#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
ABCA13	154664	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	48556330	48556330	+	Silent	SNP	T	T	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr7:48556330T>A	ENST00000435803.1	+	52	13674	c.13650T>A	c.(13648-13650)acT>acA	p.T4550T	ABCA13_ENST00000544596.1_Silent_p.T280T	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4550					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.T4495T(1)|p.T4550T(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GATATGCAACTCTTCCATGGA	0.378																																																	2	Substitution - coding silent(2)	kidney(2)											259.0	253.0	255.0					7																	48556330		1883	4105	5988	SO:0001819	synonymous_variant	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.13650T>A	7.37:g.48556330T>A		Somatic		WXS	Illumina HiSeq	Phase_I	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	T	8.889	0.953638	0.18431	.	.	ENSG00000179869	ENST00000435451	.	.	.	5.35	-3.32	0.04973	.	.	.	.	.	T	0.36580	0.0972	.	.	.	0.42422	D	0.992644	.	.	.	.	.	.	T	0.34254	-0.9836	4	.	.	.	.	0.6793	0.00872	0.2164:0.1906:0.3374:0.2555	.	.	.	.	T	71	.	.	S	+	1	0	ABCA13	48526876	0.023000	0.18921	0.032000	0.17829	0.940000	0.58332	-1.017000	0.03630	-0.506000	0.06558	0.533000	0.62120	TCT		0.378	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2		NM_152701	
ACR	49	broad.mit.edu;hgsc.bcm.edu	37	22	51178394	51178394	+	Missense_Mutation	SNP	T	T	C	rs368795913		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr22:51178394T>C	ENST00000216139.5	+	3	594	c.554T>C	c.(553-555)aTa>aCa	p.I185T	AC002056.5_ENST00000532913.1_RNA|ACR_ENST00000529621.1_Missense_Mutation_p.I185T|AC000036.4_ENST00000449652.1_RNA	NM_001097.2	NP_001088.2	P10323	ACRO_HUMAN	acrosin	185	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				acrosome matrix dispersal (GO:0002077)|acrosome reaction (GO:0007340)|activation of adenylate cyclase activity (GO:0007190)|binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|response to steroid hormone (GO:0048545)|single fertilization (GO:0007338)	acrosomal matrix (GO:0043159)|extracellular region (GO:0005576)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|protein complex (GO:0043234)	amidase activity (GO:0004040)|copper ion binding (GO:0005507)|DNA binding (GO:0003677)|drug binding (GO:0008144)|fucose binding (GO:0042806)|mannose binding (GO:0005537)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)	p.I185T(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	7		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;1.1e-06)|LUAD - Lung adenocarcinoma(64;0.247)		TGGGGATATATAGAAGAGAAA	0.617																																																	1	Substitution - Missense(1)	kidney(1)						T	THR/ILE	1,4389		0,1,2194	30.0	37.0	35.0		554	3.4	0.0	22		35	0,8590		0,0,4295	no	missense	ACR	NM_001097.2	89	0,1,6489	CC,CT,TT		0.0,0.0228,0.0077	benign	185/422	51178394	1,12979	2195	4295	6490	SO:0001583	missense	49			CR456366	CCDS14101.1	22q13.33	2012-10-23	2012-10-23		ENSG00000100312	ENSG00000100312	3.4.21.10		126	protein-coding gene	gene with protein product	"""preproacrosin"", ""acrosin light and heavy chain prepropeptide"""	102480				2298447, 12398221	Standard	NM_001097		Approved		uc003bnh.4	P10323	OTTHUMG00000150155	ENST00000216139.5:c.554T>C	22.37:g.51178394T>C	ENSP00000216139:p.Ile185Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q6ICK2	Missense_Mutation	SNP	ENST00000216139.5	37	CCDS14101.1	.	.	.	.	.	.	.	.	.	.	t	7.410	0.634585	0.14322	2.28E-4	0.0	ENSG00000100312	ENST00000216139;ENST00000529621	T;D	0.91295	0.53;-2.82	4.52	3.41	0.39046	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.836761	0.09760	N	0.759401	T	0.71099	0.3300	N	0.00815	-1.16	0.09310	N	1	B;B	0.15930	0.015;0.015	B;B	0.18263	0.021;0.021	T	0.60786	-0.7194	10	0.09843	T	0.71	-3.0196	8.7959	0.34878	0.1689:0.0:0.0:0.8311	.	185;185	E9PLV5;P10323	.;ACRO_HUMAN	T	185	ENSP00000216139:I185T;ENSP00000435120:I185T	ENSP00000216139:I185T	I	+	2	0	ACR	49525260	0.000000	0.05858	0.002000	0.10522	0.856000	0.48823	-0.166000	0.09954	2.043000	0.60533	0.374000	0.22700	ATA		0.617	ACR-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000316605.2		NM_001097	
ADH1B	125	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	100239948	100239948	+	Silent	SNP	G	G	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr4:100239948G>C	ENST00000305046.8	-	2	181	c.114C>G	c.(112-114)cgC>cgG	p.R38R	ADH1B_ENST00000394887.3_5'UTR|ADH1B_ENST00000504498.1_5'UTR			P00325	ADH1B_HUMAN	alcohol dehydrogenase 1B (class I), beta polypeptide	38					ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)	p.R38R(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	33				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	TCACCTTAATGCGAACTTCAT	0.348																																																	1	Substitution - coding silent(1)	kidney(1)											69.0	67.0	68.0					4																	100239948		2203	4300	6503	SO:0001819	synonymous_variant	125			AF153821	CCDS34033.1, CCDS68761.1	4q23	2008-02-05	2007-11-06		ENSG00000196616	ENSG00000196616	1.1.1.1	"""Alcohol dehydrogenases"""	250	protein-coding gene	gene with protein product		103720		ADH2		3006456	Standard	NM_000668		Approved		uc003hus.4	P00325	OTTHUMG00000161413	ENST00000305046.8:c.114C>G	4.37:g.100239948G>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8MYN5|B4DRS9|B4DVC3|Q13711|Q4ZGI9|Q96KI7	Silent	SNP	ENST00000305046.8	37	CCDS34033.1																																																																																				0.348	ADH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364853.1		NM_000668	
APOBEC3D	140564	hgsc.bcm.edu	37	22	39421110	39421112	+	In_Frame_Del	DEL	CTT	CTT	-	rs201748259|rs576939969	byFrequency	TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr22:39421110_39421112delCTT	ENST00000216099.8	+	3	653_655	c.246_248delCTT	c.(244-249)tgcttc>tgc	p.F83del	APOBEC3D_ENST00000427494.2_Intron|APOBEC3D_ENST00000381568.4_In_Frame_Del_p.F83del	NM_152426.3	NP_689639.2	Q96AK3	ABC3D_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D	83	CMP/dCMP deaminase zinc-binding 1.				defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)	11	Melanoma(58;0.04)					CAGAAATGTGCTTCTTATCTTGG	0.591														8	0.00159744	0.0	0.0086	5008	,	,		13843	0.0		0.001	False		,,,				2504	0.001																0										3,4261		1,1,2130						-3.3	0.0			73	28,8226		0,28,4099	no	coding	APOBEC3D	NM_152426.3		1,29,6229	A1A1,A1R,RR		0.3392,0.0704,0.2476				31,12487				SO:0001651	inframe_deletion	140564			BF832090	CCDS46709.1	22q13.1	2012-10-19	2008-05-01		ENSG00000243811	ENSG00000243811		"""Apolipoprotein B mRNA editing enzymes"""	17354	protein-coding gene	gene with protein product		609900	"""apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D (putative)"", ""apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3E pseudogene"""	APOBEC3E		11863358	Standard	NM_152426		Approved	ARP6, APOBEC3DE	uc003awt.4	Q96AK3	OTTHUMG00000151084	ENST00000216099.8:c.246_248delCTT	22.37:g.39421113_39421115delCTT	ENSP00000216099:p.Phe83del	Somatic		WXS	Illumina HiSeq	Phase_I	Q5JZ91|Q7Z2N2|Q7Z2N5|Q7Z2N6	In_Frame_Del	DEL	ENST00000216099.8	37	CCDS46709.1																																																																																				0.591	APOBEC3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321232.2		NM_152426	
