	.	ENSG00000006744	ENST00000426905;ENST00000338034;ENST00000395962;ENST00000457438	T;T;T	0.59906	0.23;0.23;0.23	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.80706	0.4674	M	0.89478	3.035	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	0.999;0.999;1.0;1.0;1.0;0.995;0.999;1.0	D;D;D;D;D;P;D;D	0.97110	0.952;0.985;0.978;0.979;1.0;0.853;0.968;0.996	D	0.83643	0.0151	10	0.87932	D	0	-19.9686	17.6123	0.88058	0.0:0.0:1.0:0.0	.	453;476;474;291;493;253;478;121	B4DPL9;E9PGJ0;G5E9D5;E7ES68;Q9BQ52;B3KSU9;B4DT15;Q9BQ52-3	.;.;.;.;RNZ2_HUMAN;.;.;.	L	453;493;474;171	ENSP00000405223:P453L;ENSP00000337445:P493L;ENSP00000379291:P474L	ENSP00000337445:P493L	P	-	2	0	ELAC2	12842496	1.000000	0.71417	0.968000	0.41197	0.987000	0.75469	8.831000	0.92068	2.769000	0.95229	0.655000	0.94253	CCG	ELAC2	-	NULL	ENSG00000006744		0.423	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ELAC2	HGNC	protein_coding	OTTHUMT00000129934.5	205	0.00	0	G			12901771	12901771	-1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000584650	ensembl	human	novel	69_37n	nonsense	70	44.44	56	SNP	0.999	A
ELK3	2004	genome.wustl.edu	37	12	96653588	96653588	+	Missense_Mutation	SNP	C	C	A			TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr12:96653588C>A	ENST00000228741.3	+	4	1408	c.1082C>A	c.(1081-1083)cCg>cAg	p.P361Q	ELK3_ENST00000549529.1_3'UTR|ELK3_ENST00000552142.1_Missense_Mutation_p.P96Q	NM_005230.2	NP_005221.2	P41970	ELK3_HUMAN	ELK3, ETS-domain protein (SRF accessory protein 2)	361					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|wound healing (GO:0042060)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	purine-rich negative regulatory element binding (GO:0032422)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.P361Q(1)		breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(5)|ovary(2)|prostate(1)|stomach(2)	20	all_cancers(2;0.00173)					CCAGTTGCTCCGCTGAGTCCT	0.498																																						dbGAP											1	Substitution - Missense(1)	breast(1)											92.0	89.0	90.0					12																	96653588		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC017371	CCDS9060.1	12q23	2006-12-30				ENSG00000111145			3325	protein-coding gene	gene with protein product		600247				7851904	Standard	NM_005230		Approved	ERP, NET, SAP2	uc001teo.1	P41970		ENST00000228741.3:c.1082C>A	12.37:g.96653588C>A	ENSP00000228741:p.Pro361Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	B2R6S6|Q6FG57|Q6GU29|Q9UD17	Missense_Mutation	SNP	pfam_Ets,smart_Ets,prints_Ets,pfscan_Ets	p.P361Q	ENST00000228741.3	37	c.1082	CCDS9060.1	12	.	.	.	.	.	.	.	.	.	.	C	28.5	4.923306	0.92319	.	.	ENSG00000111145	ENST00000228741;ENST00000552142	T;T	0.56444	0.46;0.46	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.76758	0.4032	M	0.82323	2.585	0.48830	D	0.99971	D	0.89917	1.0	D	0.91635	0.999	T	0.79405	-0.1817	10	0.87932	D	0	.	19.7824	0.96422	0.0:1.0:0.0:0.0	.	361	P41970	ELK3_HUMAN	Q	361;96	ENSP00000228741:P361Q;ENSP00000449430:P96Q	ENSP00000228741:P361Q	P	+	2	0	ELK3	95177719	1.000000	0.71417	0.978000	0.43139	0.818000	0.46254	7.469000	0.80959	2.677000	0.91161	0.561000	0.74099	CCG	ELK3	-	NULL	ENSG00000111145		0.498	ELK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ELK3	HGNC	protein_coding	OTTHUMT00000408694.1	148	0.00	0	C	NM_005230		96653588	96653588	+1	no_errors	ENST00000228741	ensembl	human	known	69_37n	missense	31	50.79	32	SNP	1.000	A
FSTL4	23105	genome.wustl.edu	37	5	132585181	132585181	+	Missense_Mutation	SNP	A	A	T			TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr5:132585181A>T	ENST00000265342.7	-	7	1064	c.815T>A	c.(814-816)gTc>gAc	p.V272D	FSTL4_ENST00000507112.1_5'UTR|CTB-49A3.5_ENST00000504312.1_RNA|CTB-49A3.5_ENST00000515122.1_RNA	NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	272	Ig-like 1.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.V272D(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GTCTCCATGGACGGCGCAGGT	0.577																																						dbGAP											1	Substitution - Missense(1)	breast(1)											104.0	80.0	88.0					5																	132585181		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB028984	CCDS34238.1	5q31.1	2013-01-29			ENSG00000053108	ENSG00000053108		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	21389	protein-coding gene	gene with protein product						10470851, 15527507	Standard	NM_015082		Approved	KIAA1061	uc003kyn.1	Q6MZW2	OTTHUMG00000162729	ENST00000265342.7:c.815T>A	5.37:g.132585181A>T	ENSP00000265342:p.Val272Asp	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8TBU0|Q9UPU1	Missense_Mutation	SNP	pfam_Ig_I-set,pfam_Immunoglobulin,pfam_Kazal-type_dom,pfam_Prot_inh_Kazal,smart_Prot_inh_Kazal,smart_Ig_sub,smart_Ig_sub2,pfscan_EF_HAND_2,pfscan_Ig-like	p.V272D	ENST00000265342.7	37	c.815	CCDS34238.1	5	.	