#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_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_annotation_transcript	i_build	i_ccds_id	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_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_type	i_havana_transcript	i_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ACSBG1	23205	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	78485853	78485853	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr15:78485853delG	ENST00000258873.4	-	5	863	c.658delC	c.(658-660)ctgfs	p.L220fs	ACSBG1_ENST00000541759.1_Intron|ACSBG1_ENST00000560817.1_Intron|ACSBG1_ENST00000558828.1_5'Flank	NM_001199377.1|NM_015162.4	NP_001186306.1|NP_055977.3	Q96GR2	ACBG1_HUMAN	acyl-CoA synthetase bubblegum family member 1	220					long-chain fatty acid metabolic process (GO:0001676)|myelination (GO:0042552)|ovarian follicle atresia (GO:0001552)|response to glucocorticoid (GO:0051384)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			endometrium(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	37						CAAACCTTCAGGATCTTTTCC	0.577																																																	0													111.0	109.0	110.0					15																	78485853		2196	4293	6489	SO:0001589	frameshift_variant	23205			AB014531	CCDS10298.1	15q23-q24	2006-02-09			ENSG00000103740	ENSG00000103740		"""Acyl-CoA synthetase family"""	29567	protein-coding gene	gene with protein product	"""bubblegum"", ""very long-chain acyl-CoA synthetase"", ""lipidosin"""	614362				9734811, 10954726	Standard	NM_015162		Approved	BGM, FLJ30320, MGC14352, BG1, KIAA0631, hBG1, hsBG	uc002bdh.3	Q96GR2	OTTHUMG00000143734	ENST00000258873.4:c.658delC	15.37:g.78485853delG	ENSP00000258873:p.Leu220fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2RB61|O75126|Q76N27|Q9HC26	Frame_Shift_Del	DEL	ENST00000258873.4	37	CCDS10298.1																																																																																				0.577	ACSBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289802.2		NM_015162	
ADRA1A	148	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	26722260	26722260	+	Missense_Mutation	SNP	G	G	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr8:26722260G>C	ENST00000519229.1	-	1	233	c.227C>G	c.(226-228)aCc>aGc	p.T76S	ADRA1A_ENST00000380581.2_Missense_Mutation_p.T76S|ADRA1A_ENST00000380587.1_Missense_Mutation_p.T76S|ADRA1A_ENST00000380586.1_Missense_Mutation_p.T76S|ADRA1A_ENST00000380582.3_Missense_Mutation_p.T76S|ADRA1A_ENST00000380572.3_Missense_Mutation_p.T76S|ADRA1A_ENST00000358857.5_Missense_Mutation_p.T76S|ADRA1A_ENST00000380573.3_Missense_Mutation_p.T76S|ADRA1A_ENST00000354550.4_Missense_Mutation_p.T76S|ADRA1A_ENST00000276393.4_Missense_Mutation_p.T76S			P25100	ADA1D_HUMAN	adrenoceptor alpha 1A	146				MTFRDLLSVSFEGPRPDSSAGGSSAGGGGGSAGGAAPSEGP AVGGVPGGAGGGGGVVGAGSGEDNRSSAGEPGSAGAGGDVN G -> MAAALRSVMMAGYLSEWRTPTYRSTEMVQRLRMEAV QHSTS (in Ref. 1). {ECO:0000305}.	adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|DNA metabolic process (GO:0006259)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure (GO:0001986)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)	p.T76S(5)		breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|skin(1)	36		all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;4.92e-10)|Colorectal(74;0.0132)|READ - Rectum adenocarcinoma(644;0.115)	Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694)	CACCGTGGAGGTGAGCAGGAG	0.607																																																	5	Substitution - Missense(5)	kidney(5)											195.0	196.0	196.0					8																	26722260		2203	4300	6503	SO:0001583	missense	148			L31774	CCDS6052.1, CCDS6053.1, CCDS6054.1, CCDS34869.1	8p21.2	2012-08-08	2012-05-09		ENSG00000120907	ENSG00000120907		"""GPCR / Class A : Adrenoceptors : alpha"""	277	protein-coding gene	gene with protein product		104221	"""adrenergic, alpha-1A-, receptor"""	ADRA1C			Standard	NM_033303		Approved	ADRA1L1	uc003xfh.1	P35348	OTTHUMG00000099459	ENST00000519229.1:c.227C>G	8.37:g.26722260G>C	ENSP00000430793:p.Thr76Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q9NPY0	Missense_Mutation	SNP	ENST00000519229.1	37		.	.	.	.	.	.	.	.	.	.	G	2.487	-0.318373	0.05386	.	.	ENSG00000120907	ENST00000380586;ENST00000380587;ENST00000380582;ENST00000380581;ENST00000519229;ENST00000354550;ENST00000276393;ENST00000380573;ENST00000380572;ENST00000358857	T;T;T;T;T;T;T;T;T;T	0.35789	1.29;1.29;1.29;1.29;1.29;1.29;1.29;1.29;1.29;1.29	4.83	4.83	0.62350	GPCR, rhodopsin-like superfamily (1);	0.050530	0.85682	D	0.000000	T	0.07683	0.0193	N	0.00159	-1.955	0.37643	D	0.922108	B;B;B;B;B;B	0.20988	0.034;0.034;0.015;0.034;0.05;0.043	B;B;B;B;B;B	0.17979	0.007;0.007;0.011;0.012;0.013;0.02	T	0.36792	-0.9733	10	0.02654	T	1	.	11.4564	0.50185	0.0847:0.0:0.9153:0.0	.	76;76;76;76;76;76	P35348-9;P35348-8;P35348;P35348-4;P35348-3;B0ZBD3	.;.;ADA1A_HUMAN;.;.;.	S	76	ENSP00000369960:T76S;ENSP00000369961:T76S;ENSP00000369956:T76S;ENSP00000369955:T76S;ENSP00000430793:T76S;ENSP00000346557:T76S;ENSP00000276393:T76S;ENSP00000369947:T76S;ENSP00000369946:T76S;ENSP00000351725:T76S	ENSP00000276393:T76S	T	-	2	0	ADRA1A	26778177	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.072000	0.71238	2.365000	0.80145	0.563000	0.77884	ACC		0.607	ADRA1A-009	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000376207.1		NM_033303	
AFAP1L1	134265	hgsc.bcm.edu;ucsc.edu	37	5	148680717	148680717	+	Missense_Mutation	SNP	G	G	A	rs61734415	byFrequency	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr5:148680717G>A	ENST00000296721.4	+	4	349	c.251G>A	c.(250-252)cGg>cAg	p.R84Q	AFAP1L1_ENST00000515000.1_Missense_Mutation_p.R84Q|AFAP1L1_ENST00000522492.1_3'UTR	NM_001146337.1|NM_152406.2	NP_001139809.1|NP_689619.1	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	84				R -> Q (in Ref. 2; BAC04664). {ECO:0000305}.		cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGTGACCTTCGGGACATGCCA	0.592													G|||	46	0.0091853	0.0015	0.0101	5008	,	,		16787	0.0		0.0338	False		,,,				2504	0.0031																0								G	GLN/ARG,GLN/ARG	43,4363	46.0+/-80.4	0,43,2160	105.0	99.0	101.0		251,251	0.6	1.0	5	dbSNP_129	101	384,8216	126.0+/-184.5	8,368,3924	yes	missense,missense	AFAP1L1	NM_001146337.1,NM_152406.2	43,43	8,411,6084	AA,AG,GG		4.4651,0.9759,3.2831	benign,benign	84/726,84/769	148680717	427,12579	2203	4300	6503	SO:0001583	missense	134265			AK094067	CCDS34274.1, CCDS54932.1	5q33.1	2013-01-10			ENSG00000157510	ENSG00000157510		"""Pleckstrin homology (PH) domain containing"""	26714	protein-coding gene	gene with protein product		614410					Standard	NM_152406		Approved	FLJ36748	uc003lqh.3	Q8TED9	OTTHUMG00000163441	ENST00000296721.4:c.251G>A	5.37:g.148680717G>A	ENSP00000296721:p.Arg84Gln	Somatic		WXS	Illumina HiSeq	Phase_I	Q08AN4|Q08AN5|Q8IW82|Q8N8Z5|Q8N9Q4	Missense_Mutation	SNP	ENST00000296721.4	37	CCDS34274.1	38	0.0173992673992674	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	30	0.0395778364116095	G	8.165	0.790456	0.16258	0.009759	0.044651	ENSG00000157510	ENST00000296721;ENST00000515000	T;T	0.40476	1.03;1.03	5.01	0.557	0.17260	.	0.349373	0.29522	N	0.011911	T	0.06325	0.0163	L	0.33485	1.01	0.34167	D	0.669394	B;B;B	0.21147	0.002;0.001;0.052	B;B;B	0.12156	0.007;0.001;0.003	T	0.26155	-1.0111	10	0.08837	T	0.75	-13.3407	10.3008	0.43650	0.487:0.0:0.513:0.0	rs61734415	84;84;84	Q8TED9-2;Q8TED9;Q8TED9-3	.;AF1L1_HUMAN;.	Q	84	ENSP00000296721:R84Q;ENSP00000424427:R84Q	ENSP00000296721:R84Q	R	+	2	0	AFAP1L1	148660910	0.995000	0.38212	0.995000	0.50966	0.906000	0.53458	0.499000	0.22546	0.162000	0.19483	-0.254000	0.11334	CGG		0.592	AFAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373443.1		NM_152406	
ANKRD35	148741	broad.mit.edu;ucsc.edu	37	1	145558859	145558859	+	Missense_Mutation	SNP	G	G	A	rs150752253	byFrequency	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr1:145558859G>A	ENST00000355594.4	+	7	565	c.478G>A	c.(478-480)Gca>Aca	p.A160T	ANKRD35_ENST00000544626.1_3'UTR	NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	160								p.A160T(1)		NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CCTGATGATCGCATCGCTGGG	0.577																																					Melanoma(9;127 754 22988 51047)												1	Substitution - Missense(1)	kidney(1)						G	THR/ALA	0,4406		0,0,2203	129.0	121.0	124.0		478	5.5	0.9	1	dbSNP_134	124	4,8596	3.7+/-12.6	0,4,4296	yes	missense	ANKRD35	NM_144698.3	58	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	probably-damaging	160/1002	145558859	4,13002	2203	4300	6503	SO:0001583	missense	148741			AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"""Ankyrin repeat domain containing"""	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.478G>A	1.37:g.145558859G>A	ENSP00000347802:p.Ala160Thr	Somatic		WXS	Illumina GAIIx	Phase_I	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.119812	0.77323	0.0	4.65E-4	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.81163	-1.46	5.51	5.51	0.81932	Ankyrin repeat-containing domain (4);	0.000000	0.45606	D	0.000347	D	0.90679	0.7076	M	0.92219	3.285	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91992	0.5604	10	0.59425	D	0.04	-11.9671	14.9105	0.70752	0.0:0.0:1.0:0.0	.	160	Q8N283	ANR35_HUMAN	T	69;160	ENSP00000347802:A160T	ENSP00000347802:A160T	A	+	1	0	ANKRD35	144270216	0.992000	0.36948	0.915000	0.36163	0.345000	0.29048	4.990000	0.63876	2.583000	0.87209	0.655000	0.94253	GCA		0.577	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1		NM_144698	
ARNT2	9915	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	80762712	80762712	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr15:80762712G>T	ENST00000303329.4	+	4	513	c.348G>T	c.(346-348)atG>atT	p.M116I	ARNT2_ENST00000533983.1_Missense_Mutation_p.M105I|ARNT2_ENST00000527771.1_Missense_Mutation_p.M105I|ARNT2_ENST00000531595.3_3'UTR	NM_014862.3	NP_055677.3	Q9HBZ2	ARNT2_HUMAN	aryl-hydrocarbon receptor nuclear translocator 2	116	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				central nervous system development (GO:0007417)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.M116I(1)		NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|pancreas(2)|prostate(2)|skin(1)	35			BRCA - Breast invasive adenocarcinoma(143;0.134)			TGAAGTCCATGAGGGGTACAG	0.592																																																	1	Substitution - Missense(1)	kidney(1)											108.0	81.0	90.0					15																	80762712		2203	4300	6503	SO:0001583	missense	9915			AB002305	CCDS32307.1	15q25.1	2013-05-21			ENSG00000172379	ENSG00000172379		"""Basic helix-loop-helix proteins"""	16876	protein-coding gene	gene with protein product		606036				11247670	Standard	NM_014862		Approved	KIAA0307, bHLHe1	uc002bfr.3	Q9HBZ2	OTTHUMG00000165478	ENST00000303329.4:c.348G>T	15.37:g.80762712G>T	ENSP00000307479:p.Met116Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B4DIS7|O15024|Q8IYC2	Missense_Mutation	SNP	ENST00000303329.4	37	CCDS32307.1	.	.	.	.	.	.	.	.	.	.	G	18.32	3.598544	0.66332	.	.	ENSG00000172379	ENST00000360062;ENST00000303329;ENST00000540859	D	0.97870	-4.58	5.0	5.0	0.66597	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.92328	0.7566	N	0.02315	-0.6	0.80722	D	1	B;B	0.18968	0.032;0.002	B;B	0.18263	0.021;0.017	D	0.88044	0.2783	10	0.44086	T	0.13	.	18.4737	0.90783	0.0:0.0:1.0:0.0	.	116;116	Q9HBZ2;Q86TN1	ARNT2_HUMAN;.	I	105;116;116	ENSP00000307479:M116I	ENSP00000307479:M116I	M	+	3	0	ARNT2	78549767	1.000000	0.71417	0.989000	0.46669	0.957000	0.61999	6.089000	0.71384	2.597000	0.87782	0.650000	0.86243	ATG		0.592	ARNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384389.2			
ATP1A2	477	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	160091025	160091025	+	Missense_Mutation	SNP	A	A	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr1:160091025A>T	ENST00000361216.3	+	3	250	c.161A>T	c.(160-162)cAa>cTa	p.Q54L	ATP1A2_ENST00000392233.3_Missense_Mutation_p.Q54L	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	54					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)	p.Q54L(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			CGCAAATACCAAGTGGACCTG	0.517																																																	1	Substitution - Missense(1)	kidney(1)											181.0	182.0	182.0					1																	160091025		2203	4300	6503	SO:0001583	missense	477			AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"""ATPases / P-type"""	800	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-2"", ""sodium pump subunit alpha-2"", ""sodium-potassium ATPase catalytic subunit alpha-2"""	182340	"""migraine, hemiplegic 2"", ""ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"""	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.161A>T	1.37:g.160091025A>T	ENSP00000354490:p.Gln54Leu	Somatic		WXS	Illumina HiSeq	Phase_I	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Missense_Mutation	SNP	ENST00000361216.3	37	CCDS1196.1	.	.	.	.	.	.	.	.	.	.	A	15.37	2.814821	0.50527	.	.	ENSG00000018625	ENST00000361216;ENST00000392233	T;T	0.79845	-1.31;-1.31	4.56	4.56	0.56223	ATPase, P-type cation-transporter, N-terminal (2);	0.347566	0.26366	N	0.024794	T	0.69369	0.3103	M	0.72479	2.2	0.36861	D	0.888409	B	0.09022	0.002	B	0.27608	0.081	T	0.73216	-0.4053	10	0.62326	D	0.03	.	7.8322	0.29349	0.9055:0.0:0.0945:0.0	.	54	P50993	AT1A2_HUMAN	L	54	ENSP00000354490:Q54L;ENSP00000376066:Q54L	ENSP00000354490:Q54L	Q	+	2	0	ATP1A2	158357649	0.914000	0.31030	1.000000	0.80357	0.997000	0.91878	1.777000	0.38604	1.915000	0.55452	0.533000	0.62120	CAA		0.517	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2		NM_000702	
CACNA1D	776	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	53777118	53777118	+	Silent	SNP	G	G	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr3:53777118G>T	ENST00000350061.5	+	22	3403	c.2892G>T	c.(2890-2892)ggG>ggT	p.G964G	CACNA1D_ENST00000288139.4_Silent_p.G984G|CACNA1D_ENST00000422281.2_Silent_p.G964G	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	964					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)	p.G984G(1)		breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TGGTGGTTGGGGTGTCTCTGG	0.433																																																	1	Substitution - coding silent(1)	kidney(1)											230.0	240.0	236.0					3																	53777118		2203	4300	6503	SO:0001819	synonymous_variant	776			AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.2892G>T	3.37:g.53777118G>T		Somatic		WXS	Illumina HiSeq	Phase_I	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Silent	SNP	ENST00000350061.5	37	CCDS46848.1																																																																																				0.433	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1		NM_000720	
CAMTA1	23261	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	7797034	7797034	+	Missense_Mutation	SNP	C	C	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr1:7797034C>T	ENST00000303635.7	+	14	3514	c.3307C>T	c.(3307-3309)Ccc>Tcc	p.P1103S	CAMTA1_ENST00000439411.2_Missense_Mutation_p.P1103S	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	1103					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P1103S(1)		breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		GGAAGTTGACCCCTTGAATGT	0.488			T	WWTR1	epitheliod hemangioendothelioma																																			Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	1	Substitution - Missense(1)	kidney(1)											146.0	128.0	134.0					1																	7797034		2203	4300	6503	SO:0001583	missense	23261			AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.3307C>T	1.37:g.7797034C>T	ENSP00000306522:p.Pro1103Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	ENST00000303635.7	37	CCDS30576.1	.	.	.	.	.	.	.	.	.	.	C	32	5.134019	0.94517	.	.	ENSG00000171735	ENST00000303635;ENST00000439411;ENST00000414738;ENST00000303646	T;T	0.35421	1.31;1.31	5.61	5.61	0.85477	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.56601	0.1996	L	0.51422	1.61	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.996;0.998;0.997	T	0.49214	-0.8963	10	0.37606	T	0.19	-19.7132	19.6383	0.95746	0.0:1.0:0.0:0.0	.	1103;190;59;1103	Q9Y6Y1-2;B4DXR3;Q7Z7P1;Q9Y6Y1	.;.;.;CMTA1_HUMAN	S	1103;1103;190;59	ENSP00000306522:P1103S;ENSP00000402561:P1103S	ENSP00000306522:P1103S	P	+	1	0	CAMTA1	7719621	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.440000	0.80464	2.631000	0.89168	0.655000	0.94253	CCC		0.488	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3		NM_015215	