AQR	9716	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	35149171	35149171	+	Missense_Mutation	SNP	C	C	T	rs573724519		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr15:35149171C>T	ENST00000156471.5	-	35	4505	c.4280G>A	c.(4279-4281)cGt>cAt	p.R1427H		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	1427					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R1427H(1)		breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		AGTTTCTTGACGGCAGCTGGT	0.498													C|||	1	0.000199681	0.0	0.0	5008	,	,		16839	0.001		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)											187.0	196.0	193.0					15																	35149171		2047	4190	6237	SO:0001583	missense	9716			AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 164"""	610548	"""aquarius homolog (mouse)"""			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.4280G>A	15.37:g.35149171C>T	ENSP00000156471:p.Arg1427His	Somatic		WXS	Illumina HiSeq	Phase_I	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Missense_Mutation	SNP	ENST00000156471.5	37	CCDS42013.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.823586	0.32237	.	.	ENSG00000021776	ENST00000543879	.	.	.	5.03	2.17	0.27698	.	0.833205	0.11008	N	0.609753	T	0.18299	0.0439	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17258	-1.0375	9	0.52906	T	0.07	-2.2197	6.3233	0.21229	0.0:0.7047:0.0:0.2953	.	1427	O60306	AQR_HUMAN	H	1427	.	ENSP00000445700:R1427H	R	-	2	0	AQR	32936463	0.368000	0.25031	0.081000	0.20488	0.018000	0.09664	0.355000	0.20163	0.845000	0.35118	-0.259000	0.10710	CGT		0.498	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2		NM_014691	
BRD8	10902	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	137502346	137502346	+	Silent	SNP	A	A	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr5:137502346A>T	ENST00000254900.5	-	10	1229	c.858T>A	c.(856-858)acT>acA	p.T286T	BRD8_ENST00000230901.5_Silent_p.T359T|BRD8_ENST00000455658.2_Silent_p.T245T|BRD8_ENST00000411594.2_Intron|BRD8_ENST00000515014.1_5'Flank|BRD8_ENST00000402931.1_Silent_p.T286T	NM_139199.1	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8	286					cell surface receptor signaling pathway (GO:0007166)|chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|intracellular receptor signaling pathway (GO:0030522)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)	p.T286T(1)|p.T359T(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(3)|urinary_tract(1)	35			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TGGCAACAGTAGTGAAGGAAG	0.502																																																	2	Substitution - coding silent(2)	kidney(2)											75.0	65.0	68.0					5																	137502346		2203	4300	6503	SO:0001819	synonymous_variant	10902			AF016270	CCDS4198.1, CCDS34241.1, CCDS54907.1	5q31	2008-02-05			ENSG00000112983	ENSG00000112983			19874	protein-coding gene	gene with protein product		602848				8611617, 9368056	Standard	NM_001164326		Approved	SMAP, p120	uc003lcf.1	Q9H0E9	OTTHUMG00000129204	ENST00000254900.5:c.858T>A	5.37:g.137502346A>T		Somatic		WXS	Illumina HiSeq	Phase_I	O43178|Q15355|Q58AB0|Q59GN0|Q969M9	Silent	SNP	ENST00000254900.5	37	CCDS4198.1																																																																																				0.502	BRD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251282.3		NM_006696	
CCNA1	8900	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	37014312	37014312	+	Silent	SNP	C	C	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr13:37014312C>T	ENST00000255465.4	+	6	1354	c.1090C>T	c.(1090-1092)Ctg>Ttg	p.L364L	CCNA1_ENST00000440264.1_Silent_p.L320L|CCNA1_ENST00000449823.1_Silent_p.L320L|CCNA1_ENST00000418263.1_Silent_p.L363L			P78396	CCNA1_HUMAN	cyclin A1	364					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|male meiosis I (GO:0007141)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)		p.L364L(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	35		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)		GACTGAGAACCTGGCTAAGGT	0.458																																																	1	Substitution - coding silent(1)	kidney(1)											113.0	111.0	112.0					13																	37014312		2203	4300	6503	SO:0001819	synonymous_variant	8900			U66838	CCDS9357.1, CCDS45031.1	13q12.3-q13	2014-01-21			ENSG00000133101	ENSG00000133101			1577	protein-coding gene	gene with protein product		604036				9041194	Standard	NM_003914		Approved	CT146	uc001uvr.4	P78396	OTTHUMG00000016733	ENST00000255465.4:c.1090C>T	13.37:g.37014312C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B7Z7E3|Q5T3V0|Q5U0G2|Q8IY91	Silent	SNP	ENST00000255465.4	37	CCDS9357.1																																																																																				0.458	CCNA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044514.2		NM_003914	
CENPC	1060	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	68380078	68380078	+	Silent	SNP	A	A	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr4:68380078A>G	ENST00000273853.6	-	8	1408	c.1158T>C	c.(1156-1158)gcT>gcC	p.A386A		NM_001812.2	NP_001803.2	Q03188	CENPC_HUMAN	centromere protein C	386					chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	centromeric DNA binding (GO:0019237)|DNA binding (GO:0003677)	p.A386A(1)									CACCTATCAAAGCATAACTTG	0.333																																																	1	Substitution - coding silent(1)	kidney(1)											79.0	67.0	71.0					4																	68380078		1814	4083	5897	SO:0001819	synonymous_variant	1060			M95724	CCDS47063.1	4q13.2	2013-11-05	2013-07-03	2013-07-03	ENSG00000145241	ENSG00000145241			1854	protein-coding gene	gene with protein product		117141	"""centromere protein C 1"""	CENPC1		7959789	Standard	XR_245245		Approved	CENP-C, hcp-4, MIF2	uc003hdd.1	Q03188	OTTHUMG00000160735	ENST00000273853.6:c.1158T>C	4.37:g.68380078A>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q8IW27|Q9P0M5	Silent	SNP	ENST00000273853.6	37	CCDS47063.1																																																																																				0.333	CENPC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362001.2			
CNKSR3	154043	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	154743778	154743778	+	Nonsense_Mutation	SNP	C	C	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr6:154743778C>T	ENST00000607772.1	-	9	1351	c.807G>A	c.(805-807)tgG>tgA	p.W269*	CNKSR3_ENST00000479339.1_Nonsense_Mutation_p.W189*|CNKSR3_ENST00000433165.2_Nonsense_Mutation_p.W94*	NM_173515.2	NP_775786.2	Q6P9H4	CNKR3_HUMAN	CNKSR family member 3	269	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)	cytoplasm (GO:0005737)|membrane (GO:0016020)		p.W269*(1)		breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	15		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;5.03e-11)|BRCA - Breast invasive adenocarcinoma(81;0.00627)		TTTTCAGCTGCCATCCCACCT	0.463																																																	1	Substitution - Nonsense(1)	kidney(1)											52.0	56.0	54.0					6																	154743778		2203	4300	6503	SO:0001587	stop_gained	154043			AK055911	CCDS5246.1	6q25.2	2013-01-10	2005-04-11	2005-04-11	ENSG00000153721	ENSG00000153721		"""Sterile alpha motif (SAM) domain containing"""	23034	protein-coding gene	gene with protein product			"""membrane associated guanylate kinase interacting protein-like 1"""	MAGI1			Standard	NM_173515		Approved	FLJ31349		Q6P9H4	OTTHUMG00000015873	ENST00000607772.1:c.807G>A	6.37:g.154743778C>T	ENSP00000475915:p.Trp269*	Somatic		WXS	Illumina HiSeq	Phase_I	Q5SGD5|Q96N65	Nonsense_Mutation	SNP	ENST00000607772.1	37	CCDS5246.1	.	.	.	.	.	.	.	.	.	.	C	39	7.905263	0.98554	.	.	ENSG00000153721	ENST00000367209;ENST00000367213;ENST00000433165;ENST00000479339;ENST00000424998;ENST00000454664	.	.	.	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.6373	0.95740	0.0:1.0:0.0:0.0	.	.	.	.	X	44;269;94;189;31;94	.	ENSP00000356178:W44X	W	-	3	0	CNKSR3	154785470	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.416000	0.80143	2.636000	0.89361	0.655000	0.94253	TGG		0.463	CNKSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042792.2		NM_173515	