.	.	.	.	.	.	.	.	.	A	18.77	3.695692	0.68386	.	.	ENSG00000053108	ENST00000265342;ENST00000360575	T	0.14516	2.5	5.51	5.51	0.81932	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.275476	0.40554	N	0.001076	T	0.33847	0.0877	M	0.88570	2.965	0.58432	D	0.999993	P	0.43633	0.813	P	0.48598	0.583	T	0.32666	-0.9898	10	0.87932	D	0	-12.8134	14.8061	0.69956	1.0:0.0:0.0:0.0	.	272	Q6MZW2	FSTL4_HUMAN	D	272;103	ENSP00000265342:V272D	ENSP00000265342:V272D	V	-	2	0	FSTL4	132613080	1.000000	0.71417	0.102000	0.21198	0.908000	0.53690	8.896000	0.92521	2.094000	0.63399	0.383000	0.25322	GTC	FSTL4	-	pfam_Ig_I-set,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like	ENSG00000053108		0.577	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FSTL4	HGNC	protein_coding	OTTHUMT00000370212.1	99	0.00	0	A	XM_048786		132585181	132585181	-1	no_errors	ENST00000265342	ensembl	human	known	69_37n	missense	10	41.18	7	SNP	0.994	T
KCNK4	50801	genome.wustl.edu	37	11	64064601	64064601	+	Missense_Mutation	SNP	T	T	A	rs145730818	byFrequency	TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr11:64064601T>A	ENST00000539216.1	+	3	684	c.324T>A	c.(322-324)aaT>aaA	p.N108K	KCNK4_ENST00000422670.2_Missense_Mutation_p.N108K|KCNK4_ENST00000394525.2_Missense_Mutation_p.N108K|KCNK4_ENST00000539651.1_3'UTR|RP11-783K16.10_ENST00000539086.1_RNA|Y_RNA_ENST00000384297.1_RNA|KCNK4_ENST00000538767.1_Missense_Mutation_p.M42K			Q9NYG8	KCNK4_HUMAN	potassium channel, subfamily K, member 4	108					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.N108K(1)		breast(2)|large_intestine(2)|lung(3)|prostate(2)|urinary_tract(1)	10						GCTATGGCAATGTGGCCCTGC	0.652																																						dbGAP											1	Substitution - Missense(1)	breast(1)											45.0	51.0	49.0					11																	64064601		2201	4297	6498	-	-	-	SO:0001583	missense	0			AF247042	CCDS8067.1	11q13	2012-03-07			ENSG00000182450	ENSG00000182450		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6279	protein-coding gene	gene with protein product		605720				10767409, 16382106	Standard	NM_033310		Approved	K2p4.1, TRAAK	uc001nzk.1	Q9NYG8	OTTHUMG00000168006	ENST00000539216.1:c.324T>A	11.37:g.64064601T>A	ENSP00000444948:p.Asn108Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	B5TJL1|Q96T94	Missense_Mutation	SNP	pfam_Ion_trans_2,prints_2pore_dom_K_chnl_TRAAK,prints_2pore_dom_K_chnl_TREK,prints_2pore_dom_K_chnl,prints_2pore_dom_K_chnl_TASK	p.N108K	ENST00000539216.1	37	c.324	CCDS8067.1	11	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.66|14.66	2.602479|2.602479	0.46423|0.46423	.|.	.|.	ENSG00000182450|ENSG00000182450	ENST00000538767|ENST00000422670;ENST00000539852;ENST00000394525;ENST00000544845;ENST00000539216	.|T;T;T	.|0.24908	.|1.83;1.83;1.83	5.19|5.19	-0.564|-0.564	0.11774|0.11774	.|Ion transport 2 (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.47414|0.47414	0.1444|0.1444	M|M	0.90705|0.90705	3.14|3.14	0.58432|0.58432	D|D	0.999999|0.999999	B;B|P	0.32467|0.46952	0.372;0.372|0.887	B;B|P	0.26864|0.55391	0.074;0.074|0.775	T|T	0.53136|0.53136	-0.8481|-0.8481	7|10	.|0.72032	.|D	.|0.01	.|.	10.9305|10.9305	0.47215|0.47215	0.0:0.7353:0.0:0.2647|0.0:0.7353:0.0:0.2647	.|.	81;42|108	B4DJC9;F5GYE0|Q9NYG8	.;.|KCNK4_HUMAN	K|K	42|108;133;108;170;108	.|ENSP00000402797:N108K;ENSP00000378033:N108K;ENSP00000444948:N108K	.|ENSP00000378033:N108K	M|N	+|+	2|3	0|2	KCNK4|KCNK4	63821177|63821177	0.786000|0.786000	0.28738|0.28738	0.773000|0.773000	0.31616|0.31616	0.993000|0.993000	0.82548|0.82548	0.473000|0.473000	0.22132|0.22132	-0.436000|-0.436000	0.07254|0.07254	0.454000|0.454000	0.30748|0.30748	ATG|AAT	KCNK4	-	pfam_Ion_trans_2,prints_2pore_dom_K_chnl	ENSG00000182450		0.652	KCNK4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	KCNK4	HGNC	protein_coding	OTTHUMT00000396430.1	31	0.00	0	T	NM_033311		64064601	64064601	+1	no_errors	ENST00000394525	ensembl	human	known	69_37n	missense	7	58.82	10	SNP	0.981	A