CASP1	834	broad.mit.edu;hgsc.bcm.edu	37	11	104897592	104897592	+	Missense_Mutation	SNP	C	C	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr11:104897592C>A	ENST00000533400.1	-	8	1128	c.1093G>T	c.(1093-1095)Gat>Tat	p.D365Y	CASP1_ENST00000534497.1_Missense_Mutation_p.D224Y|CASP1_ENST00000531166.1_Missense_Mutation_p.D49Y|CASP1_ENST00000436863.3_Missense_Mutation_p.D365Y|CASP1_ENST00000353247.5_Missense_Mutation_p.D49Y|CASP1_ENST00000527979.1_Missense_Mutation_p.D328Y|CASP1_ENST00000528974.1_3'UTR|CASP1_ENST00000525825.1_Missense_Mutation_p.D344Y|CASP1_ENST00000598974.1_Missense_Mutation_p.D365Y|CASP1_ENST00000593315.1_Missense_Mutation_p.D344Y|CASP1_ENST00000446369.1_Missense_Mutation_p.D224Y|CASP1_ENST00000415981.2_Missense_Mutation_p.D49Y|CASP1_ENST00000393136.4_Missense_Mutation_p.D344Y|CASP1_ENST00000526568.1_Missense_Mutation_p.D272Y|CASP1_ENST00000594519.1_Missense_Mutation_p.D224Y	NM_001257118.1	NP_001244047.1	P29466	CASP1_HUMAN	caspase 1, apoptosis-related cysteine peptidase	365					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic substance (GO:0071310)|execution phase of apoptosis (GO:0097194)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|membrane hyperpolarization (GO:0060081)|mitochondrial depolarization (GO:0051882)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|programmed necrotic cell death (GO:0097300)|proteolysis (GO:0006508)|pyroptosis (GO:0070269)|regulation of inflammatory response (GO:0050727)|response to ATP (GO:0033198)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|IPAF inflammasome complex (GO:0072557)|NLRP1 inflammasome complex (GO:0072558)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|endopeptidase activity (GO:0004175)	p.D365Y(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482)	Minocycline(DB01017)	TCCTCCACATCACAGGAACAG	0.403																																					NSCLC(41;1246 1743 4934)												1	Substitution - Missense(1)	kidney(1)											116.0	104.0	108.0					11																	104897592		2202	4299	6501	SO:0001583	missense	834			U13697	CCDS8329.1, CCDS8330.1, CCDS8331.1, CCDS8332.1, CCDS53704.1	11q23	2012-02-29	2012-02-29		ENSG00000137752	ENSG00000137752		"""Caspases"""	1499	protein-coding gene	gene with protein product	"""caspase-1"", ""interleukin 1, beta, convertase"""	147678	"""caspase 1, apoptosis-related cysteine protease (interleukin 1, beta, convertase)"", ""caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, convertase)"""	IL1BC		1373520, 9250871	Standard	NM_033292		Approved	ICE	uc001pim.5	P29466	OTTHUMG00000048072	ENST00000533400.1:c.1093G>T	11.37:g.104897592C>A	ENSP00000433138:p.Asp365Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	B5MDZ1|Q53EY6|Q6DMQ1|Q6GSS3|Q6PI75|Q9UCN3	Missense_Mutation	SNP	ENST00000533400.1	37	CCDS8330.1	.	.	.	.	.	.	.	.	.	.	.	12.26	1.883456	0.33255	.	.	ENSG00000137752	ENST00000532439;ENST00000526568;ENST00000527979;ENST00000533400;ENST00000436863;ENST00000415981;ENST00000446369;ENST00000353247;ENST00000393136;ENST00000525825;ENST00000531166;ENST00000534497	T;T;T;T;T;T;T;T;T;T;T;T	0.52057	3.74;3.74;3.74;3.74;3.74;0.68;0.68;0.68;3.74;3.74;0.68;0.68	4.35	1.14	0.20703	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase non-catalytic subunit p10 (1);Peptidase C14, caspase precursor p45, core (1);	0.420336	0.25264	N	0.031931	T	0.67059	0.2853	M	0.88979	2.995	0.35862	D	0.827552	D;D;D;P;P;D;P	0.89917	1.0;0.977;0.999;0.913;0.929;0.962;0.593	D;P;D;P;P;P;B	0.72338	0.977;0.742;0.973;0.541;0.757;0.733;0.323	T	0.72690	-0.4217	10	0.72032	D	0.01	.	7.2395	0.26088	0.0:0.4408:0.4587:0.1005	.	49;224;365;344;365;328;272	P29466-5;P29466-4;A8K249;P29466-2;P29466;G3V169;P29466-3	.;.;.;.;CASP1_HUMAN;.;.	Y	214;272;328;365;365;49;224;49;344;344;49;224	ENSP00000435536:D214Y;ENSP00000434250:D272Y;ENSP00000432340:D328Y;ENSP00000433138:D365Y;ENSP00000410076:D365Y;ENSP00000408446:D49Y;ENSP00000403260:D224Y;ENSP00000344132:D49Y;ENSP00000376844:D344Y;ENSP00000434779:D344Y;ENSP00000434303:D49Y;ENSP00000436875:D224Y	ENSP00000344132:D49Y	D	-	1	0	CASP1	104402802	0.001000	0.12720	0.912000	0.35992	0.346000	0.29079	-0.143000	0.10296	0.551000	0.29008	0.460000	0.39030	GAT		0.403	CASP1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388116.1		NM_033292	
SPDL1	54908	broad.mit.edu;hgsc.bcm.edu	37	5	169026150	169026150	+	Missense_Mutation	SNP	A	A	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr5:169026150A>C	ENST00000265295.4	+	10	1590	c.1311A>C	c.(1309-1311)aaA>aaC	p.K437N		NM_017785.4	NP_060255.3			spindle apparatus coiled-coil protein 1									p.K437N(1)									TGAAACTAAAATATGAACCTG	0.274																																																	1	Substitution - Missense(1)	kidney(1)											27.0	30.0	29.0					5																	169026150		2198	4296	6494	SO:0001583	missense	0			BC012568	CCDS4370.1	5q35.1	2012-09-27	2012-09-27	2012-09-27	ENSG00000040275	ENSG00000040275			26010	protein-coding gene	gene with protein product	"""spindly homolog (Drosophila)"""		"""coiled-coil domain containing 99"""	CCDC99		20427577	Standard	NM_017785		Approved	FLJ20364, hSpindly	uc003mae.4	Q96EA4	OTTHUMG00000130438	ENST00000265295.4:c.1311A>C	5.37:g.169026150A>C	ENSP00000265295:p.Lys437Asn	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000265295.4	37	CCDS4370.1	.	.	.	.	.	.	.	.	.	.	A	16.97	3.268351	0.59540	.	.	ENSG00000040275	ENST00000265295;ENST00000274631	T	0.38722	1.12	5.98	2.72	0.32119	.	0.000000	0.85682	D	0.000000	T	0.56863	0.2014	M	0.71581	2.175	0.48185	D	0.999608	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.913;0.999;0.999	T	0.56092	-0.8036	10	0.66056	D	0.02	-31.8397	5.686	0.17803	0.6241:0.0:0.3759:0.0	.	359;338;437	B4E393;Q96EA4-2;Q96EA4	.;.;SPDLY_HUMAN	N	437;338	ENSP00000265295:K437N	ENSP00000265295:K437N	K	+	3	2	CCDC99	168958728	1.000000	0.71417	1.000000	0.80357	0.519000	0.34347	1.226000	0.32563	0.779000	0.33543	-0.462000	0.05337	AAA		0.274	SPDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252829.2		NM_017785	
CD2AP	23607	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	47567071	47567071	+	Missense_Mutation	SNP	T	T	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr6:47567071T>A	ENST00000359314.5	+	13	1765	c.1309T>A	c.(1309-1311)Ttt>Att	p.F437I		NM_012120.2	NP_036252.1	Q9Y5K6	CD2AP_HUMAN	CD2-associated protein	437					mitotic nuclear division (GO:0007067)|negative regulation of transforming growth factor beta1 production (GO:0032911)|positive regulation of protein localization to nucleus (GO:1900182)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of receptor-mediated endocytosis (GO:0048259)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|substrate-dependent cell migration, cell extension (GO:0006930)|vesicle organization (GO:0016050)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)	p.F437I(1)		kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	20			Lung(136;0.105)|LUSC - Lung squamous cell carcinoma(51;0.138)			TTCATCAAAATTTGAAACTGA	0.338																																																	1	Substitution - Missense(1)	kidney(1)											52.0	53.0	53.0					6																	47567071		2203	4300	6503	SO:0001583	missense	23607			AF146277	CCDS34472.1	6p12	2008-02-05			ENSG00000198087	ENSG00000198087			14258	protein-coding gene	gene with protein product		604241				10339567	Standard	NM_012120		Approved	CMS	uc003oyw.3	Q9Y5K6	OTTHUMG00000014799	ENST00000359314.5:c.1309T>A	6.37:g.47567071T>A	ENSP00000352264:p.Phe437Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A6NL34|Q5VYA3|Q9UG97	Missense_Mutation	SNP	ENST00000359314.5	37	CCDS34472.1	.	.	.	.	.	.	.	.	.	.	T	9.173	1.021674	0.19433	.	.	ENSG00000198087	ENST00000359314	T	0.22945	1.93	5.92	3.38	0.38709	.	2.671650	0.01627	N	0.023341	T	0.07593	0.0191	L	0.27053	0.805	0.21967	N	0.999441	B	0.02656	0.0	B	0.04013	0.001	T	0.22277	-1.0221	10	0.22109	T	0.4	-7.0793	9.8098	0.40815	0.2819:0.0:0.0:0.7181	.	437	Q9Y5K6	CD2AP_HUMAN	I	437	ENSP00000352264:F437I	ENSP00000352264:F437I	F	+	1	0	CD2AP	47675030	1.000000	0.71417	0.995000	0.50966	0.212000	0.24457	1.975000	0.40569	1.025000	0.39708	0.454000	0.30748	TTT		0.338	CD2AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040817.2			
CELA1	1990	hgsc.bcm.edu	37	12	51740413	51740414	+	Frame_Shift_Ins	INS	-	-	C	rs573952082|rs386762976|rs377599213|rs370927847	byFrequency	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr12:51740413_51740414insC	ENST00000293636.1	-	1	49_50	c.9_10insG	c.(7-12)gtccttfs	p.L4fs		NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	4					exocrine pancreas development (GO:0031017)|inflammatory response (GO:0006954)|multicellular organism growth (GO:0035264)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas morphogenesis (GO:0061113)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						TTACCATAAAGGACCAGCATGT	0.515													?|-|C|unsure	1840	0.367412	0.2988	0.451	5008	,	,		13831	0.5546		0.3211	False		,,,				2504	0.2556																0																																										SO:0001589	frameshift_variant	1990				CCDS8812.1	12q13	2012-10-02	2009-05-05	2009-05-05	ENSG00000139610	ENSG00000139610			3308	protein-coding gene	gene with protein product		130120	"""elastase 1, pancreatic"""	ELA1			Standard	NM_001971		Approved		uc001ryi.1	Q9UNI1	OTTHUMG00000167523	ENST00000293636.1:c.9_10insG	12.37:g.51740413_51740414insC	ENSP00000293636:p.Leu4fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q5MLF0|Q6DJT0|Q6ISM6	Frame_Shift_Ins	INS	ENST00000293636.1	37	CCDS8812.1																																																																																				0.515	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1		NM_001971	
CELA1	1990	hgsc.bcm.edu	37	12	51740415	51740416	+	Frame_Shift_Del	DEL	AC	AC	-	rs370927847|rs386762976|rs61761206|rs55827519|rs148235680	byFrequency	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr12:51740415_51740416delAC	ENST00000293636.1	-	1	47_48	c.7_8delGT	c.(7-9)gtcfs	p.V3fs		NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	3					exocrine pancreas development (GO:0031017)|inflammatory response (GO:0006954)|multicellular organism growth (GO:0035264)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas morphogenesis (GO:0061113)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.V3fs*21(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						ACCATAAAGGACCAGCATGTTG	0.515														1840	0.367412	0.2988	0.451	5008	,	,		16016	0.5546		0.3211	False		,,,				2504	0.2556																1	Deletion - Frameshift(1)	large_intestine(1)																																								SO:0001589	frameshift_variant	1990				CCDS8812.1	12q13	2012-10-02	2009-05-05	2009-05-05	ENSG00000139610	ENSG00000139610			3308	protein-coding gene	gene with protein product		130120	"""elastase 1, pancreatic"""	ELA1			Standard	NM_001971		Approved		uc001ryi.1	Q9UNI1	OTTHUMG00000167523	ENST00000293636.1:c.7_8delGT	12.37:g.51740415_51740416delAC	ENSP00000293636:p.Val3fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q5MLF0|Q6DJT0|Q6ISM6	Frame_Shift_Del	DEL	ENST00000293636.1	37	CCDS8812.1																																																																																				0.515	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1		NM_001971	
CHD7	55636	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	61757864	61757864	+	Silent	SNP	C	C	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr8:61757864C>T	ENST00000423902.2	+	23	5585	c.5106C>T	c.(5104-5106)agC>agT	p.S1702S	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1702					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.S1702S(2)		NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			AAGCCCAGAGCACACAGCCGG	0.507																																																	2	Substitution - coding silent(2)	kidney(2)											62.0	70.0	67.0					8																	61757864		1991	4165	6156	SO:0001819	synonymous_variant	55636			AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.5106C>T	8.37:g.61757864C>T		Somatic		WXS	Illumina HiSeq	Phase_I	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Silent	SNP	ENST00000423902.2	37	CCDS47865.1																																																																																				0.507	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2		XM_098762	
CLMN	79789	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	95669872	95669872	+	Missense_Mutation	SNP	A	A	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr14:95669872A>G	ENST00000298912.4	-	9	1927	c.1814T>C	c.(1813-1815)cTa>cCa	p.L605P		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	605					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.L605P(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		CCTTTTACCTAGTTTTTCAGC	0.428																																																	1	Substitution - Missense(1)	kidney(1)											67.0	64.0	65.0					14																	95669872		2203	4300	6503	SO:0001583	missense	79789			AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.1814T>C	14.37:g.95669872A>G	ENSP00000298912:p.Leu605Pro	Somatic		WXS	Illumina HiSeq	Phase_I	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	37	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	A	4.771	0.143275	0.09083	.	.	ENSG00000165959	ENST00000298912	D	0.93426	-3.22	5.26	-7.37	0.01412	.	2.101480	0.02711	N	0.112827	D	0.86552	0.5960	L	0.27053	0.805	0.09310	N	1	B	0.15141	0.012	B	0.11329	0.006	T	0.76356	-0.2989	10	0.42905	T	0.14	.	7.5314	0.27685	0.3849:0.2846:0.3305:0.0	.	605	Q96JQ2	CLMN_HUMAN	P	605	ENSP00000298912:L605P	ENSP00000298912:L605P	L	-	2	0	CLMN	94739625	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.340000	0.07821	-2.550000	0.00480	-3.590000	0.00028	CTA		0.428	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2			
CLYBL	171425	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	100543598	100543598	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr13:100543598G>A	ENST00000376360.1	+	8	981	c.954G>A	c.(952-954)atG>atA	p.M318I	CLYBL_ENST00000339105.4_Missense_Mutation_p.M318I|CLYBL_ENST00000376354.1_Missense_Mutation_p.M284I|CLYBL_ENST00000376355.3_Missense_Mutation_p.M284I			Q8N0X4	CLYBL_HUMAN	citrate lyase beta like	318						mitochondrion (GO:0005739)	lyase activity (GO:0016829)|metal ion binding (GO:0046872)	p.M318I(1)		NS(1)|kidney(6)|large_intestine(6)|lung(10)|skin(2)	25	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					AAGGGAGTATGATCGACATGC	0.443																																																	1	Substitution - Missense(1)	kidney(1)											123.0	114.0	117.0					13																	100543598		2203	4300	6503	SO:0001583	missense	171425			AF428253	CCDS32002.1	13q32.3	2011-04-08			ENSG00000125246	ENSG00000125246			18355	protein-coding gene	gene with protein product		609686					Standard	XM_005254030		Approved	CLB	uc001vok.3	Q8N0X4	OTTHUMG00000017278	ENST00000376360.1:c.954G>A	13.37:g.100543598G>A	ENSP00000365538:p.Met318Ile	Somatic		WXS	Illumina HiSeq	Phase_I	Q5W0F7|Q8TDH8	Missense_Mutation	SNP	ENST00000376360.1	37	CCDS32002.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.199974	0.79015	.	.	ENSG00000125246	ENST00000376355;ENST00000376360;ENST00000376354;ENST00000339105;ENST00000419700;ENST00000425186	T;T;T;T;T	0.58797	1.14;1.12;1.14;1.12;0.31	5.03	5.03	0.67393	.	0.037757	0.85682	D	0.000000	T	0.80829	0.4698	M	0.90650	3.135	0.80722	D	1	D	0.76494	0.999	D	0.70016	0.967	D	0.85118	0.0967	10	0.72032	D	0.01	-15.5319	18.7527	0.91821	0.0:0.0:1.0:0.0	.	318	Q8N0X4	CLYBL_HUMAN	I	284;318;284;318;81;67	ENSP00000365533:M284I;ENSP00000365538:M318I;ENSP00000365532:M284I;ENSP00000342991:M318I;ENSP00000396574:M81I	ENSP00000342991:M318I	M	+	3	0	CLYBL	99341599	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.248000	0.95456	2.490000	0.84030	0.655000	0.94253	ATG		0.443	CLYBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045611.1			
COL1A2	1278	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	94051214	94051214	+	Missense_Mutation	SNP	A	A	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr7:94051214A>G	ENST00000297268.6	+	39	2824	c.2353A>G	c.(2353-2355)Atg>Gtg	p.M785V		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	785			Missing (in OI2). {ECO:0000269|PubMed:1339453}.		blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)	p.M785V(1)	COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	CTCTTAGGGTATGACTGGTTT	0.443										HNSCC(75;0.22)																																							1	Substitution - Missense(1)	kidney(1)											150.0	127.0	135.0					7																	94051214		2203	4300	6503	SO:0001583	missense	1278			Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.2353A>G	7.37:g.94051214A>G	ENSP00000297268:p.Met785Val	Somatic		WXS	Illumina HiSeq	Phase_I	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	37	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	A	10.11	1.261476	0.23051	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.94046	-3.34	5.35	-0.246	0.13022	.	1.181480	0.05959	N	0.640208	D	0.86297	0.5899	N	0.11756	0.17	0.09310	N	0.999994	B	0.02656	0.0	B	0.01281	0.0	T	0.73591	-0.3934	10	0.46703	T	0.11	.	10.5516	0.45092	0.4512:0.0:0.5488:0.0	.	785	P08123	CO1A2_HUMAN	V	785;786	ENSP00000297268:M785V	ENSP00000297268:M785V	M	+	1	0	COL1A2	93889150	0.000000	0.05858	0.251000	0.24312	0.983000	0.72400	-0.111000	0.10807	-0.021000	0.14009	-0.290000	0.09829	ATG		0.443	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2		NM_000089	
COL4A2	1284	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	111144511	111144511	+	Silent	SNP	T	T	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr13:111144511T>C	ENST00000360467.5	+	38	3855	c.3549T>C	c.(3547-3549)gcT>gcC	p.A1183A		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	1183	Triple-helical region.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)	p.A1183A(1)		NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			GGCCGGGAGCTCCGGGCTTAC	0.652																																																	1	Substitution - coding silent(1)	kidney(1)											33.0	48.0	43.0					13																	111144511		1967	4077	6044	SO:0001819	synonymous_variant	1284			AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"""Collagens"""	2203	protein-coding gene	gene with protein product	"""canstatin"", ""collagen type IV alpha 2"""	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.3549T>C	13.37:g.111144511T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q14052|Q548C3|Q5VZA9|Q66K23	Silent	SNP	ENST00000360467.5	37	CCDS41907.1																																																																																				0.652	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2		NM_001846	