CNOT4	4850	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	135080392	135080392	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr7:135080392T>C	ENST00000315544.5	-	9	1402	c.1123A>G	c.(1123-1125)Aca>Gca	p.T375A	CNOT4_ENST00000414802.1_Missense_Mutation_p.T375A|CNOT4_ENST00000423368.2_Missense_Mutation_p.T375A|CNOT4_ENST00000451834.1_Missense_Mutation_p.T372A|CNOT4_ENST00000428680.2_Missense_Mutation_p.T372A|CNOT4_ENST00000361528.4_Missense_Mutation_p.T372A|CNOT4_ENST00000356162.4_Missense_Mutation_p.T375A|CNOT4_ENST00000541284.1_Missense_Mutation_p.T375A	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	375					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|protein autoubiquitination (GO:0051865)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T375A(3)|p.T372A(1)		autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						ATACCTGATGTGAAGAGGCTC	0.433																																					Ovarian(51;766 1130 5502 35047 50875)												4	Substitution - Missense(4)	kidney(4)											143.0	151.0	148.0					7																	135080392		1963	4160	6123	SO:0001583	missense	4850			AF180475	CCDS43650.1, CCDS47719.1, CCDS55164.1, CCDS55165.1, CCDS55166.1, CCDS55167.1	7q33	2013-09-19			ENSG00000080802	ENSG00000080802		"""RNA binding motif (RRM) containing"""	7880	protein-coding gene	gene with protein product		604911		NOT4		10637334	Standard	NM_013316		Approved	CLONE243, NOT4H	uc011kpy.2	O95628	OTTHUMG00000155568	ENST00000315544.5:c.1123A>G	7.37:g.135080392T>C	ENSP00000326731:p.Thr375Ala	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Missense_Mutation	SNP	ENST00000315544.5	37	CCDS55166.1	.	.	.	.	.	.	.	.	.	.	T	15.25	2.777212	0.49786	.	.	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528;ENST00000414802;ENST00000356162;ENST00000428680;ENST00000315544	T;T;T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89	5.8	5.8	0.92144	.	0.042444	0.85682	D	0.000000	T	0.30324	0.0761	N	0.24115	0.695	0.80722	D	1	B;B;B;B;B;B	0.11235	0.001;0.001;0.001;0.0;0.004;0.0	B;B;B;B;B;B	0.11329	0.002;0.004;0.001;0.001;0.006;0.001	T	0.09997	-1.0649	10	0.17369	T	0.5	-13.8326	15.3291	0.74193	0.0:0.0:0.0:1.0	.	372;375;375;372;375;372	E7ET38;F8VQP3;O95628;O95628-2;O95628-4;O95628-8	.;.;CNOT4_HUMAN;.;.;.	A	375;372;375;375;372;375;375;372;375	ENSP00000445508:T375A;ENSP00000388491:T372A;ENSP00000406777:T375A;ENSP00000354673:T372A;ENSP00000416532:T375A;ENSP00000348485:T375A;ENSP00000399108:T372A;ENSP00000326731:T375A	ENSP00000262563:T375A	T	-	1	0	CNOT4	134730932	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.840000	0.62817	2.222000	0.72286	0.374000	0.22700	ACA		0.433	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding			NM_013316	
CNTN5	53942	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	99942549	99942549	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr11:99942549C>A	ENST00000524871.1	+	12	1702	c.1412C>A	c.(1411-1413)gCt>gAt	p.A471D	CNTN5_ENST00000418526.2_Missense_Mutation_p.A397D|CNTN5_ENST00000279463.3_Missense_Mutation_p.A471D|CNTN5_ENST00000528682.1_Missense_Mutation_p.A471D|CNTN5_ENST00000527185.1_Missense_Mutation_p.A471D	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	471	Ig-like C2-type 4.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)		p.A471D(2)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		TACGCTAGTGCTGAGCTGAAG	0.338																																																	2	Substitution - Missense(2)	kidney(2)											110.0	101.0	104.0					11																	99942549		1853	4126	5979	SO:0001583	missense	53942			AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.1412C>A	11.37:g.99942549C>A	ENSP00000435637:p.Ala471Asp	Somatic		WXS	Illumina HiSeq	Phase_I	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	37	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.651494	0.88056	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55;-0.55	5.48	5.48	0.80851	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.097175	0.64402	D	0.000001	D	0.88633	0.6489	M	0.93594	3.435	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.97110	0.997;0.997;1.0	D	0.91317	0.5079	10	0.87932	D	0	.	18.3469	0.90325	0.0:1.0:0.0:0.0	.	471;397;471	E9PKE8;O94779-2;O94779	.;.;CNTN5_HUMAN	D	471;471;471;397;471	ENSP00000433575:A471D;ENSP00000436185:A471D;ENSP00000435637:A471D;ENSP00000393229:A397D;ENSP00000279463:A471D	ENSP00000279463:A471D	A	+	2	0	CNTN5	99447759	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.463000	0.80869	2.573000	0.86826	0.655000	0.94253	GCT		0.338	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2		NM_014361	
COL25A1	84570	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	109783657	109783657	+	Splice_Site	SNP	C	C	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr4:109783657C>T	ENST00000399132.1	-	22	1727	c.1197G>A	c.(1195-1197)aaG>aaA	p.K399K	COL25A1_ENST00000399126.1_Splice_Site_p.K399K|COL25A1_ENST00000399127.1_Intron	NM_198721.2	NP_942014.1			collagen, type XXV, alpha 1									p.K399K(2)		NS(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	49		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		GGTTACTGACCTTTGACCCCT	0.368																																																	2	Substitution - coding silent(2)	kidney(2)											251.0	237.0	241.0					4																	109783657		1832	4092	5924	SO:0001630	splice_region_variant	84570			AF293340	CCDS43258.1, CCDS43259.1, CCDS58922.1	4q25	2013-01-16			ENSG00000188517	ENSG00000188517		"""Collagens"""	18603	protein-coding gene	gene with protein product		610004				11927537	Standard	NM_001256074		Approved		uc003hze.2	Q9BXS0	OTTHUMG00000150039	ENST00000399132.1:c.1197+1G>A	4.37:g.109783657C>T		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000399132.1	37	CCDS43258.1																																																																																				0.368	COL25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315938.2		NM_032518	Silent
CTCFL	140690	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	56089655	56089655	+	Silent	SNP	G	G	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr20:56089655G>A	ENST00000608263.1	-	6	1984	c.1323C>T	c.(1321-1323)agC>agT	p.S441S	CTCFL_ENST00000433949.3_Silent_p.S236S|CTCFL_ENST00000422869.2_Silent_p.S441S|CTCFL_ENST00000539382.1_Silent_p.S236S|CTCFL_ENST00000609232.1_Silent_p.S441S|CTCFL_ENST00000502686.2_Silent_p.S179S|CTCFL_ENST00000432255.2_Intron|CTCFL_ENST00000423479.3_Silent_p.S441S|CTCFL_ENST00000429804.3_Intron|CTCFL_ENST00000371196.2_Silent_p.S441S|CTCFL_ENST00000608425.1_Silent_p.S441S|CTCFL_ENST00000608440.1_Silent_p.S441S|CTCFL_ENST00000608858.1_5'UTR|CTCFL_ENST00000243914.3_Silent_p.S441S|CTCFL_ENST00000608903.1_Silent_p.S179S	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	441					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)	p.S441S(1)		NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			CACGTAGGTCGCTTTTCCGTG	0.483											OREG0026065	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - coding silent(1)	kidney(1)											221.0	203.0	209.0					20																	56089655		2203	4300	6503	SO:0001819	synonymous_variant	140690				CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"""Zinc fingers, C2H2-type"""	16234	protein-coding gene	gene with protein product	"""cancer/testis antigen 27"""	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.1323C>T	20.37:g.56089655G>A		Somatic	1012	WXS	Illumina HiSeq	Phase_I	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Silent	SNP	ENST00000608263.1	37	CCDS13459.1																																																																																				0.483	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1		NM_080618	