LRCH1	23143	genome.wustl.edu	37	13	47279264	47279264	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr13:47279264G>A	ENST00000389798.3	+	12	1659	c.1462G>A	c.(1462-1464)Gcc>Acc	p.A488T	LRCH1_ENST00000311191.6_Missense_Mutation_p.A488T|LRCH1_ENST00000389797.3_Missense_Mutation_p.A488T	NM_015116.2	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 1	488								p.A488T(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		ATCAGCAGAAGCCTTAGAATT	0.289																																						dbGAP											2	Substitution - Missense(2)	breast(2)											114.0	126.0	122.0					13																	47279264		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB023233	CCDS31972.1, CCDS53865.1, CCDS53866.1	13q14.11	2008-02-05	2004-05-27	2004-05-28	ENSG00000136141	ENSG00000136141			20309	protein-coding gene	gene with protein product		610368	"""calponin homology (CH) domain containing 1"""	CHDC1		10231032	Standard	NM_015116		Approved	KIAA1016	uc001vbk.3	Q9Y2L9	OTTHUMG00000016877	ENST00000389798.3:c.1462G>A	13.37:g.47279264G>A	ENSP00000374448:p.Ala488Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	B7ZLL5|F8W6F0|Q17R43|Q2KHR1|Q5TBU9|Q7Z5F6|Q7Z5F7	Missense_Mutation	SNP	pfam_Leu-rich_rpt,pfam_CH-domain,pfam_CAMSAP_CH,superfamily_CH-domain,smart_Leu-rich_rpt_typical-subtyp,smart_CH-domain,pfscan_CH-domain	p.A488T	ENST00000389798.3	37	c.1462	CCDS31972.1	13	.	.	.	.	.	.	.	.	.	.	G	12.27	1.889055	0.33348	.	.	ENSG00000136141	ENST00000311191;ENST00000389798;ENST00000389797	T;T;T	0.52526	0.66;0.72;0.68	5.95	3.1	0.35709	.	0.310735	0.34223	N	0.004141	T	0.28400	0.0702	L	0.27053	0.805	0.28356	N	0.920658	B;B;B;B	0.06786	0.0;0.001;0.001;0.0	B;B;B;B	0.08055	0.001;0.002;0.003;0.001	T	0.10989	-1.0606	10	0.16420	T	0.52	-1.3684	7.0036	0.24823	0.1572:0.1426:0.7001:0.0	.	488;488;488;488	Q17R43;Q9Y2L9-2;F8W6F0;Q9Y2L9	.;.;.;LRCH1_HUMAN	T	488	ENSP00000308493:A488T;ENSP00000374448:A488T;ENSP00000374447:A488T	ENSP00000308493:A488T	A	+	1	0	LRCH1	46177265	1.000000	0.71417	1.000000	0.80357	0.782000	0.44232	1.930000	0.40124	1.527000	0.49086	0.655000	0.94253	GCC	LRCH1	-	NULL	ENSG00000136141		0.289	LRCH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	LRCH1	HGNC	protein_coding	OTTHUMT00000044824.2	117	0.00	0	G	NM_015116		47279264	47279264	+1	no_errors	ENST00000389798	ensembl	human	known	69_37n	missense	60	64.71	110	SNP	1.000	A
LMO7	4008	genome.wustl.edu	37	13	76370783	76370783	+	Silent	SNP	A	A	G			TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr13:76370783A>G	ENST00000341547.4	+	7	1776	c.516A>G	c.(514-516)acA>acG	p.T172T	RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000465261.2_5'UTR|LMO7_ENST00000526202.1_Silent_p.T81T|LMO7_ENST00000321797.8_5'UTR|LMO7_ENST00000377534.3_Silent_p.T172T|LMO7_ENST00000357063.3_Silent_p.T172T	NM_005358.5	NP_005349.3	Q8WWI1	LMO7_HUMAN	LIM domain 7	172					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T172T(2)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		TTTTGATAACATTGTACTGGC	0.363																																						dbGAP											2	Substitution - coding silent(2)	breast(2)											80.0	75.0	77.0					13																	76370783		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000341547.4:c.516A>G	13.37:g.76370783A>G		Somatic		WXS	Illumina GAIIx	Phase_IV	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Silent	SNP	pfam_CH-domain,pfam_PDZ,superfamily_CH-domain,superfamily_PDZ,smart_CH-domain,smart_PDZ,pfscan_CH-domain,pfscan_PDZ,prints_SM22_calponin	p.T172	ENST00000341547.4	37	c.516	CCDS9454.1	13																																																																																			LMO7	-	superfamily_CH-domain,smart_CH-domain	ENSG00000136153		0.363	LMO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LMO7	HGNC	protein_coding	OTTHUMT00000045297.1	120	0.00	0	A	NM_005358		76370783	76370783	+1	no_errors	ENST00000357063	ensembl	human	known	69_37n	silent	58	46.30	50	SNP	0.317	G