COL5A3	50509	broad.mit.edu;hgsc.bcm.edu	37	19	10087919	10087919	+	Missense_Mutation	SNP	C	C	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr19:10087919C>T	ENST00000264828.3	-	44	3359	c.3274G>A	c.(3274-3276)Gat>Aat	p.D1092N		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1092	Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)	p.D1092N(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			TCTCCTTTATCGCCTTTACTC	0.607																																																	1	Substitution - Missense(1)	kidney(1)											139.0	89.0	106.0					19																	10087919		2203	4300	6503	SO:0001583	missense	50509			AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"""Collagens"""	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.3274G>A	19.37:g.10087919C>T	ENSP00000264828:p.Asp1092Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	C	11.91	1.779527	0.31502	.	.	ENSG00000080573	ENST00000264828	D	0.94184	-3.37	5.32	5.32	0.75619	.	0.138983	0.45867	D	0.000329	D	0.89605	0.6763	L	0.43701	1.375	0.50467	D	0.999871	P	0.48162	0.906	B	0.39706	0.307	D	0.88134	0.2840	10	0.20519	T	0.43	.	16.4842	0.84180	0.0:1.0:0.0:0.0	.	1092	P25940	CO5A3_HUMAN	N	1092	ENSP00000264828:D1092N	ENSP00000264828:D1092N	D	-	1	0	COL5A3	9948919	0.999000	0.42202	0.876000	0.34364	0.093000	0.18481	4.230000	0.58632	2.486000	0.83907	0.467000	0.42956	GAT		0.607	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1		NM_015719	
YBX3	8531	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	10854562	10854562	+	Missense_Mutation	SNP	T	T	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr12:10854562T>A	ENST00000228251.4	-	8	1250	c.1050A>T	c.(1048-1050)aaA>aaT	p.K350N	YBX3_ENST00000546164.1_5'UTR|YBX3_ENST00000279550.7_Missense_Mutation_p.K281N	NM_003651.4	NP_003642.3	P16989	YBOX3_HUMAN	Y box binding protein 3	350					3'-UTR-mediated mRNA stabilization (GO:0070935)|cellular hyperosmotic response (GO:0071474)|cellular response to tumor necrosis factor (GO:0071356)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of necroptotic process (GO:0060546)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cytoplasmic translation (GO:2000767)|positive regulation of organ growth (GO:0046622)|response to cold (GO:0009409)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|tight junction (GO:0005923)	double-stranded DNA binding (GO:0003690)|mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|Rho GTPase binding (GO:0017048)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)	p.K350N(1)									GATTTACCTCTTTGCCATCTT	0.507																																																	1	Substitution - Missense(1)	kidney(1)											213.0	206.0	208.0					12																	10854562		2203	4300	6503	SO:0001583	missense	8531			L29064	CCDS8630.1, CCDS44831.1	12p13.1	2013-03-13	2013-03-13	2013-03-13	ENSG00000060138	ENSG00000060138			2428	protein-coding gene	gene with protein product	"""cold-shock domain containing A1"""	603437	"""cold shock domain protein A"""	CSDA		2977358, 8710501	Standard	NM_003651		Approved	dbpA, ZONAB, CSDA1	uc001qyt.3	P16989	OTTHUMG00000168409	ENST00000228251.4:c.1050A>T	12.37:g.10854562T>A	ENSP00000228251:p.Lys350Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B2RBW6|Q14121|Q969N6|Q96B76	Missense_Mutation	SNP	ENST00000228251.4	37	CCDS8630.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.055002	0.75960	.	.	ENSG00000060138	ENST00000279550;ENST00000228251	T;T	0.29397	1.67;1.57	4.39	4.39	0.52855	.	0.000000	0.85682	D	0.000000	T	0.49592	0.1566	M	0.63843	1.955	0.47584	D	0.999468	D;D	0.76494	0.971;0.999	P;D	0.80764	0.624;0.994	T	0.46219	-0.9207	10	0.41790	T	0.15	.	11.8088	0.52171	0.0:0.0:0.0:1.0	.	281;350	P16989-2;P16989	.;DBPA_HUMAN	N	281;350	ENSP00000279550:K281N;ENSP00000228251:K350N	ENSP00000228251:K350N	K	-	3	2	CSDA	10745829	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	1.833000	0.39161	1.734000	0.51633	0.482000	0.46254	AAA		0.507	YBX3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399628.1		NM_003651	
DDX3X	1654	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	41203543	41203544	+	Frame_Shift_Ins	INS	-	-	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chrX:41203543_41203544insT	ENST00000399959.2	+	10	1771_1772	c.916_917insT	c.(916-918)attfs	p.I306fs	RN7SL15P_ENST00000582825.1_RNA|DDX3X_ENST00000441189.2_Intron|DDX3X_ENST00000542215.1_3'UTR|DDX3X_ENST00000457138.2_Frame_Shift_Ins_p.I290fs|DDX3X_ENST00000478993.1_3'UTR	NM_001193416.1|NM_001193417.1|NM_001356.3	NP_001180345.1|NP_001180346.1|NP_001347.3	O00571	DDX3X_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 3, X-linked	306	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|Interaction with GSK3B.|Necessary for interaction with XPO1.				ATP catabolic process (GO:0006200)|cellular response to arsenic-containing substance (GO:0071243)|cellular response to osmotic stress (GO:0071470)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|mature ribosome assembly (GO:0042256)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell growth (GO:0030307)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of translation (GO:0045727)|positive regulation of translational initiation (GO:0045948)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|stress granule assembly (GO:0034063)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 5'-UTR binding (GO:0048027)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|transcription factor binding (GO:0008134)|translation initiation factor binding (GO:0031369)			NS(3)|breast(8)|central_nervous_system(36)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84						TGGTGCCGATATTGGTCAGCAG	0.406										HNSCC(61;0.18)																																							0																																										SO:0001589	frameshift_variant	1654			U50553	CCDS43931.1, CCDS55404.1	Xp11.3-p11.23	2013-07-16	2013-07-16	2003-06-20	ENSG00000215301	ENSG00000215301		"""DEAD-boxes"""	2745	protein-coding gene	gene with protein product		300160	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked"""	DDX3		9381176, 9730595	Standard	NM_001193416		Approved	DBX, HLP2, DDX14	uc004dfe.3	O00571	OTTHUMG00000021369	ENST00000399959.2:c.918dupT	X.37:g.41203545_41203545dupT	ENSP00000382840:p.Ile306fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8K538|B4E3E8|O15536	Frame_Shift_Ins	INS	ENST00000399959.2	37	CCDS43931.1																																																																																				0.406	DDX3X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056253.1		NM_024005	
DEFB126	81623	hgsc.bcm.edu	37	20	126314	126314	+	Missense_Mutation	SNP	C	C	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr20:126314C>G	ENST00000382398.3	+	2	577	c.317C>G	c.(316-318)cCc>cGc	p.P106R	DEFB126_ENST00000542572.1_3'UTR	NM_030931.3	NP_112193.1	Q9BYW3	DB126_HUMAN	defensin, beta 126	106					defense response to bacterium (GO:0042742)	cell surface (GO:0009986)|extracellular region (GO:0005576)|glycocalyx (GO:0030112)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)	4		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			GCTCCTACCCCCGTTTCTCCC	0.458																																																	0													108.0	109.0	109.0					20																	126314		2203	4300	6503	SO:0001583	missense	81623				CCDS12990.1	20p13	2010-03-30	2002-05-09	2002-05-10	ENSG00000125788	ENSG00000125788		"""Defensins, beta"""	15900	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 8"""	C20orf8		11854508	Standard	NM_030931		Approved	bA530N10.1, DEFB-26	uc002wcx.3	Q9BYW3	OTTHUMG00000031616	ENST00000382398.3:c.317C>G	20.37:g.126314C>G	ENSP00000371835:p.Pro106Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q562G3|Q9H1M5	Missense_Mutation	SNP	ENST00000382398.3	37	CCDS12990.1	.	.	.	.	.	.	.	.	.	.	C	5.857	0.342300	0.11069	.	.	ENSG00000125788	ENST00000382398	T	0.40225	1.04	1.54	0.534	0.17127	.	.	.	.	.	T	0.23370	0.0565	N	0.19112	0.55	0.09310	N	1	B	0.26195	0.144	B	0.13407	0.009	T	0.14980	-1.0453	9	0.44086	T	0.13	0.0422	5.6779	0.17759	0.0:0.655:0.345:0.0	.	106	Q9BYW3	DB126_HUMAN	R	106	ENSP00000371835:P106R	ENSP00000371835:P106R	P	+	2	0	DEFB126	74314	0.000000	0.05858	0.011000	0.14972	0.008000	0.06430	0.034000	0.13776	0.202000	0.20498	-0.264000	0.10439	CCC		0.458	DEFB126-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077428.2		NM_030931	
DENND5A	23258	broad.mit.edu;ucsc.edu	37	11	9161237	9161237	+	Missense_Mutation	SNP	A	A	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr11:9161237A>G	ENST00000328194.3	-	23	4165	c.3845T>C	c.(3844-3846)gTc>gCc	p.V1282A	DENND5A_ENST00000530044.1_3'UTR|SCUBE2_ENST00000534295.1_5'Flank|DENND5A_ENST00000527700.1_Missense_Mutation_p.V625A	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	1282	RUN 2. {ECO:0000255|PROSITE- ProRule:PRU00178}.				positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.V1282A(1)		breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						GATGCCCTTGACAAGGGACGT	0.517																																																	1	Substitution - Missense(1)	kidney(1)											131.0	89.0	103.0					11																	9161237		2201	4296	6497	SO:0001583	missense	23258			AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014		"""DENN/MADD domain containing"""	19344	protein-coding gene	gene with protein product			"""RAB6 interacting protein 1"""	RAB6IP1		10470851	Standard	NM_015213		Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000328194.3:c.3845T>C	11.37:g.9161237A>G	ENSP00000328524:p.Val1282Ala	Somatic		WXS	Illumina GAIIx	Phase_I	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Missense_Mutation	SNP	ENST00000328194.3	37	CCDS31423.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.95|14.95	2.687555|2.687555	0.48097|0.48097	.|.	.|.	ENSG00000184014|ENSG00000184014	ENST00000528725;ENST00000533737|ENST00000328194;ENST00000527700	.|T;T	.|0.18960	.|3.66;2.18	5.44|5.44	5.44|5.44	0.79542|0.79542	.|RUN (1);	.|0.111293	.|0.64402	.|D	.|0.000009	T|T	0.24699|0.24699	0.0599|0.0599	L|L	0.51422|0.51422	1.61|1.61	0.49687|0.49687	D|D	0.999812|0.999812	.|B	.|0.27316	.|0.175	.|B	.|0.31016	.|0.123	T|T	0.02713|0.02713	-1.1120|-1.1120	5|10	.|0.51188	.|T	.|0.08	.|.	15.4987|15.4987	0.75677|0.75677	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|1282	.|Q6IQ26	.|DEN5A_HUMAN	P|A	181;190|1282;625	.|ENSP00000328524:V1282A;ENSP00000432549:V625A	.|ENSP00000328524:V1282A	S|V	-|-	1|2	0|0	DENND5A|DENND5A	9117813|9117813	1.000000|1.000000	0.71417|0.71417	0.979000|0.979000	0.43373|0.43373	0.980000|0.980000	0.70556|0.70556	7.576000|7.576000	0.82467|0.82467	2.064000|2.064000	0.61679|0.61679	0.460000|0.460000	0.39030|0.39030	TCA|GTC		0.517	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2		NM_015213	
EPC1	80314	hgsc.bcm.edu;ucsc.edu	37	10	32582523	32582529	+	Frame_Shift_Del	DEL	CTGACCA	CTGACCA	-	rs112553991		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	CTGACCA	CTGACCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr10:32582523_32582529delCTGACCA	ENST00000263062.8	-	3	719_725	c.450_456delTGGTCAG	c.(448-456)agtggtcagfs	p.SGQ150fs	EPC1_ENST00000319778.6_Frame_Shift_Del_p.SGQ150fs|EPC1_ENST00000375110.2_Frame_Shift_Del_p.SGQ100fs	NM_025209.2	NP_079485.1	Q9H2F5	EPC1_HUMAN	enhancer of polycomb homolog 1 (Drosophila)	150					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(5)|urinary_tract(1)	24		Prostate(175;0.0199)				GTTGTACCTGCTGACCACTGCCTTTTT	0.367																																																	0																																										SO:0001589	frameshift_variant	80314			AF277374	CCDS7172.1, CCDS60511.1, CCDS73083.1	10p11	2005-12-12			ENSG00000120616	ENSG00000120616			19876	protein-coding gene	gene with protein product		610999				10976108	Standard	NM_025209		Approved	Epl1	uc001iwg.2	Q9H2F5	OTTHUMG00000017925	ENST00000263062.8:c.450_456delTGGTCAG	10.37:g.32582523_32582529delCTGACCA	ENSP00000263062:p.Ser150fs	Somatic		WXS	Illumina HiSeq	Phase_I	B4DSC3|D3DRX7|Q5VW54|Q5VW56|Q5VW58|Q8NAQ4|Q8NE21|Q96LF4|Q96RR6|Q9H7T7	Frame_Shift_Del	DEL	ENST00000263062.8	37	CCDS7172.1																																																																																				0.367	EPC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047484.1			
EPHB6	2051	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	142563322	142563322	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr7:142563322G>A	ENST00000392957.2	+	8	1826	c.1039G>A	c.(1039-1041)Gtt>Att	p.V347I	EPHB6_ENST00000411471.2_Missense_Mutation_p.V70I|EPHB6_ENST00000442129.1_Missense_Mutation_p.V347I	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	347	Cys-rich.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)	p.V332I(1)		NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					AGCAGCCCCCGTTTGCCCCTG	0.652																																																	1	Substitution - Missense(1)	kidney(1)											36.0	36.0	36.0					7																	142563322		2203	4300	6503	SO:0001583	missense	2051			D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3396	protein-coding gene	gene with protein product		602757	"""EphB6"""				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.1039G>A	7.37:g.142563322G>A	ENSP00000376684:p.Val347Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Missense_Mutation	SNP	ENST00000392957.2	37	CCDS5873.2	.	.	.	.	.	.	.	.	.	.	G	0.019	-1.458269	0.01071	.	.	ENSG00000106123	ENST00000392957;ENST00000442129;ENST00000411471	T;T;T	0.71222	-0.5;-0.5;-0.55	5.43	-8.87	0.00792	.	1.203620	0.06175	N	0.678426	T	0.40546	0.1121	N	0.04705	-0.18	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.34775	-0.9815	10	0.11485	T	0.65	.	9.4073	0.38469	0.5527:0.2561:0.1912:0.0	.	347	O15197	EPHB6_HUMAN	I	347;347;70	ENSP00000376684:V347I;ENSP00000410789:V347I;ENSP00000409061:V70I	ENSP00000376684:V347I	V	+	1	0	EPHB6	142273444	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.698000	0.05092	-1.875000	0.01132	-1.615000	0.00797	GTT		0.652	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			
FLG	2312	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	152283596	152283596	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr1:152283596G>T	ENST00000368799.1	-	3	3801	c.3766C>A	c.(3766-3768)Caa>Aaa	p.Q1256K	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1256	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.Q1256K(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCGATGATTGTTCCTGTCCC	0.572									Ichthyosis																																								1	Substitution - Missense(1)	kidney(1)											276.0	261.0	266.0					1																	152283596		2203	4300	6503	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.3766C>A	1.37:g.152283596G>T	ENSP00000357789:p.Gln1256Lys	Somatic		WXS	Illumina HiSeq	Phase_I	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	3.540	-0.093821	0.07053	.	.	ENSG00000143631	ENST00000368799	T	0.01613	4.73	2.56	-0.918	0.10482	.	.	.	.	.	T	0.00524	0.0017	M	0.69823	2.125	0.09310	N	1	B	0.21452	0.056	B	0.18263	0.021	T	0.50939	-0.8768	9	0.06236	T	0.91	.	0.9171	0.01307	0.1554:0.2329:0.3741:0.2376	.	1256	P20930	FILA_HUMAN	K	1256	ENSP00000357789:Q1256K	ENSP00000357789:Q1256K	Q	-	1	0	FLG	150550220	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.697000	0.05098	0.292000	0.22492	-1.205000	0.01647	CAA		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1		NM_002016	
FRG2B	441581	hgsc.bcm.edu	37	10	135440117	135440119	+	In_Frame_Del	DEL	CTT	CTT	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr10:135440117_135440119delCTT	ENST00000425520.1	-	1	180_182	c.128_130delAAG	c.(127-132)aaaggc>agc	p.43_44KG>S	FRG2B_ENST00000443774.1_In_Frame_Del_p.43_44KG>S	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	43						nucleus (GO:0005634)		p.G44C(1)		endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		GCGGTCTTGCCTTTTTCTTTGAA	0.517																																																	1	Substitution - Missense(1)	lung(1)																																								SO:0001651	inframe_deletion	441581			AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899			33518	protein-coding gene	gene with protein product						15520407	Standard	NM_001080998		Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.128_130delAAG	10.37:g.135440117_135440119delCTT	ENSP00000401310:p.Lys43_Gly44delinsSer	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VSQ1	In_Frame_Del	DEL	ENST00000425520.1	37	CCDS44502.1																																																																																				0.517	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467780.1		NM_001080998	
FRG2B	441581	hgsc.bcm.edu	37	10	135440123	135440124	+	Frame_Shift_Ins	INS	-	-	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr10:135440123_135440124insT	ENST00000425520.1	-	1	175_176	c.123_124insA	c.(121-126)aaagaafs	p.E42fs	FRG2B_ENST00000443774.1_Frame_Shift_Ins_p.E42fs	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	42						nucleus (GO:0005634)				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		TTGCCTTTTTCTTTGAATGGTT	0.515																																																	0																																										SO:0001589	frameshift_variant	441581			AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899			33518	protein-coding gene	gene with protein product						15520407	Standard	NM_001080998		Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.124dupA	10.37:g.135440126_135440126dupT	ENSP00000401310:p.Glu42fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VSQ1	Frame_Shift_Ins	INS	ENST00000425520.1	37	CCDS44502.1																																																																																				0.515	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467780.1		NM_001080998	