CTNND1	1500	broad.mit.edu;ucsc.edu	37	11	57573944	57573944	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr11:57573944T>C	ENST00000399050.4	+	11	2424	c.1888T>C	c.(1888-1890)Tcc>Ccc	p.S630P	CTNND1_ENST00000529919.1_Missense_Mutation_p.S630P|CTNND1_ENST00000533667.1_Intron|CTNND1_ENST00000532245.1_Intron|CTNND1_ENST00000525902.1_Missense_Mutation_p.S307P|CTNND1_ENST00000532787.1_Intron|CTNND1_ENST00000361796.4_Intron|CTNND1_ENST00000529873.1_Intron|CTNND1_ENST00000532463.1_Intron|CTNND1_ENST00000534579.1_Intron|CTNND1_ENST00000527467.1_Missense_Mutation_p.S307P|CTNND1_ENST00000532844.1_Missense_Mutation_p.S576P|CTNND1_ENST00000529526.1_Intron|CTNND1_ENST00000399039.4_Missense_Mutation_p.S630P|CTNND1_ENST00000361391.6_Intron|CTNND1_ENST00000526938.1_Missense_Mutation_p.S630P|CTNND1_ENST00000358694.6_Intron|CTNND1_ENST00000528232.1_Missense_Mutation_p.S529P|CTNND1_ENST00000531014.1_Intron|CTNND1_ENST00000524630.1_Intron|CTNND1_ENST00000529986.1_Intron|CTNND1_ENST00000426142.2_Intron|CTNND1_ENST00000526357.1_Intron|CTNND1_ENST00000532649.1_Intron|CTNND1_ENST00000526772.1_Intron|CTNND1_ENST00000415361.2_Missense_Mutation_p.S529P|CTNND1_ENST00000360682.6_Missense_Mutation_p.S630P|CTNND1_ENST00000528621.1_Intron|CTNND1_ENST00000530748.1_Missense_Mutation_p.S576P|CTNND1_ENST00000361332.4_Intron|CTNND1_ENST00000428599.2_Intron|CTNND1_ENST00000530094.1_Intron	NM_001085458.1	NP_001078927.1	O60716	CTND1_HUMAN	catenin (cadherin-associated protein), delta 1	630					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|regulation of transcription, DNA-templated (GO:0006355)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)|zonula adherens (GO:0005915)	cadherin binding (GO:0045296)|receptor binding (GO:0005102)	p.S630P(1)		breast(5)|endometrium(8)|kidney(4)|large_intestine(7)|liver(2)|lung(16)|ovary(1)|upper_aerodigestive_tract(2)	45		all_epithelial(135;0.155)				TGAGTGGTTCTCCAGAGGTGA	0.413																																																	1	Substitution - Missense(1)	kidney(1)											126.0	112.0	116.0					11																	57573944		1903	4135	6038	SO:0001583	missense	1500			AB002382	CCDS44604.1, CCDS44605.1, CCDS44606.1, CCDS44607.1, CCDS44608.1, CCDS44609.1, CCDS53632.1, CCDS53633.1, CCDS53634.1, CCDS55763.1, CCDS55764.1, CCDS55765.1, CCDS55766.1, CCDS55767.1, CCDS73290.1	11q12.1	2013-02-14				ENSG00000198561		"""Armadillo repeat containing"""	2515	protein-coding gene	gene with protein product		601045		CTNND		8808291	Standard	NM_001085460		Approved	KIAA0384, p120, p120cas, p120ctn	uc001nmc.4	O60716		ENST00000399050.4:c.1888T>C	11.37:g.57573944T>C	ENSP00000382004:p.Ser630Pro	Somatic		WXS	Illumina GAIIx	Phase_I	A8K939|O15088|O60713|O60714|O60715|O60935|Q6DHZ7|Q6RBX8|Q9UP71|Q9UP72|Q9UP73	Missense_Mutation	SNP	ENST00000399050.4	37	CCDS44604.1	.	.	.	.	.	.	.	.	.	.	T	15.32	2.797356	0.50208	.	.	ENSG00000198561	ENST00000529919;ENST00000399039;ENST00000360682;ENST00000399050;ENST00000530748;ENST00000527467;ENST00000528232;ENST00000525902;ENST00000532844;ENST00000415361;ENST00000526938	T;T;T;T;T;T;T;T;T;T;T	0.72835	-0.32;-0.32;-0.68;-0.32;-0.32;-0.58;-0.24;-0.57;-0.33;-0.32;-0.69	4.99	3.86	0.44501	Armadillo-type fold (1);	0.511530	0.16996	N	0.191111	T	0.60287	0.2257	L	0.46157	1.445	0.80722	D	1	P;P;P	0.45176	0.852;0.769;0.769	B;B;B	0.42422	0.387;0.312;0.216	T	0.53961	-0.8364	10	0.26408	T	0.33	-9.5987	5.1781	0.15146	0.1583:0.0862:0.0:0.7556	.	630;630;630	O60716-3;O60716;C9JZR2	.;CTND1_HUMAN;.	P	630;630;630;630;576;307;529;307;576;529;630	ENSP00000434808:S630P;ENSP00000381996:S630P;ENSP00000353902:S630P;ENSP00000382004:S630P;ENSP00000436744:S576P;ENSP00000434900:S307P;ENSP00000435266:S529P;ENSP00000434672:S307P;ENSP00000433276:S576P;ENSP00000403518:S529P;ENSP00000432041:S630P	ENSP00000353902:S630P	S	+	1	0	CTNND1	57330520	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.335000	0.52105	0.933000	0.37291	0.459000	0.35465	TCC		0.413	CTNND1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393944.1		NM_001331	
DMXL1	1657	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	118484562	118484562	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr5:118484562A>G	ENST00000311085.8	+	18	3120	c.3040A>G	c.(3040-3042)Aat>Gat	p.N1014D	DMXL1_ENST00000539542.1_Missense_Mutation_p.N1014D	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	1014								p.N1014D(1)		breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		CACGTCAAAGAATGGAAAAAT	0.398																																																	1	Substitution - Missense(1)	kidney(1)											127.0	121.0	123.0					5																	118484562		2202	4300	6502	SO:0001583	missense	1657			AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.3040A>G	5.37:g.118484562A>G	ENSP00000309690:p.Asn1014Asp	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	A	0.232	-1.019948	0.02078	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.31247	1.5;1.5	5.5	4.34	0.51931	.	0.362712	0.29093	N	0.013170	T	0.11067	0.0270	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.29212	-1.0019	10	0.12430	T	0.62	-15.9349	5.394	0.16259	0.6469:0.1394:0.2137:0.0	.	1014;1014	F5H269;Q9Y485	.;DMXL1_HUMAN	D	1014	ENSP00000309690:N1014D;ENSP00000439479:N1014D	ENSP00000309690:N1014D	N	+	1	0	DMXL1	118512461	0.001000	0.12720	0.976000	0.42696	0.476000	0.33039	0.301000	0.19174	1.023000	0.39654	0.533000	0.62120	AAT		0.398	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1		NM_005509	
DRD5	1816	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	9784913	9784913	+	Silent	SNP	C	C	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr4:9784913C>T	ENST00000304374.2	+	1	1656	c.1260C>T	c.(1258-1260)ccC>ccT	p.P420P		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	420					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)	p.P420P(1)		NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	CCGTTACCCCCGGCAACCGGG	0.547																																																	1	Substitution - coding silent(1)	kidney(1)											90.0	77.0	82.0					4																	9784913		2203	4300	6503	SO:0001819	synonymous_variant	1816			X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"""GPCR / Class A : Dopamine receptors"""	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.1260C>T	4.37:g.9784913C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B2R9S3|Q8NEQ8	Silent	SNP	ENST00000304374.2	37	CCDS3405.1																																																																																				0.547	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1			
DTNBP1	84062	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	15627643	15627643	+	Nonsense_Mutation	SNP	C	C	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr6:15627643C>A	ENST00000344537.5	-	5	458	c.286G>T	c.(286-288)Gag>Tag	p.E96*	DTNBP1_ENST00000355917.3_Nonsense_Mutation_p.E96*|DTNBP1_ENST00000338950.5_Nonsense_Mutation_p.E96*	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1	96					actin cytoskeleton reorganization (GO:0031532)|anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|neuron projection morphogenesis (GO:0048812)|platelet dense granule organization (GO:0060155)|positive regulation of gene expression (GO:0010628)|positive regulation of neurotransmitter secretion (GO:0001956)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of dopamine secretion (GO:0014059)	axon (GO:0030424)|BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|growth cone (GO:0030426)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)|synaptic vesicle membrane (GO:0030672)		p.E96*(2)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	14	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			TCTTGCAGCTCCACGAGGCTT	0.488									Hermansky-Pudlak syndrome																																								2	Substitution - Nonsense(2)	kidney(2)											44.0	46.0	45.0					6																	15627643		2203	4300	6503	SO:0001587	stop_gained	84062	Familial Cancer Database	HPS, HPS1-8	AF394226	CCDS4534.1, CCDS4535.1, CCDS75404.1, CCDS75405.1	6p22.3	2013-09-27			ENSG00000047579	ENSG00000047579		"""Biogenesis of lysosomal organelles complex-1 subunits"""	17328	protein-coding gene	gene with protein product	"""dysbindin-1"", ""biogenesis of lysosomal organelles complex-1, subunit 8"""	607145				11316798	Standard	NM_032122		Approved	Dysbindin, My031, HPS7, DBND, BLOC1S8	uc003nbm.3	Q96EV8	OTTHUMG00000014295	ENST00000344537.5:c.286G>T	6.37:g.15627643C>A	ENSP00000341680:p.Glu96*	Somatic		WXS	Illumina HiSeq	Phase_I	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	Nonsense_Mutation	SNP	ENST00000344537.5	37	CCDS4534.