METTL5	29081	genome.wustl.edu	37	2	170669020	170669020	+	Intron	SNP	T	T	G			TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr2:170669020T>G	ENST00000260953.5	-	6	858				METTL5_ENST00000410097.1_Intron|METTL5_ENST00000409837.1_Intron|METTL5_ENST00000409340.1_Intron|METTL5_ENST00000392640.2_Intron|METTL5_ENST00000308099.3_Intron|METTL5_ENST00000409965.1_Intron	NM_014168.2	NP_054887.2	Q9NRN9	METL5_HUMAN	methyltransferase like 5								methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)	p.?(1)		breast(2)|central_nervous_system(1)|large_intestine(5)|lung(1)|prostate(1)	10						CGAAGTTCTGTAAAACAAAAG	0.358																																						dbGAP											1	Unknown(1)	breast(1)											118.0	120.0	119.0					2																	170669020		2203	4300	6503	-	-	-	SO:0001627	intron_variant	0			AF201938	CCDS33320.1	2q31.1	2011-01-28			ENSG00000138382	ENSG00000138382			25006	protein-coding gene	gene with protein product						11042152	Standard	XM_005246478		Approved	HSPC133	uc002ufn.3	Q9NRN9	OTTHUMG00000154117	ENST00000260953.5:c.542-4A>C	2.37:g.170669020T>G		Somatic		WXS	Illumina GAIIx	Phase_IV	D3DPC9|Q9NVX1	Missense_Mutation	SNP	NULL	p.L96F	ENST00000260953.5	37	c.288	CCDS33320.1	2	.	.	.	.	.	.	.	.	.	.	T	15.25	2.776504	0.49786	.	.	ENSG00000138382	ENST00000442181	.	.	.	5.43	-2.13	0.07144	.	.	.	.	.	T	0.39064	0.1064	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.30268	-0.9984	4	.	.	.	.	1.4684	0.02411	0.1163:0.1953:0.2418:0.4466	.	.	.	.	F	96	.	.	L	-	3	2	METTL5	170377266	0.993000	0.37304	0.884000	0.34674	0.987000	0.75469	0.250000	0.18235	-0.221000	0.09973	0.482000	0.46254	TTA	METTL5	-	NULL	ENSG00000138382		0.358	METTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	METTL5	HGNC	protein_coding	OTTHUMT00000333957.1	110	0.00	0	T	NM_014168		170669020	170669020	-1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000442181	ensembl	human	novel	69_37n	missense	118	43.60	92	SNP	0.726	G
MMRN2	79812	genome.wustl.edu	37	10	88703812	88703812	+	Silent	SNP	G	G	A			TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr10:88703812G>A	ENST00000372027.5	-	6	1050	c.729C>T	c.(727-729)ccC>ccT	p.P243P	MMRN2_ENST00000488950.1_5'UTR	NM_024756.2	NP_079032.2	Q9H8L6	MMRN2_HUMAN	multimerin 2	243					angiogenesis (GO:0001525)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.P243P(1)		breast(1)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|stomach(1)	19						TCCTCCAGATGGGGCTGAAAT	0.547																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											71.0	63.0	66.0					10																	88703812		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AK023527	CCDS7379.1	10q23.31	2004-03-10	2004-03-02	2004-03-02	ENSG00000173269	ENSG00000173269		"""EMI domain containing"""	19888	protein-coding gene	gene with protein product		608925	"""elastin microfibril interfacer 3"""	EMILIN3		11559704	Standard	NM_024756		Approved	EndoGlyx-1, FLJ13465	uc001kea.3	Q9H8L6	OTTHUMG00000018663	ENST00000372027.5:c.729C>T	10.37:g.88703812G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q504V7|Q6P2N2	Silent	SNP	pfam_C1q,pfam_EMI_domain,superfamily_Tumour_necrosis_fac-like,superfamily_tRNA-bd_arm,smart_C1q,prints_C1q,pfscan_C1q,pfscan_EMI_domain	p.P243	ENST00000372027.5	37	c.729	CCDS7379.1	10																																																																																			MMRN2	-	NULL	ENSG00000173269		0.547	MMRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MMRN2	HGNC	protein_coding	OTTHUMT00000049179.2	34	0.00	0	G	NM_024756		88703812	88703812	-1	no_errors	ENST00000372027	ensembl	human	known	69_37n	silent	14	33.33	7	SNP	1.000	A
MYH7B	57644	genome.wustl.edu	37	20	33568852	33568852	+	Silent	SNP	C	C	T			TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr20:33568852C>T	ENST00000262873.7	+	7	734	c.642C>T	c.(640-642)tcC>tcT	p.S214S	MYH7B_ENST00000481922.1_3'UTR	NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	172	Myosin motor.					membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.S214S(1)		NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			ACAACCAGTCCATGCTGATCA	0.582																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											95.0	97.0	96.0					20																	33568852		2004	4193	6197	-	-	-	SO:0001819	synonymous_variant	0			AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.642C>T	20.37:g.33568852C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	pfam_Myosin_tail,pfam_Myosin_head_motor_dom,pfam_Myosin_N,superfamily_Myosin_S1_N,superfamily_Prefoldin,superfamily_tRNA-bd_arm,superfamily_t-SNARE,smart_Myosin_head_motor_dom,pfscan_IQ_motif_EF-hand-BS,prints_Myosin_head_motor_dom	p.S214	ENST00000262873.7	37	c.642	CCDS42869.1	20																																																																																			MYH7B	-	pfam_Myosin_head_motor_dom,smart_Myosin_head_motor_dom,prints_Myosin_head_motor_dom	ENSG00000078814		0.582	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	MYH7B	HGNC	protein_coding	OTTHUMT00000078833.2	163	0.00	0	C	NM_020884		33568852	33568852	+1	no_errors	ENST00000262873	ensembl	human	novel	69_37n	silent	18	59.09	26	SNP	0.998	T