GPM6A	2823	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	176556193	176556193	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr4:176556193delC	ENST00000280187.7	-	8	745	c.700delG	c.(700-702)gttfs	p.V234fs	GPM6A_ENST00000515090.1_Frame_Shift_Del_p.V227fs|GPM6A_ENST00000506894.1_Frame_Shift_Del_p.V223fs|GPM6A_ENST00000506219.1_5'UTR|GPM6A_ENST00000393658.2_Frame_Shift_Del_p.V234fs	NM_005277.4	NP_005268.1	P51674	GPM6A_HUMAN	glycoprotein M6A	234					neural retina development (GO:0003407)|neuron migration (GO:0001764)|neuron projection morphogenesis (GO:0048812)|positive regulation of filopodium assembly (GO:0051491)|stem cell differentiation (GO:0048863)|synapse assembly (GO:0007416)	axonal growth cone (GO:0044295)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	calcium channel activity (GO:0005262)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)		GCAGACAGAACCATAAGGTAG	0.413																																																	0													69.0	65.0	67.0					4																	176556193		2203	4300	6503	SO:0001589	frameshift_variant	2823				CCDS3824.1, CCDS54822.1, CCDS58936.1	4q34	2008-08-29				ENSG00000150625			4460	protein-coding gene	gene with protein product		601275		GPM6		8661015, 18574501	Standard	NM_005277		Approved		uc003iug.4	P51674		ENST00000280187.7:c.700delG	4.37:g.176556193delC	ENSP00000280187:p.Val234fs	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z642|E9PHI5|Q92602	Frame_Shift_Del	DEL	ENST00000280187.7	37	CCDS3824.1																																																																																				0.413	GPM6A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362163.1			
KIF1A	547	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	241724433	241724433	+	Missense_Mutation	SNP	G	G	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr2:241724433G>C	ENST00000320389.7	-	7	851	c.693C>G	c.(691-693)gaC>gaG	p.D231E	KIF1A_ENST00000498729.2_Missense_Mutation_p.D231E	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	231	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)	p.D231E(1)		NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		TGGTCTCTGCGTCATGGCGCT	0.607																																																	1	Substitution - Missense(1)	kidney(1)											256.0	266.0	263.0					2																	241724433		2202	4300	6502	SO:0001583	missense	547			AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	888	protein-coding gene	gene with protein product		601255	"""axonal transport of synaptic vesicles"", ""chromosome 2 open reading frame 20"", ""spastic paraplegia 30 (autosomal recessive)"""	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.693C>G	2.37:g.241724433G>C	ENSP00000322791:p.Asp231Glu	Somatic		WXS	Illumina HiSeq	Phase_I	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Missense_Mutation	SNP	ENST00000320389.7	37	CCDS46561.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.00|13.00	2.106668|2.106668	0.37145|0.37145	.|.	.|.	ENSG00000130294|ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308;ENST00000404283|ENST00000428768	T;T;T|.	0.74315|.	-0.83;-0.83;-0.83|.	4.04|4.04	-6.54|-6.54	0.01860|0.01860	Kinesin, motor domain (4);|.	0.059543|.	0.64402|.	U|.	0.000004|.	T|T	0.51534|0.51534	0.1680|0.1680	L|L	0.42744|0.42744	1.35|1.35	0.49915|0.49915	D|D	0.99983|0.99983	B;B;B|.	0.21147|.	0.048;0.02;0.052|.	B;B;B|.	0.23716|.	0.048;0.007;0.022|.	T|T	0.56098|0.56098	-0.8035|-0.8035	10|5	0.72032|.	D|.	0.01|.	.|.	12.6682|12.6682	0.56853|0.56853	0.6434:0.0:0.3566:0.0|0.6434:0.0:0.3566:0.0	.|.	231;231;231|.	F5H045;Q12756-2;Q12756|.	.;.;KIF1A_HUMAN|.	E|G	231|39	ENSP00000322791:D231E;ENSP00000438388:D231E;ENSP00000384231:D231E|.	ENSP00000322791:D231E|.	D|R	-|-	3|1	2|0	KIF1A|KIF1A	241373106|241373106	0.001000|0.001000	0.12720|0.12720	0.827000|0.827000	0.32855|0.32855	0.691000|0.691000	0.40173|0.40173	-1.307000|-1.307000	0.02733|0.02733	-1.005000|-1.005000	0.03417|0.03417	-1.166000|-1.166000	0.01754|0.01754	GAC|CGC		0.607	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3		NM_138483	
KRTAP19-8	728299	hgsc.bcm.edu	37	21	32410670	32410671	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr21:32410670_32410671insC	ENST00000382822.2	-	1	124_125	c.92_93insG	c.(91-93)agcfs	p.S31fs		NM_001099219.1	NP_001092689.1	Q3LI54	KR198_HUMAN	keratin associated protein 19-8	31						intermediate filament (GO:0005882)				endometrium(2)|upper_aerodigestive_tract(1)	3						ACCTGCGGAAGCTGCCATAGCC	0.535																																																	0																																										SO:0001589	frameshift_variant	728299			AB096964	CCDS42917.1	21q22.11	2007-11-23			ENSG00000206102	ENSG00000206102		"""Keratin associated proteins"""	33898	protein-coding gene	gene with protein product							Standard	NM_001099219		Approved		uc010glt.3	Q3LI54	OTTHUMG00000057787	ENST00000382822.2:c.93dupG	21.37:g.32410671_32410671dupC	ENSP00000372272:p.Ser31fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Ins	INS	ENST00000382822.2	37	CCDS42917.1																																																																																				0.535	KRTAP19-8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000128239.3		NM_001099219	
MAML1	9794	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	179201812	179201812	+	Silent	SNP	C	C	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr5:179201812C>G	ENST00000292599.3	+	5	3248	c.2985C>G	c.(2983-2985)tcC>tcG	p.S995S	MAML1_ENST00000503050.1_Intron	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)									p.S995S(1)		central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGATCGACTCCCTGCTGAAGA	0.537																																																	1	Substitution - coding silent(1)	kidney(1)											101.0	93.0	96.0					5																	179201812		2203	4300	6503	SO:0001819	synonymous_variant	9794			D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"""mastermind homolog"""	605424	"""mastermind (drosophila)-like 1"""			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.2985C>G	5.37:g.179201812C>G		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000292599.3	37	CCDS34315.1																																																																																				0.537	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2		NM_014757	
MKLN1	4289	hgsc.bcm.edu;ucsc.edu	37	7	131122679	131122679	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr7:131122679delA	ENST00000352689.6	+	10	1136	c.1096delA	c.(1096-1098)attfs	p.I366fs	MKLN1_ENST00000421797.2_Frame_Shift_Del_p.I274fs	NM_013255.4	NP_037387.2	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing kelch motifs	366					signal transduction (GO:0007165)	cytoplasm (GO:0005737)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28	Melanoma(18;0.162)					TCGTTATGACATTGATACAAA	0.403																																																	0													223.0	213.0	216.0					7																	131122679		2203	4300	6503	SO:0001589	frameshift_variant	4289			AF047489	CCDS34754.1	7q32	2008-07-18			ENSG00000128585	ENSG00000128585			7109	protein-coding gene	gene with protein product		605623				10640805	Standard	NM_001145354		Approved	TWA2	uc011kpm.2	Q9UL63	OTTHUMG00000154880	ENST00000352689.6:c.1096delA	7.37:g.131122679delA	ENSP00000323527:p.Ile366fs	Somatic		WXS	Illumina HiSeq	Phase_I	A4D1M8|A6NG43|Q9NSK4|Q9NUS8	Frame_Shift_Del	DEL	ENST00000352689.6	37	CCDS34754.1																																																																																				0.403	MKLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337473.4		NM_013255	
MRPL4	51073	broad.mit.edu;ucsc.edu	37	19	10370469	10370469	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr19:10370469G>T	ENST00000253099.6	+	9	1203	c.916G>T	c.(916-918)Gcc>Tcc	p.A306S	CTD-2369P2.5_ENST00000592893.1_RNA|MRPL4_ENST00000393733.2_3'UTR|CTD-2369P2.4_ENST00000587088.1_RNA|MRPL4_ENST00000307422.5_Missense_Mutation_p.A306S	NM_015956.2|NM_146388.1	NP_057040.2|NP_666500.1	Q9BYD3	RM04_HUMAN	mitochondrial ribosomal protein L4	306					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.A306S(1)|p.A306fs>4(1)		breast(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11		Renal(1328;0.0112)	OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;1.99e-06)|all cancers(31;4.81e-06)	Lung(535;0.00705)		GGGCCCAGCGGCCACCCCGTA	0.667																																																	2	Substitution - Missense(1)|Deletion - Frameshift(1)	ovary(1)|kidney(1)											51.0	51.0	51.0					19																	10370469		2203	4300	6503	SO:0001583	missense	51073			AB049635	CCDS12230.1, CCDS42499.1	19p13.2	2012-11-14			ENSG00000105364	ENSG00000105364		"""Mitochondrial ribosomal proteins / large subunits"""	14276	protein-coding gene	gene with protein product		611823					Standard	NM_015956		Approved	CGI-28	uc002mnn.3	Q9BYD3	OTTHUMG00000180400	ENST00000253099.6:c.916G>T	19.37:g.10370469G>T	ENSP00000253099:p.Ala306Ser	Somatic		WXS	Illumina GAIIx	Phase_I	A6NNV7|Q9BW07|Q9H4N2|Q9Y317	Missense_Mutation	SNP	ENST00000253099.6	37	CCDS12230.1	.	.	.	.	.	.	.	.	.	.	g	11.21	1.571839	0.28003	.	.	ENSG00000105364	ENST00000253099;ENST00000307422	.	.	.	3.13	0.805	0.18703	.	.	.	.	.	T	0.17023	0.0409	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20472	-1.0274	8	0.87932	D	0	.	4.1345	0.10164	0.1345:0.0:0.6137:0.2518	.	306	Q9BYD3	RM04_HUMAN	S	306	.	ENSP00000253099:A306S	A	+	1	0	MRPL4	10231469	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.127000	0.15790	0.115000	0.18071	-0.422000	0.05995	GCC		0.667	MRPL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451197.1			
KMT2B	9757	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	36221724	36221724	+	Missense_Mutation	SNP	C	C	G	rs540366889		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr19:36221724C>G	ENST00000222270.7	+	26	5393	c.5393C>G	c.(5392-5394)gCa>gGa	p.A1798G	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Missense_Mutation_p.A1798G	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1798					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.A1800G(1)									CTGGAGGCTGCAGAGGAGAAC	0.592																																																	1	Substitution - Missense(1)	kidney(1)											38.0	45.0	43.0					19																	36221724		2076	4200	6276	SO:0001583	missense	9757			AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.5393C>G	19.37:g.36221724C>G	ENSP00000222270:p.Ala1798Gly	Somatic		WXS	Illumina HiSeq	Phase_I	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	37	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	C	12.60	1.985816	0.35036	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.83506	-1.73;-1.73	5.79	4.76	0.60689	.	0.000000	0.44483	D	0.000441	T	0.73063	0.3539	L	0.47716	1.5	0.09310	N	0.999998	B	0.25441	0.126	B	0.16289	0.015	T	0.55630	-0.8111	10	0.16420	T	0.52	.	8.928	0.35652	0.0:0.769:0.1515:0.0795	.	1798	Q9UMN6	MLL4_HUMAN	G	1798	ENSP00000222270:A1798G;ENSP00000398837:A1798G	ENSP00000222270:A1798G	A	+	2	0	AD000671.1	40913564	0.110000	0.22057	0.181000	0.23098	0.818000	0.46254	0.474000	0.22148	2.735000	0.93741	0.655000	0.94253	GCA		0.592	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			NM_014727	
MTMR10	54893	broad.mit.edu;ucsc.edu	37	15	31260141	31260141	+	Missense_Mutation	SNP	T	T	C	rs185348229		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr15:31260141T>C	ENST00000435680.1	-	6	644	c.547A>G	c.(547-549)Aaa>Gaa	p.K183E	MTMR10_ENST00000425768.1_Intron|MTMR10_ENST00000563714.1_Missense_Mutation_p.K101E|MTMR10_ENST00000314404.8_Intron	NM_017762.2	NP_060232.2	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	183							phosphatase activity (GO:0016791)	p.K183E(1)|p.K101E(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;2.81e-11)		all cancers(64;7.26e-15)|Epithelial(43;7.2e-11)|GBM - Glioblastoma multiforme(186;0.000158)|BRCA - Breast invasive adenocarcinoma(123;0.00426)|Lung(196;0.174)		TGGTATTTTTTCCCAACATAT	0.328													T|||	1	0.000199681	0.0	0.0	5008	,	,		19223	0.0		0.001	False		,,,				2504	0.0																2	Substitution - Missense(2)	kidney(2)											44.0	44.0	44.0					15																	31260141		1800	4076	5876	SO:0001583	missense	54893			AK000320	CCDS45204.1	15q13.3	2011-06-09				ENSG00000166912		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	25999	protein-coding gene	gene with protein product						12495846	Standard	NM_017762		Approved	FLJ20313	uc001zfh.1	Q9NXD2		ENST00000435680.1:c.547A>G	15.37:g.31260141T>C	ENSP00000402537:p.Lys183Glu	Somatic		WXS	Illumina GAIIx	Phase_I	Q6P4Q6	Missense_Mutation	SNP	ENST00000435680.1	37	CCDS45204.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	10.04	1.240402	0.22711	.	.	ENSG00000166912	ENST00000435680;ENST00000340566	D	0.92858	-3.12	5.51	4.37	0.52481	.	0.181679	0.38897	N	0.001534	D	0.82300	0.5007	N	0.19112	0.55	0.80722	D	1	B;B	0.10296	0.003;0.002	B;B	0.11329	0.006;0.003	T	0.74300	-0.3710	10	0.18276	T	0.48	.	6.2043	0.20593	0.0:0.1225:0.1554:0.722	.	101;183	Q9NXD2-2;Q9NXD2	.;MTMRA_HUMAN	E	183;101	ENSP00000402537:K183E	ENSP00000340637:K101E	K	-	1	0	MTMR10	29047433	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.673000	0.37534	2.217000	0.71921	0.482000	0.46254	AAA		0.328	MTMR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430747.1		NM_017762	
NEFH	4744	hgsc.bcm.edu	37	22	29885577	29885578	+	In_Frame_Ins	INS	-	-	AGAAGGCCAAGTCCCCTG			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr22:29885577_29885578insAGAAGGCCAAGTCCCCTG	ENST00000310624.6	+	4	1981_1982	c.1948_1949insAGAAGGCCAAGTCCCCTG	c.(1948-1950)gag>gAGAAGGCCAAGTCCCCTGag	p.650_650E>EKAKSPE		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	656	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AAAGTCCCCTGAGAAGGCCAAG	0.564																																																	0																																										SO:0001652	inframe_insertion	4744				CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	Exception_encountered	22.37:g.29885577_29885578insAGAAGGCCAAGTCCCCTG	Exception_encountered	Somatic		WXS	Illumina HiSeq	Phase_I	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	37	CCDS13858.1																																																																																				0.564	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2		NM_021076	
NFE2L2	4780	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	178098960	178098960	+	Missense_Mutation	SNP	C	C	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr2:178098960C>G	ENST00000397062.3	-	2	639	c.85G>C	c.(85-87)Gat>Cat	p.D29H	NFE2L2_ENST00000423513.1_Missense_Mutation_p.D13H|NFE2L2_ENST00000446151.2_Missense_Mutation_p.D13H|NFE2L2_ENST00000464747.1_Missense_Mutation_p.D13H|NFE2L2_ENST00000397063.4_Missense_Mutation_p.D13H	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	29					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D29H(11)|p.D29N(2)|p.D29Y(2)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			ACTCCAAGATCTATATCTTGC	0.363			Mis		"""NSCLC, HNSCC"""					HNSCC(56;0.16)																														Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	15	Substitution - Missense(15)	lung(9)|upper_aerodigestive_tract(3)|cervix(1)|liver(1)|kidney(1)											66.0	59.0	61.0					2																	178098960		1843	4100	5943	SO:0001583	missense	4780				CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"""basic leucine zipper proteins"""	7782	protein-coding gene	gene with protein product	"""NF-E2-related factor 2"""	600492	"""nuclear factor (erythroid-derived 2)-like 2"""			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.85G>C	2.37:g.178098960C>G	ENSP00000380252:p.Asp29His	Somatic		WXS	Illumina HiSeq	Phase_I	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	37	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.072800	0.76415	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000449627;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5;1.5	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.64327	0.2588	M	0.87180	2.865	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.999;0.999	T	0.69087	-0.5238	10	0.87932	D	0	.	19.9976	0.97389	0.0:1.0:0.0:0.0	.	13;13;13;29	E9PGJ7;B4DNB0;C9JFL6;Q16236	.;.;.;NF2L2_HUMAN	H	13;29;13;13;13;13;13	ENSP00000380253:D13H;ENSP00000380252:D29H;ENSP00000411575:D13H;ENSP00000391590:D13H;ENSP00000400073:D13H;ENSP00000412191:D13H;ENSP00000410015:D13H	ENSP00000380252:D29H	D	-	1	0	NFE2L2	177807206	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.487000	0.81328	2.737000	0.93849	0.563000	0.77884	GAT		0.363	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4		NM_006164	
NOTCH2	4853	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	120458045	120458045	+	Missense_Mutation	SNP	A	A	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr1:120458045A>G	ENST00000256646.2	-	34	7519	c.7300T>C	c.(7300-7302)Tct>Cct	p.S2434P		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	2434					apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)	p.S2434P(1)		breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		GACCAGTCAGAAGCAGAGTGG	0.587			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome																															Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	1	Substitution - Missense(1)	kidney(1)											104.0	100.0	102.0					1																	120458045		2203	4300	6503	SO:0001583	missense	4853	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.7300T>C	1.37:g.120458045A>G	ENSP00000256646:p.Ser2434Pro	Somatic		WXS	Illumina HiSeq	Phase_I	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.157426	0.78114	.	.	ENSG00000134250	ENST00000256646	D	0.84223	-1.82	5.66	5.66	0.87406	Domain of unknown function DUF3454, notch (1);	0.000000	0.36134	U	0.002776	D	0.91178	0.7221	M	0.80332	2.49	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92601	0.6091	10	0.87932	D	0	.	15.0762	0.72080	1.0:0.0:0.0:0.0	.	2434	Q04721	NOTC2_HUMAN	P	2434	ENSP00000256646:S2434P	ENSP00000256646:S2434P	S	-	1	0	NOTCH2	120259568	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.262000	0.95591	2.157000	0.67596	0.533000	0.62120	TCT		0.587	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1		NM_024408	