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.284429	0.80803	.	.	ENSG00000047579	ENST00000344537;ENST00000355917;ENST00000397306;ENST00000511762;ENST00000338950;ENST00000543749	.	.	.	5.58	5.58	0.84498	.	0.435086	0.20347	N	0.094138	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	.	18.3295	0.90263	0.0:1.0:0.0:0.0	.	.	.	.	X	96;96;15;61;96;96	.	ENSP00000344718:E96X	E	-	1	0	DTNBP1	15735622	0.998000	0.40836	0.101000	0.21167	0.023000	0.10783	4.258000	0.58822	2.637000	0.89404	0.650000	0.86243	GAG		0.488	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000039933.2		NM_032122	
EXTL1	2134	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	26357724	26357724	+	Silent	SNP	C	C	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr1:26357724C>T	ENST00000374280.3	+	5	2070	c.1203C>T	c.(1201-1203)ccC>ccT	p.P401P	EXTL1_ENST00000484339.1_3'UTR	NM_004455.2	NP_004446.2	Q92935	EXTL1_HUMAN	exostosin-like glycosyltransferase 1	401					protein glycosylation (GO:0006486)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)	p.P401P(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|stomach(1)|urinary_tract(1)	23		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649)		CCACAAGCCCCCAGGACTTCC	0.587																																																	1	Substitution - coding silent(1)	kidney(1)											69.0	69.0	69.0					1																	26357724		2203	4300	6503	SO:0001819	synonymous_variant	2134			U67191	CCDS271.1	1p36.1	2013-03-01	2013-03-01		ENSG00000158008	ENSG00000158008	2.4.1.224	"""Exostosin glycosyltransferase family"""	3515	protein-coding gene	gene with protein product	"""glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase"", ""alpha-N-acetylglucosaminyltransferase II"", ""glucuronyl-N-acetylglucosaminylproteoglycan alpha-1,4-N- acetylglucosaminyltransferase"", ""exostosin-L"""	601738	"""exostoses (multiple)-like 1"""			9037597	Standard	NM_004455		Approved	EXTL, MGC70794	uc001blf.3	Q92935	OTTHUMG00000007509	ENST00000374280.3:c.1203C>T	1.37:g.26357724C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q6GSC1	Silent	SNP	ENST00000374280.3	37	CCDS271.1																																																																																				0.587	EXTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019749.1		NM_004455	
FAM135B	51059	hgsc.bcm.edu	37	8	139165459	139165459	+	Splice_Site	SNP	C	C	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr8:139165459C>A	ENST00000395297.1	-	13	1429	c.1259G>T	c.(1258-1260)gGg>gTg	p.G420V		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	420										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			CAAGTTATGCCCTACAAAAAA	0.289										HNSCC(54;0.14)																																							0													28.0	26.0	27.0					8																	139165459		1800	4065	5865	SO:0001630	splice_region_variant	51059			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.1259-1G>T	8.37:g.139165459C>A		Somatic		WXS	Illumina HiSeq	Phase_I	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	C	8.107	0.778027	0.16120	.	.	ENSG00000147724	ENST00000395297	T	0.16073	2.37	5.42	4.54	0.55810	.	1.230090	0.05570	N	0.571034	T	0.28699	0.0711	L	0.42245	1.32	0.51767	D	0.999937	D	0.67145	0.996	P	0.59643	0.861	T	0.05818	-1.0862	10	0.17832	T	0.49	.	7.9747	0.30149	0.0:0.808:0.0:0.192	.	420	Q49AJ0	F135B_HUMAN	V	420	ENSP00000378710:G420V	ENSP00000276737:G420V	G	-	2	0	FAM135B	139234641	0.769000	0.28531	0.099000	0.21106	0.144000	0.21451	1.149000	0.31626	1.301000	0.44836	-0.140000	0.14226	GGG		0.289	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3		NM_015912	Missense_Mutation
FAT2	2196	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	150925180	150925180	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr5:150925180G>C	ENST00000261800.5	-	9	5520	c.5508C>G	c.(5506-5508)ttC>ttG	p.F1836L		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1836	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F1836L(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CACAGAATTGGAAAGAGGGCA	0.448																																																	1	Substitution - Missense(1)	kidney(1)											67.0	72.0	70.0					5																	150925180		2203	4300	6503	SO:0001583	missense	2196			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.5508C>G	5.37:g.150925180G>C	ENSP00000261800:p.Phe1836Leu	Somatic		WXS	Illumina HiSeq	Phase_I	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	12.27	1.887023	0.33348	.	.	ENSG00000086570	ENST00000261800	T	0.52983	0.64	5.07	3.26	0.37387	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000015	T	0.47395	0.1443	M	0.74389	2.26	0.45216	D	0.99822	B	0.16603	0.018	B	0.22386	0.039	T	0.40887	-0.9539	10	0.44086	T	0.13	.	10.3989	0.44218	0.0737:0.135:0.7913:0.0	.	1836	Q9NYQ8	FAT2_HUMAN	L	1836	ENSP00000261800:F1836L	ENSP00000261800:F1836L	F	-	3	2	FAT2	150905373	1.000000	0.71417	0.941000	0.38009	0.909000	0.53808	2.448000	0.44926	0.513000	0.28278	0.467000	0.42956	TTC		0.448	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1		NM_001447	
FLRT2	23768	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	86089519	86089519	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr14:86089519T>C	ENST00000330753.4	+	2	2428	c.1661T>C	c.(1660-1662)gTg>gCg	p.V554A	FLRT2_ENST00000554746.1_Missense_Mutation_p.V554A	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	554					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)	p.V554A(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		GTGATATTTGTGCTGGTGGTC	0.587																																																	1	Substitution - Missense(1)	kidney(1)											75.0	79.0	78.0					14																	86089519		2203	4300	6503	SO:0001583	missense	23768			AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"""Fibronectin type III domain containing"""	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1661T>C	14.37:g.86089519T>C	ENSP00000332879:p.Val554Ala	Somatic		WXS	Illumina HiSeq	Phase_I	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	37	CCDS9877.1	.	.	.	.	.	.	.	.	.	.	T	19.56	3.850758	0.71719	.	.	ENSG00000185070	ENST00000330753;ENST00000554746;ENST00000535800	T;T	0.63744	-0.06;-0.06	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.60379	0.2264	M	0.62723	1.935	0.58432	D	0.999999	P	0.38767	0.646	B	0.33339	0.162	T	0.65981	-0.6036	10	0.87932	D	0	-19.394	16.8222	0.85835	0.0:0.0:0.0:1.0	.	554	O43155	FLRT2_HUMAN	A	554;554;207	ENSP00000332879:V554A;ENSP00000451050:V554A	ENSP00000332879:V554A	V	+	2	0	FLRT2	85159272	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	8.039000	0.88947	2.371000	0.80710	0.533000	0.62120	GTG		0.587	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			