PDE2A	5138	genome.wustl.edu	37	11	72290428	72290428	+	Splice_Site	SNP	C	C	G			TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr11:72290428C>G	ENST00000334456.5	-	27	2502		c.e27-1		PDE2A_ENST00000444035.2_Splice_Site|PDE2A_ENST00000418754.2_Splice_Site|PDE2A_ENST00000540345.1_Splice_Site|PDE2A_ENST00000544570.1_Splice_Site|PDE2A_ENST00000376450.3_Splice_Site	NM_002599.4	NP_002590.1	O00408	PDE2A_HUMAN	phosphodiesterase 2A, cGMP-stimulated						blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to drug (GO:0035690)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to mechanical stimulus (GO:0071260)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP catabolic process (GO:0046069)|cGMP-mediated signaling (GO:0019934)|establishment of endothelial barrier (GO:0061028)|metabolic process (GO:0008152)|monocyte differentiation (GO:0030224)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vascular permeability (GO:0043116)|positive regulation of inflammatory response (GO:0050729)|positive regulation of vascular permeability (GO:0043117)|protein targeting to mitochondrion (GO:0006626)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel activity (GO:0005262)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|drug binding (GO:0008144)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)	p.?(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	36			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Caffeine(DB00201)|Tofisopam(DB08811)	GCTGATAGTCCTGAGGCGAGG	0.602																																						dbGAP											1	Unknown(1)	breast(1)											70.0	62.0	64.0					11																	72290428		2200	4293	6493	-	-	-	SO:0001630	splice_region_variant	0			U67733	CCDS8216.1, CCDS44670.1, CCDS53678.1, CCDS73345.1	11q13.1-q14.1	2008-05-14			ENSG00000186642	ENSG00000186642	3.1.4.17	"""Phosphodiesterases"""	8777	protein-coding gene	gene with protein product		602658				9210593	Standard	NM_002599		Approved		uc010rrc.2	O00408	OTTHUMG00000102045	ENST00000334456.5:c.2257-1G>C	11.37:g.72290428C>G		Somatic		WXS	Illumina GAIIx	Phase_IV	B2R646|B3KRV5|E9PGI1|F6W5Z0|Q5J791|Q5J792|Q5J793|Q6ZMR1	Splice_Site	SNP	-	e27-1	ENST00000334456.5	37	c.2257-1	CCDS8216.1	11	.	.	.	.	.	.	.	.	.	.	C	17.86	3.491701	0.64074	.	.	ENSG00000186642	ENST00000334456;ENST00000376450;ENST00000444035;ENST00000429363;ENST00000544570;ENST00000418754;ENST00000540345;ENST00000420501;ENST00000441209	.	.	.	5.24	5.24	0.73138	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.3995	0.87455	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PDE2A	71968076	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	7.642000	0.83385	2.455000	0.83008	0.555000	0.69702	.	PDE2A	-	-	ENSG00000186642		0.602	PDE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PDE2A	HGNC	protein_coding	OTTHUMT00000219839.2	42	0.00	0	C	NM_002599	Intron	72290428	72290428	-1	no_errors	ENST00000334456	ensembl	human	known	69_37n	splice_site	8	38.46	5	SNP	1.000	G
PIK3CA	5290	genome.wustl.edu	37	3	178936082	178936082	+	Missense_Mutation	SNP	G	G	A	rs121913273		TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr3:178936082G>A	ENST00000263967.3	+	10	1781	c.1624G>A	c.(1624-1626)Gaa>Aaa	p.E542K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	542	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> K (in CLOVE, KERSEB, CRC and BC; also found in glioblastoma multiforme and endometrial carcinoma; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N- terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|E -> Q (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.