PARN	5073	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	14711480	14711480	+	Nonsense_Mutation	SNP	G	G	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr16:14711480G>A	ENST00000437198.2	-	6	496	c.355C>T	c.(355-357)Cag>Tag	p.Q119*	PARN_ENST00000420015.2_Nonsense_Mutation_p.Q73*|PARN_ENST00000341484.7_Nonsense_Mutation_p.Q58*|PARN_ENST00000539279.1_Intron|PARN_ENST00000566021.1_Intron	NM_001134477.2|NM_002582.3	NP_001127949.1|NP_002573.1	O95453	PARN_HUMAN	poly(A)-specific ribonuclease	119					female gamete generation (GO:0007292)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA metabolic process (GO:0016070)|RNA modification (GO:0009451)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|nuclease activity (GO:0004518)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(A)-specific ribonuclease activity (GO:0004535)|protein kinase binding (GO:0019901)	p.Q119*(2)		cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|urinary_tract(1)	21						TCAAATCCCTGGCTTGCTAGA	0.368																																																	2	Substitution - Nonsense(2)	kidney(2)											68.0	65.0	66.0					16																	14711480		1829	4086	5915	SO:0001587	stop_gained	5073			AJ005698	CCDS45419.1, CCDS45420.1, CCDS58425.1	16p13	2014-08-08	2011-07-07		ENSG00000140694	ENSG00000140694	3.1.13.4		8609	protein-coding gene	gene with protein product	"""deadenylation nuclease"""	604212	"""poly(A)-specific ribonuclease (deadenylation nuclease)"""			10640832	Standard	NM_002582		Approved	DAN	uc010uzd.2	O95453	OTTHUMG00000173199	ENST00000437198.2:c.355C>T	16.37:g.14711480G>A	ENSP00000387911:p.Gln119*	Somatic		WXS	Illumina HiSeq	Phase_I	B2RCB3|B4DDG8|B4DWR4|B4E1H6	Nonsense_Mutation	SNP	ENST00000437198.2	37	CCDS45419.1	.	.	.	.	.	.	.	.	.	.	G	39	7.386878	0.98252	.	.	ENSG00000140694	ENST00000437198;ENST00000341484;ENST00000420015;ENST00000538472	.	.	.	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-15.7619	19.3813	0.94536	0.0:0.0:1.0:0.0	.	.	.	.	X	119;58;73;102	.	ENSP00000345456:Q58X	Q	-	1	0	PARN	14618981	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.465000	0.90383	2.824000	0.97209	0.655000	0.94253	CAG		0.368	PARN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422383.1		NM_002582	
PASD1	139135	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	150842545	150842545	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chrX:150842545G>T	ENST00000370357.4	+	15	2307	c.2062G>T	c.(2062-2064)Gat>Tat	p.D688Y		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	688						nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.D688Y(2)		breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					GACCCCACAGGATTACATCCG	0.498																																																	2	Substitution - Missense(2)	kidney(2)											127.0	117.0	121.0					X																	150842545		2203	4300	6503	SO:0001583	missense	139135			AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"""cancer/testis antigen 63"""					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.2062G>T	X.37:g.150842545G>T	ENSP00000359382:p.Asp688Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	Q3MNE0|Q69HD7|Q8N7X9	Missense_Mutation	SNP	ENST00000370357.4	37	CCDS35431.1	.	.	.	.	.	.	.	.	.	.	G	11.52	1.661900	0.29515	.	.	ENSG00000166049	ENST00000370357	T	0.53206	0.63	3.37	1.59	0.23543	.	.	.	.	.	T	0.49081	0.1536	L	0.27053	0.805	0.09310	N	1	D	0.89917	1.0	D	0.71414	0.973	T	0.30208	-0.9986	9	0.87932	D	0	-12.8714	5.0366	0.14438	0.289:0.0:0.711:0.0	.	688	Q8IV76	PASD1_HUMAN	Y	688	ENSP00000359382:D688Y	ENSP00000359382:D688Y	D	+	1	0	PASD1	150593201	0.001000	0.12720	0.003000	0.11579	0.004000	0.04260	0.699000	0.25586	0.290000	0.22444	-0.192000	0.12808	GAT		0.498	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2		NM_173493	
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52588818	52588818	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr3:52588818delG	ENST00000296302.7	-	27	4532	c.4531delC	c.(4531-4533)cagfs	p.Q1511fs	PBRM1_ENST00000409057.1_Frame_Shift_Del_p.Q1456fs|PBRM1_ENST00000394830.3_Frame_Shift_Del_p.Q1404fs|RNU6-856P_ENST00000516959.1_RNA|PBRM1_ENST00000409767.1_Intron|PBRM1_ENST00000410007.1_Frame_Shift_Del_p.Q1431fs|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000356770.4_Frame_Shift_Del_p.Q1424fs|PBRM1_ENST00000409114.3_Intron|PBRM1_ENST00000337303.4_Intron			Q86U86	PB1_HUMAN	polybromo 1	1511	Pro-rich.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TGAAGTGGCTGCATGCTGCCC	0.592			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	0													49.0	48.0	49.0					3																	52588818		2203	4300	6503	SO:0001589	frameshift_variant	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.4531delC	3.37:g.52588818delG	ENSP00000296302:p.Gln1511fs	Somatic		WXS	Illumina HiSeq	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Del	DEL	ENST00000296302.7	37																																																																																					0.592	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PCDHB10	56126	broad.mit.edu;hgsc.bcm.edu	37	5	140569080	140569080	+	5'Flank	SNP	G	G	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr5:140569080G>T	ENST00000239446.4	+	0	0					NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10						calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GTGCCCGAGGGTCCTTTTCCA	0.657																																																	0													76.0	92.0	86.0					5																	140569080		2203	4300	6503	SO:0001631	upstream_gene_variant	56127			AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"""Cadherins / Protocadherins : Clustered"""	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626		5.37:g.140569080G>T	Exception_encountered	Somatic		WXS	Illumina HiSeq	Phase_I	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1																																																																																				0.657	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1		NM_018930	
PCDHGB4	8641	hgsc.bcm.edu	37	5	140767492	140767497	+	In_Frame_Del	DEL	TGCCAG	TGCCAG	-	rs145222727|rs370380135	byFrequency	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	TGCCAG	TGCCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr5:140767492_140767497delTGCCAG	ENST00000519479.1	+	1	41_46	c.41_46delTGCCAG	c.(40-48)ctgccagtg>ctg	p.PV15del	PCDHGA6_ENST00000517434.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	15					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P15_V16delPV(1)		endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTGAGAGGCTGCCAGTGCTCTTTCT	0.617											OREG0016859	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		166	0.033147	0.0045	0.0476	5008	,	,		16199	0.0		0.0944	False		,,,				2504	0.0327																1	Deletion - In frame(1)	prostate(1)							,,,,,,,,,,,	50,3074		6,38,1518					,,,,,,,,,,,	3.7	0.9		dbSNP_134	6	518,6570		64,390,3090	no	coding,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding	PCDHGB4,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_032098.1,NM_018924.2,NM_018923.2,NM_018922.2,NM_018920.2,NM_018919.2,NM_018918.2,NM_018917.2,NM_018916.3,NM_018915.2,NM_018912.2,NM_003736.2	,,,,,,,,,,,	70,428,4608	A1A1,A1R,RR		7.3081,1.6005,5.5621	,,,,,,,,,,,	,,,,,,,,,,,		568,9644				SO:0001651	inframe_deletion	8641			AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"""Cadherins / Protocadherins : Clustered"""	8711	other	protocadherin	"""fibroblast cadherin FIB2"", ""cadherin 20"""	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.41_46delTGCCAG	5.37:g.140767492_140767497delTGCCAG	ENSP00000428288:p.Pro15_Val16del	Somatic	1658	WXS	Illumina HiSeq	Phase_I	O15099|Q2M267|Q9UN64	In_Frame_Del	DEL	ENST00000519479.1	37	CCDS54928.1																																																																																				0.617	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1		NM_003736	
PDE11A	50940	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	178936671	178936671	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr2:178936671G>A	ENST00000286063.6	-	1	811	c.494C>T	c.(493-495)cCc>cTc	p.P165L	PDE11A_ENST00000358450.4_Intron	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	165					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)	p.P165L(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	TGTGGTGGGGGGCAGGGAGCT	0.577									Primary Pigmented Nodular Adrenocortical Disease, Familial																																								1	Substitution - Missense(1)	kidney(1)											69.0	67.0	68.0					2																	178936671		2203	4300	6503	SO:0001583	missense	50940	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"""Phosphodiesterases"""	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.494C>T	2.37:g.178936671G>A	ENSP00000286063:p.Pro165Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Missense_Mutation	SNP	ENST00000286063.6	37	CCDS33334.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.708416	0.89018	.	.	ENSG00000128655	ENST00000286063	T	0.68624	-0.34	4.92	4.92	0.64577	.	0.384943	0.31936	N	0.006829	T	0.77294	0.4109	L	0.55990	1.75	0.80722	D	1	D	0.76494	0.999	D	0.64144	0.922	T	0.79764	-0.1666	10	0.66056	D	0.02	.	17.1044	0.86658	0.0:0.0:1.0:0.0	.	165	Q9HCR9	PDE11_HUMAN	L	165	ENSP00000286063:P165L	ENSP00000286063:P165L	P	-	2	0	PDE11A	178644917	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.257000	0.95545	2.281000	0.76405	0.655000	0.94253	CCC		0.577	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2			
PENK	5179	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	57354177	57354177	+	Missense_Mutation	SNP	G	G	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr8:57354177G>C	ENST00000314922.3	-	2	534	c.458C>G	c.(457-459)tCc>tGc	p.S153C	PENK_ENST00000523274.1_5'UTR|PENK_ENST00000451791.2_Missense_Mutation_p.S153C	NM_006211.3	NP_006202.1	P01210	PENK_HUMAN	proenkephalin	153					aggressive behavior (GO:0002118)|behavioral fear response (GO:0001662)|locomotory behavior (GO:0007626)|neuropeptide signaling pathway (GO:0007218)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|startle response (GO:0001964)	extracellular region (GO:0005576)	neuropeptide hormone activity (GO:0005184)	p.S153C(1)		central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	21		all_lung(136;0.229)	Epithelial(17;0.000873)|all cancers(17;0.0069)			CAGGTCTGAGGAATTGGCCAG	0.527																																																	1	Substitution - Missense(1)	kidney(1)											108.0	107.0	107.0					8																	57354177		2203	4300	6503	SO:0001583	missense	5179				CCDS6168.1	8q23-q24	2013-02-26				ENSG00000181195		"""Endogenous ligands"""	8831	protein-coding gene	gene with protein product	"""preproenkephalin"""	131330				6281660	Standard	NM_006211		Approved		uc003xsz.2	P01210		ENST00000314922.3:c.458C>G	8.37:g.57354177G>C	ENSP00000324248:p.Ser153Cys	Somatic		WXS	Illumina HiSeq	Phase_I	B2RC23|Q6FHC6|Q6FHE6	Missense_Mutation	SNP	ENST00000314922.3	37	CCDS6168.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.708779	0.48517	.	.	ENSG00000181195	ENST00000539312;ENST00000314922;ENST00000451791	T;T	0.19938	2.11;2.11	5.81	5.81	0.92471	.	0.220511	0.39475	N	0.001355	T	0.43678	0.1258	M	0.67569	2.06	0.80722	D	1	D	0.76494	0.999	P	0.59825	0.864	T	0.17471	-1.0368	10	0.56958	D	0.05	-20.2407	19.0666	0.93114	0.0:0.0:1.0:0.0	.	153	P01210	PENK_HUMAN	C	153	ENSP00000324248:S153C;ENSP00000400894:S153C	ENSP00000324248:S153C	S	-	2	0	PENK	57516731	1.000000	0.71417	0.973000	0.42090	0.358000	0.29455	3.664000	0.54525	2.736000	0.93811	0.655000	0.94253	TCC		0.527	PENK-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378645.1			
PHYH	5264	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	13325777	13325777	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr10:13325777G>T	ENST00000263038.4	-	7	799	c.741C>A	c.(739-741)caC>caA	p.H247Q	PHYH_ENST00000396913.2_Missense_Mutation_p.H147Q|PHYH_ENST00000396920.3_Missense_Mutation_p.H230Q	NM_006214.3	NP_006205.1	O14832	PAHX_HUMAN	phytanoyl-CoA 2-hydroxylase	247					cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|isoprenoid metabolic process (GO:0006720)|methyl-branched fatty acid metabolic process (GO:0097089)|small molecule metabolic process (GO:0044281)	mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|electron carrier activity (GO:0009055)|L-ascorbic acid binding (GO:0031418)|metal ion binding (GO:0046872)|phytanoyl-CoA dioxygenase activity (GO:0048244)	p.H247Q(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	25		Ovarian(717;0.0448)			Antihemophilic Factor(DB00025)|Vitamin C(DB00126)	CCATCACCAGGTGCACCCGGG	0.502																																																	1	Substitution - Missense(1)	kidney(1)											266.0	269.0	268.0					10																	13325777		2203	4300	6503	SO:0001583	missense	5264				CCDS7097.1, CCDS41489.1	10p13	2010-04-27	2006-01-09		ENSG00000107537	ENSG00000107537	1.14.11.18		8940	protein-coding gene	gene with protein product	"""Refsum disease"", ""phytanoyl-CoA dioxygenase"""	602026	"""phytanoyl-CoA hydroxylase (Refsum disease)"", ""phytanoyl-CoA hydroxylase"""			9326939	Standard	XM_005252469		Approved	PAHX, RD, PHYH1	uc001imf.3	O14832	OTTHUMG00000017693	ENST00000263038.4:c.741C>A	10.37:g.13325777G>T	ENSP00000263038:p.His247Gln	Somatic		WXS	Illumina HiSeq	Phase_I	A8MTS8|B1ALH5	Missense_Mutation	SNP	ENST00000263038.4	37	CCDS7097.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.500741	0.64298	.	.	ENSG00000107537	ENST00000396913;ENST00000263038;ENST00000396920;ENST00000453759	D;D;D;D	0.89123	-2.47;-2.47;-2.47;-2.47	5.75	5.75	0.90469	.	0.044760	0.85682	D	0.000000	D	0.94693	0.8288	M	0.88570	2.965	0.80722	D	1	D;D	0.63046	0.966;0.992	P;D	0.71184	0.855;0.972	D	0.94477	0.7690	10	0.49607	T	0.09	-32.2325	13.1752	0.59621	0.0728:0.0:0.9272:0.0	.	230;247	B1ALH6;O14832	.;PAHX_HUMAN	Q	147;247;230;147	ENSP00000380121:H147Q;ENSP00000263038:H247Q;ENSP00000380126:H230Q;ENSP00000412525:H147Q	ENSP00000263038:H247Q	H	-	3	2	PHYH	13365783	1.000000	0.71417	0.993000	0.49108	0.680000	0.39746	2.487000	0.45268	2.707000	0.92482	0.591000	0.81541	CAC		0.502	PHYH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046845.2			
PIF1	80119	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	65114788	65114788	+	Missense_Mutation	SNP	G	G	A	rs201996206		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr15:65114788G>A	ENST00000268043.4	-	3	674	c.580C>T	c.(580-582)Cct>Tct	p.P194S	PIF1_ENST00000559239.1_Missense_Mutation_p.P194S|PIF1_ENST00000333425.6_Missense_Mutation_p.P194S					PIF1 5'-to-3' DNA helicase									p.P194S(2)		kidney(1)|lung(1)	2						CTCTTCACAGGCAGGGGCCAC	0.607																																																	2	Substitution - Missense(2)	kidney(2)											38.0	38.0	38.0					15																	65114788		2202	4299	6501	SO:0001583	missense	80119			AK026345	CCDS10195.2, CCDS66797.1	15q22.1	2013-05-13	2013-05-13	2006-11-24	ENSG00000140451	ENSG00000140451	3.6.4.12		26220	protein-coding gene	gene with protein product		610953	"""chromosome 15 open reading frame 20"", ""PIF1 5'-to-3' DNA helicase homolog (S. cerevisiae)"""	C15orf20		10926538, 16522649	Standard	NM_025049		Approved	FLJ22692	uc002ant.2	Q9H611	OTTHUMG00000132974	ENST00000268043.4:c.580C>T	15.37:g.65114788G>A	ENSP00000268043:p.Pro194Ser	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000268043.4	37	CCDS10195.2	.	.	.	.	.	.	.	.	.	.	G	15.02	2.708494	0.48517	.	.	ENSG00000140451	ENST00000268043;ENST00000333425	T;T	0.54479	0.57;0.57	4.53	4.53	0.55603	.	0.112678	0.56097	D	0.000021	T	0.56426	0.1984	L	0.54323	1.7	0.80722	D	1	D;P	0.57571	0.98;0.704	P;B	0.50617	0.646;0.296	T	0.53592	-0.8417	10	0.29301	T	0.29	-4.1718	15.1739	0.72896	0.0:0.0:1.0:0.0	.	194;194	Q9H611-2;Q9H611	.;PIF1_HUMAN	S	194	ENSP00000268043:P194S;ENSP00000328174:P194S	ENSP00000268043:P194S	P	-	1	0	PIF1	62901841	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.412000	0.44609	2.509000	0.84616	0.561000	0.74099	CCT		0.607	PIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256533.1		NM_025049	
POT1	25913	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	124493109	124493109	+	Silent	SNP	C	C	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr7:124493109C>T	ENST00000357628.3	-	10	1384	c.786G>A	c.(784-786)gaG>gaA	p.E262E	POT1_ENST00000393329.1_Silent_p.E131E	NM_015450.2	NP_056265.2	Q9NUX5	POTE1_HUMAN	protection of telomeres 1	262					DNA duplex unwinding (GO:0032508)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of DNA strand elongation (GO:0060383)|positive regulation of helicase activity (GO:0051096)|positive regulation of telomerase activity (GO:0051973)|positive regulation of telomere maintenance via telomerase (GO:0032212)|telomere capping (GO:0016233)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|single-stranded telomeric DNA binding (GO:0043047)|telomerase inhibitor activity (GO:0010521)	p.E262E(2)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(4)|liver(1)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47						GAAGATGAAACTCTAAACTTA	0.358																																					Esophageal Squamous(149;1032 1141 16047 36610 40540 42429 44687 51642)												2	Substitution - coding silent(2)	kidney(2)											109.0	102.0	104.0					7																	124493109		2203	4300	6503	SO:0001819	synonymous_variant	25913			AK022580	CCDS5793.1	7q31.33	2013-01-21	2013-01-21		ENSG00000128513	ENSG00000128513			17284	protein-coding gene	gene with protein product		606478	"""protection of telomeres 1 homolog (S. pombe)"""			11349150, 12391173	Standard	NR_003102		Approved	hPot1, DKFZp586D211	uc003vlm.3	Q9NUX5	OTTHUMG00000157194	ENST00000357628.3:c.786G>A	7.37:g.124493109C>T		Somatic		WXS	Illumina HiSeq	Phase_I	O95018|Q5MJ36|Q9H662|Q9NW19|Q9UG95	Silent	SNP	ENST00000357628.3	37	CCDS5793.1																																																																																				0.358	POT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347861.1			