GCC2	9648	broad.mit.edu;hgsc.bcm.edu	37	2	109113518	109113518	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr2:109113518C>G	ENST00000309863.6	+	21	5449	c.4735C>G	c.(4735-4737)Ctt>Gtt	p.L1579V		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	1579	Mediates interaction with RAB6A.|Mediates interaction with RAB9A.				Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)	p.L1579V(1)		breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						AAACGGCCTGCTTCGGGAAAC	0.448																																																	1	Substitution - Missense(1)	kidney(1)											116.0	122.0	120.0					2																	109113518		2203	4300	6503	SO:0001583	missense	9648			BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"""GRIP and coiled-coil domain-containing 2"""			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.4735C>G	2.37:g.109113518C>G	ENSP00000307939:p.Leu1579Val	Somatic		WXS	Illumina HiSeq	Phase_I	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Missense_Mutation	SNP	ENST00000309863.6	37	CCDS33268.1	.	.	.	.	.	.	.	.	.	.	C	19.09	3.759321	0.69763	.	.	ENSG00000135968	ENST00000309863	T	0.50548	0.74	5.15	5.15	0.70609	.	0.000000	0.64402	D	0.000001	T	0.66742	0.2820	M	0.72118	2.19	0.52099	D	0.999943	D	0.67145	0.996	D	0.65140	0.932	T	0.64162	-0.6472	10	0.33141	T	0.24	.	18.9876	0.92779	0.0:1.0:0.0:0.0	.	1579	Q8IWJ2	GCC2_HUMAN	V	1579	ENSP00000307939:L1579V	ENSP00000307939:L1579V	L	+	1	0	GCC2	108479950	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	5.369000	0.66138	2.550000	0.86006	0.561000	0.74099	CTT		0.448	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3		NM_014635	
GNL3L	54552	broad.mit.edu;hgsc.bcm.edu	37	X	54585053	54585053	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chrX:54585053C>T	ENST00000336470.4	+	15	1770	c.1631C>T	c.(1630-1632)gCc>gTc	p.A544V	GNL3L_ENST00000360845.2_Missense_Mutation_p.A544V	NM_019067.5	NP_061940.1	Q9NVN8	GNL3L_HUMAN	guanine nucleotide binding protein-like 3 (nucleolar)-like	544					GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)	p.A544V(1)		NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	30						CTGGCATCTGCCCTGAAAAAT	0.542																																																	1	Substitution - Missense(1)	kidney(1)											37.0	30.0	32.0					X																	54585053		2203	4300	6503	SO:0001583	missense	54552			AK001475	CCDS14360.1	Xp11.22	2010-03-17			ENSG00000130119	ENSG00000130119			25553	protein-coding gene	gene with protein product		300873				12477932	Standard	NM_019067		Approved	FLJ10613	uc004dth.2	Q9NVN8	OTTHUMG00000021629	ENST00000336470.4:c.1631C>T	X.37:g.54585053C>T	ENSP00000338573:p.Ala544Val	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000336470.4	37	CCDS14360.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.442446	0.83993	.	.	ENSG00000130119	ENST00000336470;ENST00000360845	T;T	0.24350	1.86;1.86	4.76	4.76	0.60689	.	0.000000	0.85682	D	0.000000	T	0.38026	0.1025	L	0.34521	1.04	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	T	0.07635	-1.0762	10	0.42905	T	0.14	-10.6679	12.6205	0.56600	0.0:1.0:0.0:0.0	.	544	Q9NVN8	GNL3L_HUMAN	V	544	ENSP00000338573:A544V;ENSP00000354091:A544V	ENSP00000338573:A544V	A	+	2	0	GNL3L	54601778	0.999000	0.42202	0.955000	0.39395	0.817000	0.46193	5.272000	0.65559	2.275000	0.75901	0.513000	0.50165	GCC		0.542	GNL3L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056805.1		NM_019067	
IGSF11	152404	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	118621704	118621704	+	Missense_Mutation	SNP	C	C	T	rs374674136		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr3:118621704C>T	ENST00000393775.2	-	7	1264	c.959G>A	c.(958-960)cGa>cAa	p.R320Q	IGSF11_ENST00000489689.1_Missense_Mutation_p.R296Q|IGSF11_ENST00000491903.1_Missense_Mutation_p.R292Q|IGSF11_ENST00000425327.2_Missense_Mutation_p.R319Q|IGSF11_ENST00000354673.2_Missense_Mutation_p.R319Q|IGSF11_ENST00000441144.2_Missense_Mutation_p.R295Q	NM_001015887.1	NP_001015887.1	Q5DX21	IGS11_HUMAN	immunoglobulin superfamily, member 11	320					cell adhesion (GO:0007155)|regulation of growth (GO:0040008)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R319Q(1)|p.R320Q(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						GCTCCAGTATCGACTGTTGTA	0.458																																																	2	Substitution - Missense(2)	kidney(2)						C	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	136.0	141.0	139.0		959,956	4.5	1.0	3		139	0,8600		0,0,4300	no	missense,missense	IGSF11	NM_001015887.1,NM_152538.2	43,43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	320/432,319/431	118621704	1,13005	2203	4300	6503	SO:0001583	missense	152404			AB079879	CCDS2983.1, CCDS46891.1	3q21.2	2013-01-11			ENSG00000144847	ENSG00000144847		"""Immunoglobulin superfamily / I-set domain containing"""	16669	protein-coding gene	gene with protein product	"""cancer/testis antigen 119"""	608351				12207903	Standard	XM_006713516		Approved	BT-IgSF, MGC35227, Igsf13, VSIG3, CT119	uc003ebw.3	Q5DX21	OTTHUMG00000159387	ENST00000393775.2:c.959G>A	3.37:g.118621704C>T	ENSP00000377370:p.Arg320Gln	Somatic		WXS	Illumina HiSeq	Phase_I	C9JZN0|Q8N4F1|Q8N7T8|Q8NDD2	Missense_Mutation	SNP	ENST00000393775.2	37	CCDS46891.1	.	.	.	.	.	.	.	.	.	.	C	18.76	3.691748	0.68271	2.27E-4	0.0	ENSG00000144847	ENST00000425327;ENST00000393775;ENST00000489689;ENST00000354673;ENST00000441144;ENST00000491903	T;T;D;T;D;D	0.84223	-0.93;-1.15;-1.82;-0.93;-1.76;-1.65	5.37	4.5	0.54988	.	0.168025	0.53938	N	0.000044	D	0.84669	0.5523	L	0.29908	0.895	0.53005	D	0.999963	D;B;D;B;D	0.89917	0.999;0.032;1.0;0.076;0.999	P;B;D;B;P	0.66847	0.886;0.01;0.947;0.007;0.886	T	0.80859	-0.1194	10	0.20519	T	0.43	.	9.5885	0.39532	0.0:0.8432:0.0:0.1568	.	292;295;319;296;320	C9JBA5;Q5DX21-3;Q5DX21-2;C9JMW0;Q5DX21	.;.;.;.;IGS11_HUMAN	Q	319;320;296;319;295;292	ENSP00000406092:R319Q;ENSP00000377370:R320Q;ENSP00000420486:R296Q;ENSP00000346700:R319Q;ENSP00000401240:R295Q;ENSP00000417413:R292Q	ENSP00000346700:R319Q	R	-	2	0	IGSF11	120104394	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	2.937000	0.48979	1.520000	0.48965	0.655000	0.94253	CGA		0.458	IGSF11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355075.2			
JRKL	8690	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	96124831	96124831	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr11:96124831G>T	ENST00000332349.4	+	2	1265	c.1018G>T	c.(1018-1020)Gca>Tca	p.A340S	JRKL_ENST00000458427.1_Missense_Mutation_p.A340S|JRKL_ENST00000546177.1_Intron|CCDC82_ENST00000525786.1_5'Flank|CCDC82_ENST00000542662.1_5'Flank	NM_001261833.1	NP_001248762.1	Q9Y4A0	JERKL_HUMAN	JRK-like	340	DDE.				central nervous system development (GO:0007417)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A340S(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)		BRCA - Breast invasive adenocarcinoma(274;0.148)		AAATTATCGTGCAGGTCTTCT	0.403																																																	1	Substitution - Missense(1)	kidney(1)											82.0	78.0	79.0					11																	96124831		2201	4298	6499	SO:0001583	missense	8690			AF004715	CCDS8308.1	11q21	2014-03-28	2014-03-28		ENSG00000183340	ENSG00000183340			6200	protein-coding gene	gene with protein product		603211	"""erky (mouse) homolog-like"", ""jerky homolog-like (mouse)"""			9240447	Standard	NM_003772		Approved	HHMJG	uc009ywu.4	Q9Y4A0	OTTHUMG00000154950	ENST00000332349.4:c.1018G>T	11.37:g.96124831G>T	ENSP00000333350:p.Ala340Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A8K3G4|B2RAJ3|Q32MC2	Missense_Mutation	SNP	ENST00000332349.4	37	CCDS8308.1	.	.	.	.	.	.	.	.	.	.	G	2.218	-0.379050	0.05000	.	.	ENSG00000183340	ENST00000332349;ENST00000458427	T;T	0.28666	1.6;1.6	4.44	2.28	0.28536	.	0.000000	0.39687	N	0.001287	T	0.16385	0.0394	N	0.17594	0.5	0.21627	N	0.999612	B	0.25772	0.134	B	0.24848	0.056	T	0.14227	-1.0480	10	0.41790	T	0.15	-9.5199	6.6225	0.22810	0.0:0.2002:0.5935:0.2062	.	340	Q9Y4A0	JERKL_HUMAN	S	340	ENSP00000333350:A340S;ENSP00000389989:A340S	ENSP00000333350:A340S	A	+	1	0	JRKL	95764479	0.989000	0.36119	0.655000	0.29622	0.986000	0.74619	1.726000	0.38085	0.916000	0.36871	0.313000	0.20887	GCA		0.403	JRKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337775.2		NM_003772	