|E -> V (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E542K(545)|p.E542Q(10)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TCCTCTCTCTGAAATCACTGA	0.333	E542K(BT483_BREAST)|E542K(CAL51_BREAST)|E542K(HGC27_STOMACH)|E542K(IM95_STOMACH)|E542K(JHUEM1_ENDOMETRIUM)|E542K(NCIH1341_LUNG)|E542K(SW948_LARGE_INTESTINE)|E542K(T84_LARGE_INTESTINE)|E542K(VMCUB1_URINARY_TRACT)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	dbGAP		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	555	Substitution - Missense(555)	breast(176)|large_intestine(166)|urinary_tract(45)|endometrium(37)|skin(19)|lung(18)|stomach(16)|ovary(16)|thyroid(14)|upper_aerodigestive_tract(9)|central_nervous_system(7)|cervix(6)|liver(6)|oesophagus(5)|penis(4)|kidney(3)|soft_tissue(2)|haematopoietic_and_lymphoid_tissue(2)|prostate(2)|biliary_tract(1)|pituitary(1)											56.0	56.0	56.0					3																	178936082		1809	4069	5878	-	-	-	SO:0001583	missense	0				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1624G>A	3.37:g.178936082G>A	ENSP00000263967:p.Glu542Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q14CW1|Q99762	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,pfam_PI3K_adapt-bd_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.E542K	ENST00000263967.3	37	c.1624	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	G	34	5.360420	0.95877	.	.	ENSG00000121879	ENST00000263967	T	0.62105	0.05	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69287	0.3094	L	0.41356	1.27	0.80722	D	1	D	0.65815	0.995	D	0.63192	0.912	T	0.60296	-0.7291	10	0.09843	T	0.71	-23.9623	20.0024	0.97423	0.0:0.0:1.0:0.0	.	542	P42336	PK3CA_HUMAN	K	542	ENSP00000263967:E542K	ENSP00000263967:E542K	E	+	1	0	PIK3CA	180418776	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAA	PIK3CA	-	pfam_PInositide-3_kin_accessory_dom,superfamily_ARM-type_fold,smart_PInositide-3_kin_accessory_dom	ENSG00000121879		0.333	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	36	0.00	0	G			178936082	178936082	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	69	52.41	76	SNP	1.000	A
SCN2A	6326	genome.wustl.edu	37	2	166245338	166245338	+	Silent	SNP	C	C	T	rs186157680	byFrequency	TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr2:166245338C>T	ENST00000375437.2	+	27	5312	c.5022C>T	c.(5020-5022)taC>taT	p.Y1674Y	SCN2A_ENST00000283256.6_Silent_p.Y1674Y|SCN2A_ENST00000375427.2_Silent_p.Y1674Y|SCN2A_ENST00000357398.3_Silent_p.Y1674Y	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1674					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.Y1674Y(2)		NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGTTCATCTACGCCATCTTTG	0.473													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		20111	0.0		0.0	False		,,,				2504	0.0					dbGAP											2	Substitution - coding silent(2)	breast(2)											186.0	175.0	179.0					2																	166245338		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10588	protein-coding gene	gene with protein product		182390	"""sodium channel, voltage-gated, type II, alpha 2 polypeptide"", ""sodium channel, voltage-gated, type II, alpha 1 polypeptide"""	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.5022C>T	2.37:g.166245338C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Silent	SNP	pfam_Ion_trans_dom,pfam_Na_trans_assoc,pfam_DUF3451,pfam_PKD1_2_channel,smart_IQ_motif_EF-hand-BS,prints_Na_channel_asu,prints_PKD_2,pfscan_IQ_motif_EF-hand-BS	p.Y1674	ENST00000375437.2	37	c.5022	CCDS33314.1	2																																																																																			SCN2A	-	pfam_Ion_trans_dom,pfam_PKD1_2_channel	ENSG00000136531		0.473	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SCN2A	HGNC	protein_coding	OTTHUMT00000102659.2	854	0.00	0	C	NM_021007		166245338	166245338	+1	no_errors	ENST00000283256	ensembl	human	known	69_37n	silent	144	45.66	121	SNP	0.954	T
SIK3	23387	genome.wustl.edu	37	11	116732018	116732018	+	Frame_Shift_Del	DEL	G	G	-			TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr11:116732018delG	ENST00000292055.4	-	18	2114	c.2079delC	c.(2077-2079)cccfs	p.P693fs	SIK3_ENST00000446921.2_Frame_Shift_Del_p.P751fs|SIK3_ENST00000434315.2_Frame_Shift_Del_p.P592fs|SIK3_ENST00000375288.1_Intron|SIK3_ENST00000375300.1_Frame_Shift_Del_p.P751fs|SIK3_ENST00000542607.1_Frame_Shift_Del_p.P693fs|SIK3_ENST00000488337.1_Intron	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	693	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						CACTGCTCATGGGGGGAGGAC	0.483																																						dbGAP											0													79.0	85.0	83.0					11																	116732018		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.2079delC	11.37:g.116732018delG	ENSP00000292055:p.Pro693fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Frame_Shift_Del	DEL	pfam_Prot_kinase_cat_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_cat_dom	p.M752fs	ENST00000292055.4	37	c.2253	CCDS8379.1	11																																																																																			SIK3	-	NULL	ENSG00000160584		0.483	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	SIK3	HGNC	protein_coding		67	0.00	0	G	NM_025164		116732018	116732018	-1	no_errors	ENST00000375300	ensembl	human	known	69_37n	frame_shift_del	8	76.47	26	DEL	0.024	-