PTPDC1	138639	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	96860800	96860800	+	Missense_Mutation	SNP	T	T	A	rs201009690		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr9:96860800T>A	ENST00000375360.3	+	7	2130	c.1790T>A	c.(1789-1791)cTa>cAa	p.L597Q	PTPDC1_ENST00000288976.3_Missense_Mutation_p.L649Q	NM_001253830.1|NM_177995.2	NP_001240759.1|NP_818931.1	A2A3K4	PTPC1_HUMAN	protein tyrosine phosphatase domain containing 1	597					cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)		protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.L649Q(1)|p.L597Q(1)		endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	32						GCCAAAGCCCTAGCAAATTTA	0.388																																																	2	Substitution - Missense(2)	kidney(2)											64.0	71.0	69.0					9																	96860800		2203	4300	6503	SO:0001583	missense	138639			BC051654	CCDS6707.1, CCDS6708.1, CCDS75860.1	9q22.32	2011-06-09			ENSG00000158079	ENSG00000158079		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"""	30184	protein-coding gene	gene with protein product	"""protein tyrosine phosphatase PTP9Q22"""					14702039	Standard	NM_152422		Approved	PTP9Q22, FLJ37312	uc010mrj.2	A2A3K4	OTTHUMG00000020258	ENST00000375360.3:c.1790T>A	9.37:g.96860800T>A	ENSP00000364509:p.Leu597Gln	Somatic		WXS	Illumina HiSeq	Phase_I	Q5T3M4|Q6NXE8|Q8IWM1|Q8N1X4|Q8N9F5	Missense_Mutation	SNP	ENST00000375360.3	37	CCDS6707.1	.	.	.	.	.	.	.	.	.	.	.	21.7	4.193348	0.78902	.	.	ENSG00000158079	ENST00000375360;ENST00000288976	T;T	0.17213	2.29;2.29	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.44074	0.1276	M	0.75264	2.295	0.53688	D	0.999974	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.992;0.997;0.992;0.992	T	0.38628	-0.9652	10	0.87932	D	0	-14.0943	15.7905	0.78357	0.0:0.0:0.0:1.0	.	651;649;651;597	E7EN59;A2A3K4-2;A8K0X7;A2A3K4	.;.;.;PTPC1_HUMAN	Q	597;649	ENSP00000364509:L597Q;ENSP00000288976:L649Q	ENSP00000288976:L649Q	L	+	2	0	PTPDC1	95900621	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.801000	0.75170	2.324000	0.78689	0.533000	0.62120	CTA		0.388	PTPDC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215007.1		NM_177995, NM_152422	
PRRC2B	84726	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	134357757	134357757	+	Splice_Site	SNP	G	G	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr9:134357757G>A	ENST00000357304.4	+	20	5038		c.e20-1		PRRC2B_ENST00000372249.1_Splice_Site|PRRC2B_ENST00000458550.1_Splice_Site|PRRC2B_ENST00000405995.1_Splice_Site	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B								poly(A) RNA binding (GO:0044822)	p.?(2)		cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						GCTCTGCACAGCAGGGTTTTA	0.537																																																	2	Unknown(2)	kidney(2)											132.0	139.0	137.0					9																	134357757		2013	4183	6196	SO:0001630	splice_region_variant	84726			AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.4984-1G>A	9.37:g.134357757G>A		Somatic		WXS	Illumina HiSeq	Phase_I	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Splice_Site	SNP	ENST00000357304.4	37	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	G	16.24	3.068421	0.55539	.	.	ENSG00000130723	ENST00000405995;ENST00000357304;ENST00000458550	.	.	.	4.68	3.77	0.43336	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.0524	0.25081	0.0873:0.0:0.7396:0.173	.	.	.	.	.	-1	.	.	.	+	.	.	PRRC2B	133347578	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.865000	0.48412	0.947000	0.37659	-0.314000	0.08810	.		0.537	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				Intron
RAB33A	9363	broad.mit.edu;hgsc.bcm.edu	37	X	129306194	129306194	+	Missense_Mutation	SNP	C	C	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chrX:129306194C>T	ENST00000257017.4	+	1	572	c.158C>T	c.(157-159)aCc>aTc	p.T53I		NM_004794.2	NP_004785.1	Q14088	RB33A_HUMAN	RAB33A, member RAS oncogene family	53					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.T53I(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(5)	11						ACCTGCCTGACCTTCCGCTTC	0.572																																																	1	Substitution - Missense(1)	kidney(1)											93.0	73.0	80.0					X																	129306194		2203	4300	6503	SO:0001583	missense	9363			D14889	CCDS14621.1	Xq26	2008-02-05			ENSG00000134594	ENSG00000134594		"""RAB, member RAS oncogene"""	9773	protein-coding gene	gene with protein product		300333				7688322, 9512502	Standard	NM_004794		Approved	RabS10	uc004evl.3	Q14088	OTTHUMG00000022391	ENST00000257017.4:c.158C>T	X.37:g.129306194C>T	ENSP00000257017:p.Thr53Ile	Somatic		WXS	Illumina HiSeq	Phase_I	Q5JUZ6|Q92465	Missense_Mutation	SNP	ENST00000257017.4	37	CCDS14621.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.738447	0.89573	.	.	ENSG00000134594	ENST00000257017	T	0.76186	-1.0	4.59	4.59	0.56863	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.66489	0.2794	N	0.00808	-1.17	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82061	-0.0644	10	0.72032	D	0.01	-14.3675	16.9479	0.86235	0.0:1.0:0.0:0.0	.	53	Q14088	RB33A_HUMAN	I	53	ENSP00000257017:T53I	ENSP00000257017:T53I	T	+	2	0	RAB33A	129133875	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.738000	0.55067	2.266000	0.75297	0.600000	0.82982	ACC		0.572	RAB33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058246.1		NM_004794	
RRS1	23212	broad.mit.edu;hgsc.bcm.edu	37	8	67342089	67342089	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr8:67342089G>T	ENST00000320270.2	+	1	827	c.723G>T	c.(721-723)aaG>aaT	p.K241N	RP11-346I3.4_ENST00000499642.1_lincRNA|ADHFE1_ENST00000415254.1_5'Flank|ADHFE1_ENST00000396623.3_5'Flank|ADHFE1_ENST00000379385.4_5'Flank	NM_015169.3	NP_055984.1	Q15050	RRS1_HUMAN	RRS1 ribosome biogenesis regulator homolog (S. cerevisiae)	241					hematopoietic progenitor cell differentiation (GO:0002244)|mitotic metaphase plate congression (GO:0007080)|ribosome biogenesis (GO:0042254)	condensed nuclear chromosome (GO:0000794)|endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.K241N(1)		kidney(2)|lung(2)	4		Lung NSC(129;0.197)	Epithelial(68;0.0391)|all cancers(69;0.0898)|BRCA - Breast invasive adenocarcinoma(89;0.111)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			GCCTCCCCAAGGAGAAGGTGC	0.607																																																	1	Substitution - Missense(1)	kidney(1)											19.0	24.0	23.0					8																	67342089		2192	4293	6485	SO:0001583	missense	23212			BC001811	CCDS6189.1	8q13.1	2013-10-22			ENSG00000179041	ENSG00000179041			17083	protein-coding gene	gene with protein product						7788527, 10688653	Standard	NM_015169		Approved	KIAA0112	uc003xwa.3	Q15050	OTTHUMG00000164765	ENST00000320270.2:c.723G>T	8.37:g.67342089G>T	ENSP00000322396:p.Lys241Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q9BUX8	Missense_Mutation	SNP	ENST00000320270.2	37	CCDS6189.1	.	.	.	.	.	.	.	.	.	.	G	14.59	2.579380	0.46006	.	.	ENSG00000179041	ENST00000320270	D	0.87179	-2.22	5.56	4.68	0.58851	.	0.046425	0.85682	D	0.000000	D	0.83501	0.5268	L	0.43646	1.37	0.58432	D	0.999999	P	0.34462	0.454	B	0.39379	0.298	T	0.79374	-0.1830	10	0.22109	T	0.4	-29.9676	12.9467	0.58376	0.0785:0.0:0.9215:0.0	.	241	Q15050	RRS1_HUMAN	N	241	ENSP00000322396:K241N	ENSP00000322396:K241N	K	+	3	2	RRS1	67504643	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	1.992000	0.40737	1.360000	0.45960	0.650000	0.86243	AAG		0.607	RRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380126.1		NM_015169	
SAFB2	9667	broad.mit.edu;ucsc.edu	37	19	5613494	5613494	+	Silent	SNP	C	C	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr19:5613494C>T	ENST00000252542.4	-	5	852	c.588G>A	c.(586-588)ttG>ttA	p.L196L	SAFB2_ENST00000591310.1_5'Flank	NM_014649.2	NP_055464.1	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	196					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.L196L(1)		endometrium(3)|kidney(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		CTTTGAAGTTCAACGATGAAG	0.418																																					Ovarian(127;888 1728 23957 44128 52668)												1	Substitution - coding silent(1)	kidney(1)											139.0	114.0	122.0					19																	5613494		2203	4300	6503	SO:0001819	synonymous_variant	9667			D50928	CCDS32879.1	19p13.3	2013-02-12				ENSG00000130254		"""RNA binding motif (RRM) containing"""	21605	protein-coding gene	gene with protein product		608066				12660241	Standard	NM_014649		Approved	KIAA0138	uc002mcd.3	Q14151		ENST00000252542.4:c.588G>A	19.37:g.5613494C>T		Somatic		WXS	Illumina GAIIx	Phase_I	B4DKG3|Q8TB13	Silent	SNP	ENST00000252542.4	37	CCDS32879.1																																																																																				0.418	SAFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451016.1		NM_014649	
SCUBE2	57758	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	9091015	9091015	+	Missense_Mutation	SNP	T	T	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr11:9091015T>A	ENST00000309263.3	-	5	617	c.545A>T	c.(544-546)cAc>cTc	p.H182L	SCUBE2_ENST00000520467.1_Missense_Mutation_p.H182L|SCUBE2_ENST00000457346.2_Missense_Mutation_p.H182L|SCUBE2_ENST00000450649.2_Missense_Mutation_p.H182L			Q9NQ36	SCUB2_HUMAN	signal peptide, CUB domain, EGF-like 2	182	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.H182L(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(15)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		ACTACAGCCGTGATCCTTATT	0.577																																																	1	Substitution - Missense(1)	kidney(1)											122.0	108.0	113.0					11																	9091015		2201	4296	6497	SO:0001583	missense	57758			AK131552	CCDS7797.1, CCDS7797.2, CCDS53599.1	11p15.4	2014-09-04			ENSG00000175356	ENSG00000175356			30425	protein-coding gene	gene with protein product		611747				12270931, 11528127	Standard	NM_020974		Approved	Cegf1, Cegb1, FLJ16792	uc001mhi.2	Q9NQ36	OTTHUMG00000163880	ENST00000309263.3:c.545A>T	11.37:g.9091015T>A	ENSP00000310658:p.His182Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q2NKQ8|Q6ZWI1	Missense_Mutation	SNP	ENST00000309263.3	37		.	.	.	.	.	.	.	.	.	.	T	29.1	4.977091	0.92982	.	.	ENSG00000175356	ENST00000457346;ENST00000309263;ENST00000450649;ENST00000520467	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	4.79	4.79	0.61399	Epidermal growth factor-like (1);	0.000000	0.85682	D	0.000000	D	0.92280	0.7551	M	0.82630	2.6	0.80722	D	1	B;P;D	0.69078	0.357;0.635;0.997	B;P;P	0.60173	0.316;0.495;0.87	D	0.92126	0.5708	10	0.38643	T	0.18	.	14.6129	0.68529	0.0:0.0:0.0:1.0	.	182;182;182	Q9NQ36-3;Q9NQ36-2;Q9NQ36	.;.;SCUB2_HUMAN	L	182	ENSP00000390481:H182L;ENSP00000310658:H182L;ENSP00000415187:H182L;ENSP00000429969:H182L	ENSP00000310658:H182L	H	-	2	0	SCUBE2	9047591	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	7.854000	0.86942	1.926000	0.55796	0.533000	0.62120	CAC		0.577	SCUBE2-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000385812.2		NM_020974	
SELE	6401	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	169701065	169701065	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr1:169701065G>A	ENST00000333360.7	-	4	579	c.440C>T	c.(439-441)tCc>tTc	p.S147F	SELE_ENST00000367774.1_Missense_Mutation_p.S147F|SELE_ENST00000367782.4_Missense_Mutation_p.S147F|SELE_ENST00000367776.1_Missense_Mutation_p.S147F|SELE_ENST00000367775.1_Missense_Mutation_p.S147F|SELE_ENST00000367780.4_Missense_Mutation_p.S147F|SELE_ENST00000367777.1_Missense_Mutation_p.S147F|C1orf112_ENST00000498289.1_Intron|SELE_ENST00000367779.4_Missense_Mutation_p.S147F|SELE_ENST00000367781.4_Missense_Mutation_p.S147F	NM_000450.2	NP_000441.2	P16581	LYAM2_HUMAN	selectin E	147	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				actin filament-based process (GO:0030029)|activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of receptor internalization (GO:0002092)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)	caveola (GO:0005901)|coated pit (GO:0005905)|cortical cytoskeleton (GO:0030863)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	oligosaccharide binding (GO:0070492)|phospholipase binding (GO:0043274)|sialic acid binding (GO:0033691)|transmembrane signaling receptor activity (GO:0004888)	p.S147F(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(3)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	all_hematologic(923;0.208)				Carvedilol(DB01136)	GCCACTGCAGGATGTATTGGT	0.443																																																	1	Substitution - Missense(1)	kidney(1)											117.0	99.0	105.0					1																	169701065		2203	4300	6503	SO:0001583	missense	6401			M30640	CCDS1283.1	1q22-q25	2008-07-31	2008-07-31		ENSG00000007908	ENSG00000007908		"""CD molecules"""	10718	protein-coding gene	gene with protein product		131210	"""endothelial adhesion molecule 1"""	ELAM1, ELAM		1375831	Standard	NM_000450		Approved	ESEL, CD62E	uc001ggm.4	P16581	OTTHUMG00000034851	ENST00000333360.7:c.440C>T	1.37:g.169701065G>A	ENSP00000331736:p.Ser147Phe	Somatic		WXS	Illumina HiSeq	Phase_I	A2RRD6|P16111	Missense_Mutation	SNP	ENST00000333360.7	37	CCDS1283.1	.	.	.	.	.	.	.	.	.	.	G	17.28	3.348803	0.61183	.	.	ENSG00000007908	ENST00000367781;ENST00000367782;ENST00000367780;ENST00000367779;ENST00000333360;ENST00000367777;ENST00000367775;ENST00000367776;ENST00000367774	D;D;D;D;D;D;D;D;D	0.92348	-3.02;-3.02;-3.02;-3.02;-3.02;-3.02;-3.02;-3.02;-3.02	5.5	5.5	0.81552	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.40144	N	0.001175	D	0.96716	0.8928	M	0.90922	3.16	0.58432	D	0.99999	D	0.89917	1.0	D	0.87578	0.998	D	0.97318	0.9942	10	0.87932	D	0	-15.8882	16.9766	0.86315	0.0:0.0:1.0:0.0	.	147	P16581	LYAM2_HUMAN	F	147	ENSP00000356755:S147F;ENSP00000356756:S147F;ENSP00000356754:S147F;ENSP00000356753:S147F;ENSP00000331736:S147F;ENSP00000356751:S147F;ENSP00000356749:S147F;ENSP00000356750:S147F;ENSP00000356748:S147F	ENSP00000331736:S147F	S	-	2	0	SELE	167967689	1.000000	0.71417	0.989000	0.46669	0.457000	0.32468	4.909000	0.63314	2.601000	0.87937	0.586000	0.80456	TCC		0.443	SELE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084333.1		NM_000450	
SETX	23064	broad.mit.edu;ucsc.edu	37	9	135202159	135202159	+	Missense_Mutation	SNP	C	C	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr9:135202159C>A	ENST00000224140.5	-	10	5008	c.4826G>T	c.(4825-4827)gGt>gTt	p.G1609V	SETX_ENST00000393220.1_Missense_Mutation_p.G1609V|SETX_ENST00000372169.2_Missense_Mutation_p.G1609V	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	1609					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.G1609V(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		TTTAGAAAGACCAGCAATTCG	0.408																																																	1	Substitution - Missense(1)	kidney(1)											100.0	96.0	97.0					9																	135202159		2203	4300	6503	SO:0001583	missense	23064			AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"""amyotrophic lateral sclerosis 4"", ""spinocerebellar ataxia, recessive, non-Friedreich type 1"""	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.4826G>T	9.37:g.135202159C>A	ENSP00000224140:p.Gly1609Val	Somatic		WXS	Illumina GAIIx	Phase_I	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	C	5.181	0.218920	0.09810	.	.	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	D;D;D	0.86230	-1.99;-2.09;-1.7	4.72	-0.998	0.10212	.	1.919010	0.02419	N	0.082386	T	0.78253	0.4254	N	0.22421	0.69	0.22926	N	0.998557	B;B;B	0.34015	0.435;0.037;0.062	B;B;B	0.33620	0.167;0.023;0.052	T	0.65973	-0.6038	10	0.31617	T	0.26	.	6.0283	0.19667	0.0:0.4118:0.24:0.3482	.	1609;1609;1609	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	V	1609	ENSP00000224140:G1609V;ENSP00000361242:G1609V;ENSP00000376913:G1609V	ENSP00000224140:G1609V	G	-	2	0	SETX	134191980	0.000000	0.05858	0.338000	0.25549	0.215000	0.24574	-0.284000	0.08422	-0.109000	0.12044	-0.302000	0.09304	GGT		0.408	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3		NM_015046	
SH3RF1	57630	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	170190302	170190302	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr4:170190302G>A	ENST00000284637.9	-	2	403	c.62C>T	c.(61-63)gCt>gTt	p.A21V	SH3RF1_ENST00000508685.1_5'Flank	NM_020870.3	NP_065921.2	Q7Z6J0	SH3R1_HUMAN	SH3 domain containing ring finger 1	21					negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|protein ubiquitination (GO:0016567)|regulation of JNK cascade (GO:0046328)	cell projection (GO:0042995)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.A21V(1)		NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31		Prostate(90;0.00267)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)		CTTCGCAGAAGCATCAAGGCG	0.458																																																	1	Substitution - Missense(1)	kidney(1)											62.0	62.0	62.0					4																	170190302		2203	4300	6503	SO:0001583	missense	57630			BC033203	CCDS34099.1	4q32.3	2013-01-09	2006-02-13	2006-02-13	ENSG00000154447	ENSG00000154447		"""RING-type (C3HC4) zinc fingers"""	17650	protein-coding gene	gene with protein product	"""plenty of SH3 domains"""		"""SH3 multiple domains 2"""	SH3MD2		9482736	Standard	NM_020870		Approved	POSH, RNF142, KIAA1494	uc003isa.1	Q7Z6J0	OTTHUMG00000161010	ENST00000284637.9:c.62C>T	4.37:g.170190302G>A	ENSP00000284637:p.Ala21Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q05BT2|Q8IW46|Q9HAM2|Q9P234	Missense_Mutation	SNP	ENST00000284637.9	37	CCDS34099.1	.	.	.	.	.	.	.	.	.	.	G	17.33	3.361191	0.61403	.	.	ENSG00000154447	ENST00000284637;ENST00000502315;ENST00000510806	D;D;D	0.86030	-2.06;-2.06;-2.06	5.24	4.39	0.52855	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	T	0.76521	0.3999	N	0.19112	0.55	0.58432	D	0.999999	B	0.28470	0.213	B	0.34824	0.19	T	0.69614	-0.5098	10	0.16420	T	0.52	-9.8633	14.1581	0.65430	0.0732:0.0:0.9268:0.0	.	21	Q7Z6J0	SH3R1_HUMAN	V	21	ENSP00000284637:A21V;ENSP00000427585:A21V;ENSP00000421714:A21V	ENSP00000284637:A21V	A	-	2	0	SH3RF1	170426877	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.967000	0.87967	1.198000	0.43158	0.561000	0.74099	GCT		0.458	SH3RF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363382.3		NM_020870	