KIAA2018	205717	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	113374665	113374665	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr3:113374665G>T	ENST00000478658.1	-	5	5881	c.5864C>A	c.(5863-5865)tCt>tAt	p.S1955Y	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Missense_Mutation_p.S1955Y			Q68DE3	K2018_HUMAN	KIAA2018	1955						membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.S1955Y(1)		NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						ATGAGACACAGATGGATGTGG	0.537																																																	1	Substitution - Missense(1)	kidney(1)											94.0	91.0	92.0					3																	113374665		2146	4252	6398	SO:0001583	missense	205717			AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.5864C>A	3.37:g.113374665G>T	ENSP00000420721:p.Ser1955Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	37	CCDS43133.1	.	.	.	.	.	.	.	.	.	.	g	15.30	2.793730	0.50102	.	.	ENSG00000176542	ENST00000316407;ENST00000478658	T;T	0.16743	2.32;2.32	5.56	5.56	0.83823	.	0.354630	0.29529	N	0.011895	T	0.20007	0.0481	N	0.24115	0.695	0.49213	D	0.999766	D	0.56521	0.976	P	0.47744	0.556	T	0.00888	-1.1526	10	0.62326	D	0.03	-4.7613	19.8795	0.96891	0.0:0.0:1.0:0.0	.	1955	Q68DE3	K2018_HUMAN	Y	1955	ENSP00000320794:S1955Y;ENSP00000420721:S1955Y	ENSP00000320794:S1955Y	S	-	2	0	KIAA2018	114857355	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	7.150000	0.77403	2.775000	0.95449	0.558000	0.71614	TCT		0.537	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1		NM_001009899	
LAMC3	10319	broad.mit.edu;hgsc.bcm.edu	37	9	133911651	133911651	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr9:133911651G>A	ENST00000361069.4	+	4	1041	c.908G>A	c.(907-909)cGc>cAc	p.R303H	LAMC3_ENST00000480883.1_3'UTR	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	303	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)	p.R303H(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		GACTGTGAGCGCTGCCTGCCC	0.687																																																	1	Substitution - Missense(1)	kidney(1)											28.0	31.0	30.0					9																	133911651		2200	4298	6498	SO:0001583	missense	10319			AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.908G>A	9.37:g.133911651G>A	ENSP00000354360:p.Arg303His	Somatic		WXS	Illumina HiSeq	Phase_I	B1APX9|B1APY0|Q59H72	Missense_Mutation	SNP	ENST00000361069.4	37	CCDS6938.1	.	.	.	.	.	.	.	.	.	.	G	10.78	1.445631	0.25987	.	.	ENSG00000050555	ENST00000361069;ENST00000355048;ENST00000320021	T	0.64260	-0.09	5.06	1.72	0.24424	EGF-like, laminin (4);	0.474905	0.21551	N	0.072731	T	0.51381	0.1671	L	0.49699	1.58	0.19575	N	0.999969	B	0.33022	0.394	B	0.30572	0.117	T	0.44802	-0.9304	10	0.48119	T	0.1	.	9.3915	0.38376	0.3959:0.0:0.6041:0.0	.	303	Q9Y6N6	LAMC3_HUMAN	H	303	ENSP00000354360:R303H	ENSP00000325873:R303H	R	+	2	0	LAMC3	132901472	0.000000	0.05858	1.000000	0.80357	0.365000	0.29674	-0.002000	0.12924	0.538000	0.28769	-0.369000	0.07265	CGC		0.687	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3		NM_006059	
LILRB4	11006	hgsc.bcm.edu	37	19	55179244	55179244	+	Splice_Site	DEL	G	G	-	rs571881532|rs386810941	byFrequency	TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr19:55179244delG	ENST00000391736.1	+	13	1515	c.1200delG	c.(1198-1200)gag>ga	p.E400fs	LILRB4_ENST00000391733.3_Splice_Site_p.E401fs|LILRB4_ENST00000270452.2_Splice_Site_p.E400fs|LILRB4_ENST00000430952.2_Splice_Site_p.E399fs|LILRB4_ENST00000391734.3_Intron	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	400					immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		TGGACACTGAGGTGAGTCCTT	0.617													?|GG|G|unsure	97	0.019369	0.0461	0.0144	5008	,	,		16664	0.002		0.0169	False		,,,				2504	0.0072																0									,	175,4085		12,151,1967	99.0	93.0	95.0		,	1.0	0.0	19		95	101,8151		5,91,4030	no	frameshift-near-splice,frameshift-near-splice	LILRB4	NM_006847.3,NM_001081438.1	,	17,242,5997	A1A1,A1R,RR		1.2239,4.108,2.2059	,	,	55179244	276,12236	2193	4296	6489	SO:0001630	splice_region_variant	11006			U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.1200+1G>-	19.37:g.55179244delG		Somatic		WXS	Illumina HiSeq	Phase_I	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Frame_Shift_Del	DEL	ENST00000391736.1	37	CCDS12902.1																																																																																				0.617	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3			Frame_Shift_Del
LOXL1	4016	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	74239485	74239485	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr15:74239485A>G	ENST00000261921.7	+	4	1753	c.1427A>G	c.(1426-1428)cAc>cGc	p.H476R		NM_005576.2	NP_005567.2	Q08397	LOXL1_HUMAN	lysyl oxidase-like 1	476	Lysyl-oxidase like.				extracellular matrix organization (GO:0030198)|oxidation-reduction process (GO:0055114)|protein deamination (GO:0018277)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor (GO:0016641)	p.H476R(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10						GCCGAGGGCCACAAGGCCAGT	0.587																																																	1	Substitution - Missense(1)	kidney(1)											80.0	71.0	74.0					15																	74239485		2198	4297	6495	SO:0001583	missense	4016			L21186	CCDS10253.1	15q24-q25	2008-07-18			ENSG00000129038	ENSG00000129038			6665	protein-coding gene	gene with protein product		153456				7689553	Standard	NM_005576		Approved	LOXL, LOL	uc002awc.1	Q08397	OTTHUMG00000137595	ENST00000261921.7:c.1427A>G	15.37:g.74239485A>G	ENSP00000261921:p.His476Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q6NUL3|Q96BW7	Missense_Mutation	SNP	ENST00000261921.7	37	CCDS10253.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.296368	0.81025	.	.	ENSG00000129038	ENST00000261921;ENST00000395162	T	0.39056	1.1	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.64338	0.2589	M	0.79258	2.445	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	T	0.69584	-0.5106	10	0.87932	D	0	.	13.2143	0.59849	1.0:0.0:0.0:0.0	.	476	Q08397	LOXL1_HUMAN	R	476;338	ENSP00000261921:H476R	ENSP00000261921:H476R	H	+	2	0	LOXL1	72026538	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.057000	0.93889	1.804000	0.52760	0.379000	0.24179	CAC		0.587	LOXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268995.2		NM_005576	
LRGUK	136332	hgsc.bcm.edu;ucsc.edu	37	7	133848194	133848198	+	Frame_Shift_Del	DEL	GCCCT	GCCCT	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	GCCCT	GCCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr7:133848194_133848198delGCCCT	ENST00000285928.2	+	7	910_914	c.841_845delGCCCT	c.(841-846)gccctgfs	p.AL281fs		NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	281						cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)			breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	49						GGATCTGAAAGCCCTGCAGAACCTG	0.415																																																	0																																										SO:0001589	frameshift_variant	136332			AK057348	CCDS5830.1	7q33	2006-10-27			ENSG00000155530	ENSG00000155530			21964	protein-coding gene	gene with protein product							Standard	NM_144648		Approved	FLJ32786	uc003vrm.1	Q96M69	OTTHUMG00000155320	ENST00000285928.2:c.841_845delGCCCT	7.37:g.133848194_133848198delGCCCT	ENSP00000285928:p.Ala281fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q2M3I1	Frame_Shift_Del	DEL	ENST00000285928.2	37	CCDS5830.1																																																																																				0.415	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1		NM_144648	