TMEM120B	144404	genome.wustl.edu	37	12	122212588	122212588	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr12:122212588G>A	ENST00000449592.2	+	10	898	c.797G>A	c.(796-798)cGg>cAg	p.R266Q	TMEM120B_ENST00000540377.1_5'UTR	NM_001080825.2	NP_001074294.2	A0PK00	T120B_HUMAN	transmembrane protein 120B	266						integral component of membrane (GO:0016021)		p.R266Q(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(6)	11	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;5.75e-05)|Epithelial(86;0.000128)|BRCA - Breast invasive adenocarcinoma(302;0.238)		TGGATGTGGCGGGGCCTCACC	0.632																																						dbGAP											2	Substitution - Missense(2)	breast(2)											48.0	55.0	52.0					12																	122212588		1903	4104	6007	-	-	-	SO:0001583	missense	0			BC127768	CCDS41852.1	12q24.31	2007-08-01			ENSG00000188735	ENSG00000188735			32008	protein-coding gene	gene with protein product							Standard	NM_001080825		Approved		uc001ubc.4	A0PK00	OTTHUMG00000169076	ENST00000449592.2:c.797G>A	12.37:g.122212588G>A	ENSP00000404991:p.Arg266Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	A0PK01|B3KX33	Missense_Mutation	SNP	pfam_TMPIT	p.R266Q	ENST00000449592.2	37	c.797	CCDS41852.1	12	.	.	.	.	.	.	.	.	.	.	G	36	5.870951	0.97049	.	.	ENSG00000188735	ENST00000449592	T	0.33865	1.39	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.69717	0.3142	M	0.92268	3.29	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.74636	-0.3599	10	0.45353	T	0.12	-36.5014	18.5112	0.90917	0.0:0.0:1.0:0.0	.	266	A0PK00	T120B_HUMAN	Q	266	ENSP00000404991:R266Q	ENSP00000345152:R266Q	R	+	2	0	TMEM120B	120696971	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	7.807000	0.86032	2.665000	0.90641	0.561000	0.74099	CGG	TMEM120B	-	pfam_TMPIT	ENSG00000188735		0.632	TMEM120B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	TMEM120B	HGNC	protein_coding	OTTHUMT00000402158.1	114	0.00	0	G	NM_001080825		122212588	122212588	+1	no_errors	ENST00000342607	ensembl	human	known	69_37n	missense	32	54.29	38	SNP	1.000	A
ZKSCAN1	7586	genome.wustl.edu	37	7	99631717	99631717	+	Missense_Mutation	SNP	C	C	G			TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr7:99631717C>G	ENST00000324306.6	+	6	1823	c.1589C>G	c.(1588-1590)tCc>tGc	p.S530C	ZKSCAN1_ENST00000535170.1_Missense_Mutation_p.S317C|ZKSCAN1_ENST00000426572.1_Missense_Mutation_p.S494C	NM_003439.1	NP_003430.1	P17029	ZKSC1_HUMAN	zinc finger with KRAB and SCAN domains 1	530					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S530C(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(5)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			ACCCGCAGCTCCACCCTCACT	0.517																																						dbGAP											1	Substitution - Missense(1)	breast(1)											83.0	79.0	81.0					7																	99631717		2203	4300	6503	-	-	-	SO:0001583	missense	0			X52349	CCDS34698.1, CCDS69349.1, CCDS75640.1	7q22	2013-01-09	2004-11-16	2004-11-17	ENSG00000106261	ENSG00000106261		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13101	protein-coding gene	gene with protein product		601260	"""zinc finger protein 36 (KOX 18)"""	ZNF139, ZNF36			Standard	NM_001287055		Approved	KOX18, PHZ-37, ZSCAN33	uc003usk.1	P17029	OTTHUMG00000156534	ENST00000324306.6:c.1589C>G	7.37:g.99631717C>G	ENSP00000323148:p.Ser530Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	A4D294|P52745|Q2M1U1|Q8TBW5|Q8TEK7	Missense_Mutation	SNP	pfam_Tscrpt_reg_SCAN,pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Retrov_capsid_C,superfamily_Krueppel-associated_box,smart_Tscrpt_reg_SCAN,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box,pfscan_Tscrpt_reg_SCAN	p.S530C	ENST00000324306.6	37	c.1589	CCDS34698.1	7	.	.	.	.	.	.	.	.	.	.	C	15.01	2.705447	0.48412	.	.	