SLC7A2	6542	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	17409424	17409424	+	Silent	SNP	G	G	A	rs573592866		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr8:17409424G>A	ENST00000494857.1	+	7	1202	c.984G>A	c.(982-984)gcG>gcA	p.A328A	SLC7A2_ENST00000470360.1_Silent_p.A368A|SLC7A2_ENST00000398090.3_Silent_p.A368A|SLC7A2_ENST00000004531.10_Silent_p.A368A|SLC7A2_ENST00000522656.1_Silent_p.A328A	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	328					amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|macrophage activation (GO:0042116)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide production involved in inflammatory response (GO:0002537)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	basic amino acid transmembrane transporter activity (GO:0015174)|high-affinity arginine transmembrane transporter activity (GO:0005289)|L-lysine transmembrane transporter activity (GO:0015189)|L-ornithine transmembrane transporter activity (GO:0000064)	p.A328A(1)|p.A368A(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|stomach(1)	25				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)	TTCCTGTAGCGTTTGAATATG	0.502																																																	2	Substitution - coding silent(2)	kidney(2)											135.0	131.0	132.0					8																	17409424		2203	4300	6503	SO:0001819	synonymous_variant	6542			D29990	CCDS6002.2, CCDS34852.1, CCDS55203.1	8p22	2013-05-22			ENSG00000003989	ENSG00000003989		"""Solute carriers"""	11060	protein-coding gene	gene with protein product		601872		ATRC2		8954799	Standard	NM_001164771		Approved	CAT-2, HCAT2	uc011kye.2	P52569	OTTHUMG00000130819	ENST00000494857.1:c.984G>A	8.37:g.17409424G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Silent	SNP	ENST00000494857.1	37	CCDS34852.1																																																																																				0.502	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3		NM_003046	
SLC7A3	84889	broad.mit.edu;ucsc.edu	37	X	70147708	70147708	+	Missense_Mutation	SNP	A	A	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chrX:70147708A>C	ENST00000374299.3	-	6	1127	c.983T>G	c.(982-984)aTt>aGt	p.I328S	SLC7A3_ENST00000298085.4_Missense_Mutation_p.I328S			Q8WY07	CTR3_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 3	328					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)|L-lysine transmembrane transporter activity (GO:0015189)	p.I328S(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|urinary_tract(1)	31	Renal(35;0.156)				L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	AGCCCATCCAATGTAGAGAAA	0.493																																																	1	Substitution - Missense(1)	kidney(1)											66.0	54.0	58.0					X																	70147708		2202	4297	6499	SO:0001583	missense	84889			AF320612	CCDS14404.1	Xq12	2013-05-22			ENSG00000165349	ENSG00000165349		"""Solute carriers"""	11061	protein-coding gene	gene with protein product		300443				11591158	Standard	NM_001048164		Approved	CAT-3, ATRC3, FLJ14541	uc004dyn.3	Q8WY07	OTTHUMG00000021780	ENST00000374299.3:c.983T>G	X.37:g.70147708A>C	ENSP00000363417:p.Ile328Ser	Somatic		WXS	Illumina GAIIx	Phase_I	D3DVU7|Q5JQR2|Q8N185|Q8NCA7|Q96SZ7	Missense_Mutation	SNP	ENST00000374299.3	37	CCDS14404.1	.	.	.	.	.	.	.	.	.	.	A	9.804	1.181433	0.21787	.	.	ENSG00000165349	ENST00000374299;ENST00000298085	D;D	0.89617	-2.54;-2.54	5.15	-1.89	0.07689	Amino acid permease domain (1);	0.555395	0.19643	N	0.109416	D	0.84772	0.5546	M	0.63169	1.94	0.09310	N	1	B	0.12630	0.006	B	0.32149	0.141	T	0.74399	-0.3678	10	0.51188	T	0.08	.	5.0068	0.14291	0.4985:0.2645:0.237:0.0	.	328	Q8WY07	CTR3_HUMAN	S	328	ENSP00000363417:I328S;ENSP00000298085:I328S	ENSP00000298085:I328S	I	-	2	0	SLC7A3	70064433	0.571000	0.26659	0.000000	0.03702	0.724000	0.41520	4.225000	0.58600	-0.667000	0.05303	-1.639000	0.00775	ATT		0.493	SLC7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057080.1		NM_032803	
SLCO4A1	28231	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	61299368	61299368	+	Missense_Mutation	SNP	A	A	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr20:61299368A>T	ENST00000370507.1	+	8	1739	c.1643A>T	c.(1642-1644)tAc>tTc	p.Y548F	SLCO4A1_ENST00000470412.1_3'UTR|RP11-93B14.5_ENST00000451648.1_RNA|RP11-93B14.5_ENST00000433126.1_RNA|RP11-93B14.5_ENST00000411824.1_RNA|SLCO4A1_ENST00000217159.1_Missense_Mutation_p.Y548F			Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family, member 4A1	548	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.Y548F(1)		endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(3)|prostate(2)	21	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)		Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	TCCCAGGTGTACCGAGACTGT	0.582																																					Pancreas(168;741 2006 10379 40139 45334)												1	Substitution - Missense(1)	kidney(1)											179.0	171.0	174.0					20																	61299368		2203	4300	6503	SO:0001583	missense	28231			AB031051	CCDS13501.1	20q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000101187	ENSG00000101187		"""Solute carriers"""	10953	protein-coding gene	gene with protein product		612436	"""solute carrier family 21 (organic anion transporter), member 12"""	SLC21A12		10873595	Standard	NM_016354		Approved	OATP-E, OATP4A1	uc002ydb.1	Q96BD0	OTTHUMG00000032923	ENST00000370507.1:c.1643A>T	20.37:g.61299368A>T	ENSP00000359538:p.Tyr548Phe	Somatic		WXS	Illumina HiSeq	Phase_I	Q9H4T7|Q9H4T8|Q9H8P2|Q9NWX8|Q9UI35|Q9UIG7	Missense_Mutation	SNP	ENST00000370507.1	37	CCDS13501.1	.	.	.	.	.	.	.	.	.	.	A	15.30	2.793673	0.50102	.	.	ENSG00000101187	ENST00000217159;ENST00000370512;ENST00000370507;ENST00000342674	T;T	0.04119	3.7;3.7	4.97	4.97	0.65823	Proteinase inhibitor I1, Kazal (1);Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);Protease inhibitor, Kazal-type (1);	0.140112	0.49305	D	0.000147	T	0.06462	0.0166	L	0.46885	1.475	0.51012	D	0.999907	B	0.14805	0.011	B	0.23574	0.047	T	0.30707	-0.9969	10	0.15952	T	0.53	.	14.6308	0.68655	1.0:0.0:0.0:0.0	.	548	Q96BD0	SO4A1_HUMAN	F	548;548;548;400	ENSP00000217159:Y548F;ENSP00000359538:Y548F	ENSP00000217159:Y548F	Y	+	2	0	SLCO4A1	60769813	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	3.018000	0.49625	1.850000	0.53721	0.482000	0.46254	TAC		0.582	SLCO4A1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080048.2		NM_016354	
SLIT2	9353	broad.mit.edu;ucsc.edu	37	4	20512749	20512749	+	Silent	SNP	T	T	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr4:20512749T>C	ENST00000504154.1	+	11	1299	c.1047T>C	c.(1045-1047)tcT>tcC	p.S349S	SLIT2_ENST00000273739.5_Silent_p.S353S|SLIT2_ENST00000503837.1_Silent_p.S353S|SLIT2_ENST00000503823.1_Silent_p.S349S	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	349					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)	p.S349S(1)		NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						GACTACGCTCTCTGAATTCAC	0.383																																																	1	Substitution - coding silent(1)	kidney(1)											88.0	86.0	87.0					4																	20512749		2203	4300	6503	SO:0001819	synonymous_variant	9353			AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.1047T>C	4.37:g.20512749T>C		Somatic		WXS	Illumina GAIIx	Phase_I	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Silent	SNP	ENST00000504154.1	37	CCDS3426.1																																																																																				0.383	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			
SRP72	6731	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	57349375	57349375	+	Missense_Mutation	SNP	C	C	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr4:57349375C>T	ENST00000342756.5	+	9	1617	c.896C>T	c.(895-897)tCc>tTc	p.S299F	SRP72_ENST00000510663.1_Missense_Mutation_p.S238F	NM_006947.3	NP_008878.3	O76094	SRP72_HUMAN	signal recognition particle 72kDa	299					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)	p.S299F(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(7)|ovary(2)	22	Glioma(25;0.08)|all_neural(26;0.101)					TTTAAGCTTTCCAAGAAACAA	0.348																																																	1	Substitution - Missense(1)	kidney(1)											77.0	76.0	76.0					4																	57349375		2203	4299	6502	SO:0001583	missense	6731			AF069765	CCDS3506.1, CCDS58898.1	4q11	2013-01-10	2002-08-29		ENSG00000174780	ENSG00000174780		"""Tetratricopeptide (TTC) repeat domain containing"""	11303	protein-coding gene	gene with protein product		602122	"""signal recognition particle 72kD"""			9224693, 9857079	Standard	NM_006947		Approved		uc003hbv.3	O76094	OTTHUMG00000128843	ENST00000342756.5:c.896C>T	4.37:g.57349375C>T	ENSP00000342181:p.Ser299Phe	Somatic		WXS	Illumina HiSeq	Phase_I	G5E9Z8|Q7Z3C0	Missense_Mutation	SNP	ENST00000342756.5	37	CCDS3506.1	.	.	.	.	.	.	.	.	.	.	C	19.82	3.898229	0.72639	.	.	ENSG00000174780	ENST00000342756;ENST00000537129;ENST00000510663	T;T	0.80123	-1.34;-1.26	5.72	5.72	0.89469	.	0.159818	0.56097	D	0.000029	T	0.76328	0.3972	L	0.35854	1.095	0.41235	D	0.986605	P;B	0.51057	0.941;0.083	P;B	0.51385	0.668;0.034	T	0.71839	-0.4471	10	0.06494	T	0.89	.	13.0113	0.58733	0.0:0.8379:0.1621:0.0	.	238;299	G5E9Z8;O76094	.;SRP72_HUMAN	F	299;244;238	ENSP00000342181:S299F;ENSP00000424576:S238F	ENSP00000342181:S299F	S	+	2	0	SRP72	57044132	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.800000	0.62524	2.694000	0.91930	0.655000	0.94253	TCC		0.348	SRP72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250782.7			
TMEM59	9528	broad.mit.edu;ucsc.edu|broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	54509109	54509110	+	Missense_Mutation	DNP	GC	GC	AT			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr1:54509109_54509110GC>AT	ENST00000234831.5	-	4	728_729	c.479_480GC>AT	c.(478-480)aGC>aAT	p.S160N	TMEM59_ENST00000371348.1_Missense_Mutation_p.S29N|TMEM59_ENST00000371341.1_Missense_Mutation_p.S29N|TMEM59_ENST00000371344.1_Missense_Mutation_p.S29N	NM_004872.3	NP_004863.2	Q9BXS4	TMM59_HUMAN	transmembrane protein 59	160					autophagy (GO:0006914)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of protein glycosylation in Golgi (GO:0090285)|negative regulation of protein processing (GO:0010955)|positive regulation of autophagy (GO:0010508)	extracellular vesicular exosome (GO:0070062)|Golgi cis cisterna (GO:0000137)|Golgi medial cisterna (GO:0005797)|Golgi trans cisterna (GO:0000138)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	endopeptidase activity (GO:0004175)	p.S160N(1)|p.S160S(1)		kidney(3)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7						AGGTTATGAAGCTCTGTGCGGA	0.396																																																	2	Substitution - Missense(1)|Substitution - coding silent(1)	kidney(2)																																								SO:0001583	missense	9528			AF047439	CCDS586.1	1p32.3	2008-05-14	2005-07-22	2005-07-22	ENSG00000116209	ENSG00000116209			1239	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 8"""	C1orf8		9653160	Standard	NM_004872		Approved	HSPC001	uc001cwp.3	Q9BXS4	OTTHUMG00000008437	ENST00000234831.5:c.479_480delinsAT	1.37:g.54509109_54509110delinsAT	ENSP00000234831:p.Ser160Asn	Somatic		WXS	Illumina GAIIx|Illumina HiSeq	Phase_I	B3KQL7|O75393|Q4VBP9|Q5T705|Q96KX7	Silent|Missense_Mutation	SNP	ENST00000234831.5	37	CCDS586.1																																																																																				0.396	TMEM59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023254.2		NM_004872	
WDFY3	23001	hgsc.bcm.edu;ucsc.edu	37	4	85738690	85738690	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr4:85738690delT	ENST00000295888.4	-	13	2149	c.1742delA	c.(1741-1743)aagfs	p.K581fs	WDFY3_ENST00000322366.6_Frame_Shift_Del_p.K581fs	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	581					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		TTGAGGGTACTTTACTATATT	0.448																																																	0													130.0	129.0	129.0					4																	85738690		2203	4300	6503	SO:0001589	frameshift_variant	23001			AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.1742delA	4.37:g.85738690delT	ENSP00000295888:p.Lys581fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Frame_Shift_Del	DEL	ENST00000295888.4	37	CCDS3609.1																																																																																				0.448	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2		NM_014991	
ZNF331	55422	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	54080261	54080261	+	Missense_Mutation	SNP	T	T	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr19:54080261T>G	ENST00000253144.9	+	7	1780	c.447T>G	c.(445-447)caT>caG	p.H149Q	ZNF331_ENST00000512387.1_Missense_Mutation_p.H149Q|ZNF331_ENST00000513265.1_Intron|ZNF331_ENST00000449416.1_Missense_Mutation_p.H149Q|ZNF331_ENST00000513999.1_Missense_Mutation_p.H149Q|ZNF331_ENST00000511593.2_Missense_Mutation_p.H149Q|ZNF331_ENST00000511154.1_Missense_Mutation_p.H149Q|ZNF331_ENST00000411977.2_Missense_Mutation_p.H149Q	NM_001253801.1|NM_018555.5	NP_001240730.1|NP_061025.5	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	149					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.H149Q(1)		NS(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	10				GBM - Glioblastoma multiforme(134;0.00555)		TTAGTCAACATCAGAAAATCC	0.413			T	?	follicular thyroid adenoma																																			Dom	yes		19	19q13.3-q13.4	55422	zinc finger protein 331		E	1	Substitution - Missense(1)	kidney(1)											98.0	104.0	102.0					19																	54080261		2203	4300	6503	SO:0001583	missense	55422			AF251515	CCDS33102.1	19q13	2013-12-10				ENSG00000130844		"""Zinc fingers, C2H2-type"", ""-"""	15489	protein-coding gene	gene with protein product	"""rearranged in thyroid adenomas"""	606043					Standard	NM_001079906		Approved	RITA, ZNF463, ZNF361	uc021uzh.1	Q9NQX6		ENST00000253144.9:c.447T>G	19.37:g.54080261T>G	ENSP00000253144:p.His149Gln	Somatic		WXS	Illumina HiSeq	Phase_I	Q96GJ4	Missense_Mutation	SNP	ENST00000253144.9	37	CCDS33102.1	.	.	.	.	.	.	.	.	.	.	T	15.82	2.945267	0.53079	.	.	ENSG00000130844	ENST00000253144;ENST00000511593;ENST00000449416;ENST00000411977;ENST00000511154;ENST00000513999;ENST00000512387;ENST00000514022;ENST00000505949	D;D;D;D;D;D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18	3.68	0.303	0.15791	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35903	N	0.002920	D	0.94364	0.8188	H	0.97214	3.96	0.24470	N	0.994396	D	0.89917	1.0	D	0.77557	0.99	D	0.86899	0.2053	10	0.87932	D	0	.	6.7817	0.23650	0.0:0.3291:0.0:0.6709	.	149	Q9NQX6	ZN331_HUMAN	Q	149	ENSP00000253144:H149Q;ENSP00000427439:H149Q;ENSP00000393817:H149Q;ENSP00000393336:H149Q;ENSP00000421014:H149Q;ENSP00000423156:H149Q;ENSP00000421728:H149Q;ENSP00000422471:H149Q;ENSP00000427532:H149Q	ENSP00000253144:H149Q	H	+	3	2	ZNF331	58772073	0.013000	0.17824	0.926000	0.36857	0.940000	0.58332	0.055000	0.14229	-0.115000	0.11915	0.460000	0.39030	CAT		0.413	ZNF331-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371366.1		NM_018555	
ZNF704	619279	hgsc.bcm.edu;ucsc.edu	37	8	81577290	81577298	+	In_Frame_Del	DEL	ATCACTGTA	ATCACTGTA	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	ATCACTGTA	ATCACTGTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr8:81577290_81577298delATCACTGTA	ENST00000327835.3	-	6	910_918	c.679_687delTACAGTGAT	c.(679-687)tacagtgatdel	p.YSD227del	ZNF704_ENST00000520336.1_5'Flank	NM_001033723.2	NP_001028895.1	Q6ZNC4	ZN704_HUMAN	zinc finger protein 704	227							metal ion binding (GO:0046872)			lung(9)|skin(1)|upper_aerodigestive_tract(1)	11	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)			CCTCTTCTCCATCACTGTAGTCAGAGTCT	0.493																																																	0																																										SO:0001651	inframe_deletion	619279			AK131274	CCDS34913.1	8q21.13	2008-05-02			ENSG00000164684	ENSG00000164684			32291	protein-coding gene	gene with protein product							Standard	NM_001033723		Approved	FLJ16218, Gig1	uc003yby.2	Q6ZNC4	OTTHUMG00000164733	ENST00000327835.3:c.679_687delTACAGTGAT	8.37:g.81577290_81577298delATCACTGTA	ENSP00000331462:p.Tyr227_Asp229del	Somatic		WXS	Illumina HiSeq	Phase_I	B2RNE6|B9EGW6	In_Frame_Del	DEL	ENST00000327835.3	37	CCDS34913.1																																																																																				0.493	ZNF704-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379964.2		NM_001033723	
ZNF805	390980	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	57752278	57752278	+	Missense_Mutation	SNP	G	G	T	rs533627612		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr19:57752278G>T	ENST00000414468.2	+	1	19	c.19G>T	c.(19-21)Gac>Tac	p.D7Y	ZNF805_ENST00000535550.1_5'UTR|ZNF805_ENST00000354309.4_5'UTR	NM_001023563.3	NP_001018857.2	Q5CZA5	ZN805_HUMAN	zinc finger protein 805	7					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D7Y(1)		breast(1)|endometrium(3)|kidney(3)|lung(1)|stomach(1)	9						GGCTTTGACGGACCCGGCGCA	0.682																																																	1	Substitution - Missense(1)	kidney(1)											49.0	52.0	51.0					19																	57752278		692	1591	2283	SO:0001583	missense	390980			AF024708	CCDS46207.1, CCDS46208.1	19q13.43	2013-01-08			ENSG00000204524	ENSG00000204524		"""Zinc fingers, C2H2-type"", ""-"""	23272	protein-coding gene	gene with protein product							Standard	NM_001023563		Approved		uc010ygt.2	Q5CZA5		ENST00000414468.2:c.19G>T	19.37:g.57752278G>T	ENSP00000412999:p.Asp7Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	B4DNM5	Missense_Mutation	SNP	ENST00000414468.2	37	CCDS46207.1	.	.	.	.	.	.	.	.	.	.	G	11.88	1.771374	0.31320	.	.	ENSG00000204524	ENST00000414468	T	0.05580	3.42	3.2	2.16	0.27623	Krueppel-associated box (1);	.	.	.	.	T	0.06690	0.0171	L	0.38838	1.175	0.31184	N	0.701676	P	0.50943	0.94	P	0.44990	0.466	T	0.19063	-1.0317	9	0.56958	D	0.05	.	6.376	0.21507	0.1379:0.0:0.8621:0.0	.	7	Q5CZA5	ZN805_HUMAN	Y	7	ENSP00000412999:D7Y	ENSP00000412999:D7Y	D	+	1	0	ZNF805	62444090	0.570000	0.26651	0.100000	0.21137	0.016000	0.09150	1.044000	0.30329	0.907000	0.36646	0.655000	0.94253	GAC		0.682	ZNF805-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465722.1		NM_001023563	
B4GALNT4	338707	broad.mit.edu	37	11	379925	379925	+	Missense_Mutation	SNP	C	C	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr11:379925C>T	ENST00000329962.6	+	16	2548	c.2548C>T	c.(2548-2550)Cgc>Tgc	p.R850C		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	850					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)	p.R850C(1)		endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GCTGCACGCGCGCACCGGGGA	0.687																																																	1	Substitution - Missense(1)	kidney(1)											33.0	36.0	35.0					11																	379925		2202	4296	6498	SO:0001583	missense	338707			AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"""Beta 4-glycosyltransferases"""	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.2548C>T	11.37:g.379925C>T	ENSP00000328277:p.Arg850Cys	Somatic		WXS	Illumina GAIIx	Phase_I	Q96LV2	Missense_Mutation	SNP	ENST00000329962.6	37	CCDS7694.1	.	.	.	.	.	.	.	.	.	.	c	11.85	1.763055	0.31228	.	.	ENSG00000182272	ENST00000329962	T	0.36157	1.27	3.73	3.73	0.42828	.	1.152560	0.06091	N	0.663715	T	0.33469	0.0864	N	0.17082	0.46	0.09310	N	1	D	0.71674	0.998	P	0.51866	0.682	T	0.22277	-1.0221	10	0.54805	T	0.06	-8.5595	6.9118	0.24338	0.3786:0.4741:0.1473:0.0	.	850	Q76KP1	B4GN4_HUMAN	C	850	ENSP00000328277:R850C	ENSP00000328277:R850C	R	+	1	0	B4GALNT4	369925	0.001000	0.12720	0.333000	0.25482	0.287000	0.27160	0.605000	0.24179	2.073000	0.62155	0.561000	0.74099	CGC		0.687	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2		NM_178537	
CASZ1	54897	broad.mit.edu	37	1	10711096	10711097	+	Frame_Shift_Ins	INS	-	-	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr1:10711096_10711097insG	ENST00000377022.3	-	12	3034_3035	c.2717_2718insC	c.(2716-2718)ccgfs	p.P906fs	CASZ1_ENST00000344008.5_Frame_Shift_Ins_p.P906fs|RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	906					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		TCACTTGGGCCGGGGGGAACCT	0.698																																																	0																																										SO:0001589	frameshift_variant	54897			AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.2718dupC	1.37:g.10711102_10711102dupG	ENSP00000366221:p.Pro906fs	Somatic		WXS	Illumina GAIIx	Phase_I	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Frame_Shift_Ins	INS	ENST00000377022.3	37	CCDS41246.1																																																																																				0.698	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2		NM_017766	
HRNR	388697	broad.mit.edu	37	1	152188024	152188024	+	Silent	SNP	C	C	G	rs142170860		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr1:152188024C>G	ENST00000368801.2	-	3	6156	c.6081G>C	c.(6079-6081)tcG>tcC	p.S2027S	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2027					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.S2027S(2)		autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGCCACAGCTCGATGACTGTC	0.562																																																	2	Substitution - coding silent(2)	lung(1)|kidney(1)											348.0	495.0	444.0					1																	152188024		2158	4162	6320	SO:0001819	synonymous_variant	388697			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.6081G>C	1.37:g.152188024C>G		Somatic		WXS	Illumina GAIIx	Phase_I	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																				0.562	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1		XM_373868	
UVSSA	57654	broad.mit.edu	37	4	1343562	1343562	+	Missense_Mutation	SNP	G	G	A	rs201486316		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr4:1343562G>A	ENST00000389851.4	+	3	796	c.349G>A	c.(349-351)Gtg>Atg	p.V117M	UVSSA_ENST00000507531.1_Missense_Mutation_p.V117M|UVSSA_ENST00000511216.1_Missense_Mutation_p.V117M	NM_020894.2	NP_065945.2	Q2YD98	UVSSA_HUMAN	UV-stimulated scaffold protein A	117	VHS-like.				protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)	RNA polymerase II core binding (GO:0000993)	p.V117M(1)									CACCCGGGCCGTGGAAGGGTG	0.627													G|||	1	0.000199681	0.0	0.0	5008	,	,		13312	0.001		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)											30.0	36.0	34.0					4																	1343562		2203	4300	6503	SO:0001583	missense	0			BC021930	CCDS33938.1	4p16.3	2012-04-27	2012-04-27	2012-04-27		ENSG00000163945			29304	protein-coding gene	gene with protein product		614632	"""KIAA1530"""	KIAA1530		10819331, 22466610, 22466611, 22466612	Standard	NM_020894		Approved		uc003gde.4	Q2YD98		ENST00000389851.4:c.349G>A	4.37:g.1343562G>A	ENSP00000374501:p.Val117Met	Somatic		WXS	Illumina GAIIx	Phase_I	A8K9E6|B2RU11|Q8WTX4|Q9P1Z8	Missense_Mutation	SNP	ENST00000389851.4	37	CCDS33938.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	12.73	2.025870	0.35701	.	.	ENSG00000163945	ENST00000511216;ENST00000389851;ENST00000507531	T;T;T	0.24151	1.87;1.87;1.87	4.89	3.01	0.34805	.	0.129672	0.51477	D	0.000087	T	0.34542	0.0901	L	0.48218	1.51	0.80722	D	1	D	0.76494	0.999	P	0.57371	0.819	T	0.03945	-1.0990	10	0.41790	T	0.15	.	10.9687	0.47426	0.1639:0.0:0.8361:0.0	.	117	Q2YD98	K1530_HUMAN	M	117	ENSP00000425130:V117M;ENSP00000374501:V117M;ENSP00000421741:V117M	ENSP00000374501:V117M	V	+	1	0	KIAA1530	1333562	0.988000	0.35896	0.054000	0.19295	0.107000	0.19398	1.927000	0.40094	0.948000	0.37687	0.591000	0.81541	GTG		0.627	UVSSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359480.1		NM_020894	
MUC4	4585	broad.mit.edu	37	3	195513468	195513468	+	Missense_Mutation	SNP	G	G	C	rs76596008	byFrequency	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr3:195513468G>C	ENST00000463781.3	-	2	5442	c.4983C>G	c.(4981-4983)caC>caG	p.H1661Q	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H1661Q	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.H1661Q(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGCGTGACCTGTGG	0.587																																																	2	Substitution - Missense(2)	kidney(1)|endometrium(1)											26.0	31.0	30.0					3																	195513468		688	1577	2265	SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4983C>G	3.37:g.195513468G>C	ENSP00000417498:p.His1661Gln	Somatic		WXS	Illumina GAIIx	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	3.800	-0.041898	0.07452	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.28255	1.66;1.62	0.595	-0.863	0.10669	.	.	.	.	.	T	0.16685	0.0401	N	0.02539	-0.55	0.09310	N	1	P	0.49358	0.923	P	0.53518	0.728	T	0.14868	-1.0457	8	.	.	.	.	5.1757	0.15133	0.2702:0.0:0.7298:0.0	.	1661	E7ESK3	.	Q	1661	ENSP00000417498:H1661Q;ENSP00000420243:H1661Q	.	H	-	3	2	MUC4	196997863	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	0.163000	0.16520	-0.313000	0.08728	0.089000	0.15464	CAC		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
PCK1	5105	broad.mit.edu	37	20	56140965	56140967	+	3'UTR	DEL	ATC	ATC	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	ATC	ATC	ATC	-	ATC	ATC	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr20:56140965_56140967delATC	ENST00000319441.4	+	0	2138_2140				PCK1_ENST00000543666.1_3'UTR	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)						carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			CACCATAATAATCATCACCACAC	0.429																																																	0																																										SO:0001624	3_prime_UTR_variant	5105				CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.*107ATC>-	20.37:g.56140968_56140970delATC		Somatic		WXS	Illumina GAIIx	Phase_I	A8K437|B4DT64|Q8TCA3|Q9UJD2	3'UTR	DEL	ENST00000319441.4	37	CCDS13460.1																																																																																				0.429	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			
PRRX1	5396	broad.mit.edu	37	1	170695367	170695367	+	Missense_Mutation	SNP	T	T	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr1:170695367T>C	ENST00000239461.6	+	3	737	c.424T>C	c.(424-426)Ttt>Ctt	p.F142L	PRRX1_ENST00000497230.2_Missense_Mutation_p.F142L|PRRX1_ENST00000476867.2_3'UTR|PRRX1_ENST00000367760.3_Missense_Mutation_p.F142L	NM_022716.2	NP_073207.1	P54821	PRRX1_HUMAN	paired related homeobox 1	142					artery morphogenesis (GO:0048844)|cartilage development (GO:0051216)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|inner ear morphogenesis (GO:0042472)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|palate development (GO:0060021)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)	nucleolus (GO:0005730)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)	p.F142L(2)		large_intestine(2)|ovary(1)	3	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CCAGGTGTGGTTTCAGAACCG	0.448																																																	2	Substitution - Missense(2)	kidney(2)											52.0	50.0	50.0					1																	170695367		2203	4300	6503	SO:0001583	missense	5396			M95929	CCDS1290.1, CCDS1291.1	1q24.3	2011-06-20	2003-11-12	2003-11-14	ENSG00000116132	ENSG00000116132		"""Homeoboxes / PRD class"""	9142	protein-coding gene	gene with protein product		167420	"""paired mesoderm homeo box 1"""	PMX1		1509260	Standard	NM_006902		Approved	PHOX1	uc001ghf.3	P54821	OTTHUMG00000035231	ENST00000239461.6:c.424T>C	1.37:g.170695367T>C	ENSP00000239461:p.Phe142Leu	Somatic		WXS	Illumina GAIIx	Phase_I	B5BUM7|O60807	Missense_Mutation	SNP	ENST00000239461.6	37	CCDS1290.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.500349	0.85176	.	.	ENSG00000116132	ENST00000367760;ENST00000239461;ENST00000497230	D;D;D	0.99741	-6.6;-6.6;-6.6	5.5	4.36	0.52297	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.100268	0.64402	D	0.000002	D	0.99866	0.9937	H	0.99830	4.82	0.80722	D	1	D;B	0.57257	0.979;0.033	D;B	0.71414	0.973;0.014	D	0.96806	0.9593	10	0.87932	D	0	.	11.6755	0.51427	0.0:0.0:0.1485:0.8515	.	142;142	P54821;P54821-2	PRRX1_HUMAN;.	L	142	ENSP00000356734:F142L;ENSP00000239461:F142L;ENSP00000450762:F142L	ENSP00000239461:F142L	F	+	1	0	PRRX1	168961991	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.743000	0.68655	0.894000	0.36317	0.454000	0.30748	TTT		0.448	PRRX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085236.3		NM_006902	
RASA2	5922	broad.mit.edu	37	3	141295907	141295907	+	Missense_Mutation	SNP	G	G	A	rs201190266		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr3:141295907G>A	ENST00000452898.1	+	15	1584	c.1549G>A	c.(1549-1551)Gta>Ata	p.V517I	RASA2_ENST00000286364.3_Missense_Mutation_p.V517I	NM_006506.2	NP_006497.2	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	517	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)	p.V517I(2)		NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	34						TGCTGTAGCCGTAGTATCACC	0.353																																																	2	Substitution - Missense(2)	kidney(2)											228.0	215.0	219.0					3																	141295907		2203	4300	6503	SO:0001583	missense	5922			AF115573	CCDS3117.1	3q22-q23	2013-01-10			ENSG00000155903	ENSG00000155903		"""Pleckstrin homology (PH) domain containing"""	9872	protein-coding gene	gene with protein product		601589				8699317	Standard	NM_006506		Approved	GAP1M	uc003etz.1	Q15283	OTTHUMG00000160221	ENST00000452898.1:c.1549G>A	3.37:g.141295907G>A	ENSP00000391677:p.Val517Ile	Somatic		WXS	Illumina GAIIx	Phase_I	A8K7K1|G3V0F9|O00695|Q15284|Q92594|Q99577|Q9UEQ2	Missense_Mutation	SNP	ENST00000452898.1	37		.	.	.	.	.	.	.	.	.	.	G	7.080	0.570046	0.13560	.	.	ENSG00000155903	ENST00000286364;ENST00000452898;ENST00000423660	T;T	0.71934	-0.61;-0.61	6.03	4.24	0.50183	Ras GTPase-activating protein, conserved site (1);Rho GTPase activation protein (1);Ras GTPase-activating protein (4);	0.059991	0.64402	N	0.000004	T	0.35653	0.0939	N	0.00808	-1.17	0.49213	D	0.999769	B;B;B;B	0.21147	0.052;0.005;0.004;0.005	B;B;B;B	0.21917	0.037;0.012;0.007;0.012	T	0.43376	-0.9395	10	0.02654	T	1	.	12.1791	0.54202	0.1391:0.0:0.8609:0.0	.	109;517;517;517	E7EU60;A8K7K1;G3V0F9;Q15283	.;.;.;RASA2_HUMAN	I	517;517;109	ENSP00000286364:V517I;ENSP00000391677:V517I	ENSP00000286364:V517I	V	+	1	0	RASA2	142778597	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.269000	0.72558	0.870000	0.35726	0.557000	0.71058	GTA		0.353	RASA2-201	KNOWN	basic	protein_coding	protein_coding			NM_006506	
CDR2	1039	broad.mit.edu	37	16	22444123	22444123	+	5'UTR	SNP	G	G	A	rs200715642		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr16:22444123G>A	ENST00000569045.1	-	0	509				RRN3P3_ENST00000551766.1_RNA			Q01850	CDR2_HUMAN	cerebellar degeneration-related protein 2, 62kDa							cytoplasm (GO:0005737)				endometrium(3)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	11				GBM - Glioblastoma multiforme(48;0.0188)		ATCACTATCCGCTCAAAATTC	0.333																																																	0																																										SO:0001623	5_prime_UTR_variant	100131998			M63256	CCDS32404.1	16p13.1-p12	2008-02-05	2002-08-29			ENSG00000140743			1799	protein-coding gene	gene with protein product	"""Yo paraneoplastic antigen"""	117340	"""cerebellar degeneration-related protein (62kD)"""			2014264	Standard	NM_001802		Approved	CDR62, Yo	uc002dkn.3	Q01850		ENST00000569045.1:c.-317C>T	16.37:g.22444123G>A		Somatic		WXS	Illumina GAIIx	Phase_I	A8K8A8|Q13977	RNA	SNP	ENST00000569045.1	37																																																																																					0.333	CDR2-006	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000430087.1			
LOC101929232	101929232	broad.mit.edu	37	15	29084045	29084045	+	IGR	SNP	T	T	G	rs75345913		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr15:29084045T>G								RP11-578F21.12 (30601 upstream) : GOLGA6L7P (6061 downstream)																							TTATTCGTATTTTTTGGTAAC	0.313																																																	0																																										SO:0001628	intergenic_variant	0																															15.37:g.29084045T>G		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.313									
SMG1P7	100506060	broad.mit.edu	37	16	70268080	70268080	+	RNA	SNP	T	T	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr16:70268080T>C	ENST00000459379.1	-	0	0																											GTCTTACTGTTGGCTAAAAGG	0.373																																																	0																																												0																															16.37:g.70268080T>C		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000459379.1	37																																																																																					0.373	snoU13.216-201	NOVEL	basic	snoRNA	snoRNA				
AC015849.16	0	broad.mit.edu	37	17	34235676	34235676	+	lincRNA	SNP	C	C	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr17:34235676C>A	ENST00000587132.1	-	0	2351																											CAGACTGCACCAGTGAATTCT	0.453																																																	0																																												0																															17.37:g.34235676C>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000587132.1	37																																																																																					0.453	AC015849.16-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000449325.1			
LOC285484	285484	broad.mit.edu	37	4	6239041	6239041	+	lincRNA	DEL	G	G	-	rs34405068	byFrequency	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr4:6239041delG	ENST00000508601.1	+	0	1544				RP11-1406H17.1_ENST00000602577.1_lincRNA	NR_037863.1																						TGGAGGAAGAGGAGGGACAAA	0.522													GG|GG|G|deletion	1092	0.218051	0.1982	0.1816	5008	,	,		19335	0.006		0.3926	False		,,,				2504	0.3098																0																																												0																															4.37:g.6239041delG		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	DEL	ENST00000508601.1	37																																																																																					0.522	RP11-586D19.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000359673.1			
ZNF688	146542	broad.mit.edu	37	16	30581350	30581351	+	Frame_Shift_Ins	INS	-	-	C	rs528760504		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45d5c746-60e3-4531-8db0-fd648811d45f	fe4271a8-7eda-4760-b5fb-c3f160edde4a	g.chr16:30581350_30581351insC	ENST00000223459.6	-	3	1821_1822	c.717_718insG	c.(715-720)gggcggfs	p.R240fs	ZNF688_ENST00000395219.1_Frame_Shift_Ins_p.R226fs|AC002310.7_ENST00000486926.1_RNA|AC002310.7_ENST00000492040.1_RNA	NM_145271.3	NP_660314.1	P0C7X2	ZN688_HUMAN	zinc finger protein 688	240					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(2)|lung(2)|ovary(1)	8						CGGCCCCGCCGCCCCCCGGAGC	0.708																																																	0																																										SO:0001589	frameshift_variant	146542			AK122680	CCDS10684.1	16p11.2	2013-01-08			ENSG00000229809	ENSG00000229809		"""Zinc fingers, C2H2-type"", ""-"""	30489	protein-coding gene	gene with protein product						10493829	Standard	XM_005255139		Approved		uc002dys.2	P0C7X2	OTTHUMG00000132408	ENST00000223459.6:c.718dupG	16.37:g.30581356_30581356dupC	ENSP00000223459:p.Arg240fs	Somatic		WXS	Illumina GAIIx	Phase_I	A8MV39|B3KV51|O75701|Q8IW91|Q8WV14|Q96MN0	Frame_Shift_Ins	INS	ENST00000223459.6	37	CCDS10684.1																																																																																				0.708	ZNF688-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255544.2		NM_145271	