ENSG00000106261	ENST00000324306;ENST00000426572;ENST00000535170	T;T;T	0.37058	1.22;1.22;1.22	4.96	4.96	0.65561	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47852	D	0.000210	T	0.30386	0.0763	N	0.08118	0	0.09310	N	0.99999	D	0.69078	0.997	P	0.55824	0.785	T	0.13098	-1.0522	10	0.87932	D	0	.	9.4791	0.38889	0.0:0.9056:0.0:0.0944	.	530	P17029	ZKSC1_HUMAN	C	530;494;317	ENSP00000323148:S530C;ENSP00000409172:S494C;ENSP00000443508:S317C	ENSP00000323148:S530C	S	+	2	0	ZKSCAN1	99469653	0.020000	0.18652	0.996000	0.52242	0.903000	0.53119	1.315000	0.33608	2.743000	0.94032	0.563000	0.77884	TCC	ZKSCAN1	-	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2	ENSG00000106261		0.517	ZKSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZKSCAN1	HGNC	protein_coding	OTTHUMT00000344550.2	58	0.00	0	C	NM_003439		99631717	99631717	+1	no_errors	ENST00000324306	ensembl	human	known	69_37n	missense	34	35.85	19	SNP	0.227	G
WEE2	494551	genome.wustl.edu	37	7	141427142	141427142	+	Silent	SNP	A	A	T			TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr7:141427142A>T	ENST00000397541.2	+	10	1837	c.1431A>T	c.(1429-1431)gcA>gcT	p.A477A	WEE2-AS1_ENST00000486906.1_RNA|RNU1-82P_ENST00000390851.1_RNA|WEE2-AS1_ENST00000478332.1_RNA|WEE2-AS1_ENST00000484172.1_RNA|WEE2-AS1_ENST00000465110.1_RNA|WEE2-AS1_ENST00000471512.1_RNA|WEE2-AS1_ENST00000459753.1_RNA|WEE2-AS1_ENST00000488785.1_RNA|WEE2-AS1_ENST00000495800.1_RNA|WEE2-AS1_ENST00000462383.1_RNA	NM_001105558.1	NP_001099028.1	P0C1S8	WEE2_HUMAN	WEE1 homolog 2 (S. pombe)	477	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				female meiotic division (GO:0007143)|female pronucleus assembly (GO:0035038)|mitotic nuclear division (GO:0007067)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of oocyte maturation (GO:1900194)|regulation of meiosis I (GO:0060631)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)	p.A477A(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31	Melanoma(164;0.0171)					GACCTTCTGCAGCAGCTCTGG	0.468																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											131.0	128.0	129.0					7																	141427142		1868	4120	5988	-	-	-	SO:0001819	synonymous_variant	0			AK131218	CCDS43660.1	7q32	2008-07-02			ENSG00000214102	ENSG00000214102			19684	protein-coding gene	gene with protein product		614084					Standard	NM_001105558		Approved	FLJ16107	uc003vwn.2	P0C1S8	OTTHUMG00000157536	ENST00000397541.2:c.1431A>T	7.37:g.141427142A>T		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pirsf_Wee1-like_protein_kinase,pfscan_Prot_kinase_cat_dom	p.A477	ENST00000397541.2	37	c.1431	CCDS43660.1	7																																																																																			WEE2	-	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pirsf_Wee1-like_protein_kinase,pfscan_Prot_kinase_cat_dom	ENSG00000214102		0.468	WEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WEE2	HGNC	protein_coding	OTTHUMT00000349091.1	63	0.00	0	A	NM_001105558		141427142	141427142	+1	no_errors	ENST00000397541	ensembl	human	known	69_37n	silent	34	39.29	22	SNP	0.315	T
TRBV4-1	28617	genome.wustl.edu	37	7	142013464	142013464	+	RNA	SNP	C	C	T			TCGA-BH-A0W3-01A-11D-A10G-09	TCGA-BH-A0W3-10A-01X-A10H-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3fa14183-e0c5-4dc2-bb4a-d8dd42f6578b	6f5bdee8-4595-46eb-960a-3001189bb761	g.chr7:142013464C>T	ENST00000390357.3	+	0	348									T cell receptor beta variable 4-1																		AGACTCAGCCCTGTATCTCTG	0.572																																						dbGAP											0													79.0	86.0	84.0					7																	142013464		1921	4131	6052	-	-	-			0			U07977		7q34	2012-02-07			ENSG00000211710	ENSG00000211710		"""T cell receptors / TRB locus"""	12215	other	T cell receptor gene						8650574	Standard	NG_001333		Approved	TRBV41, TCRBV4S1, TCRBV7S1A1N2T, BV07S1J2.7			OTTHUMG00000158522		7.37:g.142013464C>T		Somatic		WXS	Illumina GAIIx	Phase_IV		Silent	SNP	pfam_Ig_V-set,pfscan_Ig-like	p.L107	ENST00000390357.3	37	c.319		7																																																																																			TRBV4-1	-	pfam_Ig_V-set,pfscan_Ig-like	ENSG00000211710		0.572	TRBV4-1-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TRBV4-1	HGNC	TR_V_gene	OTTHUMT00000351228.2	41	0.00	0	C	NG_001333		142013464	142013464	+1	no_stop_codon:bad_bp_length_for_coding_region	ENST00000390357	ensembl	human	known	69_37n	silent	23	48.89	22	SNP	0.000	T