MAP3K4	4216	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	161513128	161513128	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr6:161513128G>T	ENST00000392142.4	+	13	3370	c.3222G>T	c.(3220-3222)atG>atT	p.M1074I	MAP3K4_ENST00000366919.2_Missense_Mutation_p.M1074I|MAP3K4_ENST00000366920.2_Missense_Mutation_p.M1074I|MAP3K4_ENST00000348824.7_Missense_Mutation_p.M1074I	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	1074					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)	p.M1074I(2)		breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		GGAAGTGGATGAATTATGTCC	0.398																																																	2	Substitution - Missense(2)	kidney(2)											210.0	221.0	217.0					6																	161513128		2203	4300	6503	SO:0001583	missense	4216			AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.3222G>T	6.37:g.161513128G>T	ENSP00000375986:p.Met1074Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Missense_Mutation	SNP	ENST00000392142.4	37	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.616573	0.87359	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	T;T;T;T	0.75154	-0.9;-0.83;-0.9;-0.91	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.82962	0.5151	M	0.71036	2.16	0.80722	D	1	P;B;D;D	0.61080	0.942;0.349;0.962;0.989	P;B;D;D	0.68483	0.885;0.061;0.946;0.958	T	0.77566	-0.2540	10	0.30854	T	0.27	-48.2391	20.5827	0.99408	0.0:0.0:1.0:0.0	.	1074;64;1074;1074	F5H538;Q9P1M2;Q9Y6R4-2;Q9Y6R4	.;.;.;M3K4_HUMAN	I	1074	ENSP00000355886:M1074I;ENSP00000375986:M1074I;ENSP00000355887:M1074I;ENSP00000297332:M1074I	ENSP00000297332:M1074I	M	+	3	0	MAP3K4	161433118	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.420000	0.97426	2.941000	0.99782	0.655000	0.94253	ATG		0.398	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			
MAU2	23383	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	19459978	19459978	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr19:19459978G>A	ENST00000392313.6	+	15	1552	c.1373G>A	c.(1372-1374)cGa>cAa	p.R458Q	MAU2_ENST00000262815.8_Missense_Mutation_p.R458Q	NM_015329.3	NP_056144.3	Q9Y6X3	SCC4_HUMAN	MAU2 sister chromatid cohesion factor	458					maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	protein N-terminus binding (GO:0047485)	p.R458Q(1)		NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	18						CACTGCCTCCGAGCAGCCGCC	0.582																																																	1	Substitution - Missense(1)	kidney(1)											79.0	66.0	71.0					19																	19459978		2203	4300	6503	SO:0001583	missense	23383			AB020699	CCDS32969.2	19p13.11	2013-08-28	2013-08-28	2013-08-28	ENSG00000129933	ENSG00000129933			29140	protein-coding gene	gene with protein product	"""sister chromatid cohesion 4"""	614560	"""KIAA0892"", ""MAU2 chromatid cohesion factor homolog (C. elegans)"""	KIAA0892		10048485	Standard	NM_015329		Approved	MGC75361, mau-2, MAU2L, SCC4	uc002nmk.4	Q9Y6X3	OTTHUMG00000150188	ENST00000392313.6:c.1373G>A	19.37:g.19459978G>A	ENSP00000376127:p.Arg458Gln	Somatic		WXS	Illumina HiSeq	Phase_I	Q66PT1|Q6P3S7|Q6ZTT2|Q9UFX8	Missense_Mutation	SNP	ENST00000392313.6	37	CCDS32969.2	.	.	.	.	.	.	.	.	.	.	G	14.68	2.606449	0.46527	.	.	ENSG00000129933	ENST00000392313;ENST00000262815	T;T	0.62941	-0.01;-0.01	4.86	3.83	0.44106	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.48572	0.1507	L	0.52364	1.645	0.58432	D	0.999995	B;B;P	0.46656	0.44;0.35;0.882	B;B;B	0.35353	0.025;0.009;0.201	T	0.45440	-0.9261	10	0.16420	T	0.52	.	12.087	0.53702	0.0851:0.0:0.9149:0.0	.	34;63;458	Q9Y6X3-3;Q9Y6X3-2;Q9Y6X3	.;.;SCC4_HUMAN	Q	458	ENSP00000376127:R458Q;ENSP00000262815:R458Q	ENSP00000262815:R458Q	R	+	2	0	MAU2	19320978	1.000000	0.71417	0.155000	0.22561	0.348000	0.29142	9.006000	0.93592	1.188000	0.43014	0.655000	0.94253	CGA		0.582	MAU2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316748.6		NM_015329	
MTSS1	9788	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	125565825	125565825	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr8:125565825C>T	ENST00000518547.1	-	14	2149	c.1676G>A	c.(1675-1677)cGa>cAa	p.R559Q	MTSS1_ENST00000378017.3_Missense_Mutation_p.R534Q|MTSS1_ENST00000395508.2_Missense_Mutation_p.R333Q|MTSS1_ENST00000524090.1_Missense_Mutation_p.R449Q|MTSS1_ENST00000325064.5_Missense_Mutation_p.R563Q|NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000354184.4_Missense_Mutation_p.R277Q|MTSS1_ENST00000431961.2_Missense_Mutation_p.R277Q|MTSS1_ENST00000523587.1_5'UTR	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	559					actin cytoskeleton organization (GO:0030036)|actin filament polymerization (GO:0030041)|adherens junction maintenance (GO:0034334)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|cellular response to fluid shear stress (GO:0071498)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|filopodium assembly (GO:0046847)|glomerulus morphogenesis (GO:0072102)|in utero embryonic development (GO:0001701)|magnesium ion homeostasis (GO:0010960)|microspike assembly (GO:0030035)|negative regulation of epithelial cell proliferation (GO:0050680)|nephron tubule epithelial cell differentiation (GO:0072160)|positive regulation of actin filament bundle assembly (GO:0032233)|renal tubule morphogenesis (GO:0061333)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)	p.R559Q(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			GAACATCCGTCGGTAGGACTG	0.557																																					Esophageal Squamous(160;622 1893 3862 8546 12509)												1	Substitution - Missense(1)	kidney(1)											81.0	56.0	64.0					8																	125565825		2203	4300	6503	SO:0001583	missense	9788			AF086645	CCDS6353.1, CCDS64968.1, CCDS64969.1	8p22	2008-02-05			ENSG00000170873	ENSG00000170873			20443	protein-coding gene	gene with protein product		608486				12482861, 12082544	Standard	XM_005251111		Approved	KIAA0429, MIMA, MIMB, MIM	uc003yrk.2	O43312	OTTHUMG00000048189	ENST00000518547.1:c.1676G>A	8.37:g.125565825C>T	ENSP00000429064:p.Arg559Gln	Somatic		WXS	Illumina HiSeq	Phase_I	J3KNK6|Q8TCA2|Q96RX2	Missense_Mutation	SNP	ENST00000518547.1	37	CCDS6353.1	.	.	.	.	.	.	.	.	.	.	C	17.61	3.432402	0.62844	.	.	ENSG00000170873	ENST00000378017;ENST00000518547;ENST00000354184;ENST00000395508;ENST00000325064;ENST00000431961;ENST00000524090	T;T;T;T;T;T;T	0.51071	0.84;0.72;0.9;0.81;0.72;0.9;0.78	6.04	5.17	0.71159	.	0.123853	0.52532	D	0.000070	T	0.63105	0.2483	L	0.56280	1.765	0.50813	D	0.999891	D;D;D;D;D;D;D	0.89917	0.983;1.0;1.0;1.0;1.0;0.999;1.0	P;D;D;D;D;D;D	0.87578	0.492;0.997;0.996;0.992;0.998;0.99;0.994	T	0.60100	-0.7329	10	0.28530	T	0.3	-12.4428	15.3659	0.74523	0.0:0.9335:0.0:0.0665	.	449;333;534;559;534;277;208	E7EWW5;B7Z3B6;A5YM41;O43312;O43312-4;O43312-2;Q6ZTG0	.;.;.;MTSS1_HUMAN;.;.;.	Q	534;559;277;333;563;277;449	ENSP00000367256:R534Q;ENSP00000429064:R559Q;ENSP00000346119:R277Q;ENSP00000378884:R333Q;ENSP00000322804:R563Q;ENSP00000393606:R277Q;ENSP00000428319:R449Q	ENSP00000322804:R563Q	R	-	2	0	MTSS1	125635006	1.000000	0.71417	0.948000	0.38648	0.033000	0.12548	7.625000	0.83145	1.573000	0.49748	-0.258000	0.10820	CGA		0.557	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3		NM_014751	
MTUS2	23281	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	29599346	29599346	+	Nonsense_Mutation	SNP	G	G	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr13:29599346G>T	ENST00000431530.3	+	1	599	c.541G>T	c.(541-543)Gaa>Taa	p.E181*		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	171						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)	p.E181*(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						TGACAATGAGGAACTGAGGAG	0.532																																																	1	Substitution - Nonsense(1)	kidney(1)											76.0	79.0	78.0					13																	29599346		2038	4199	6237	SO:0001587	stop_gained	23281			AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"""+TIP of 150 kDa"", ""cardiac zipper protein"""		"""KIAA0774"""	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.541G>T	13.37:g.29599346G>T	ENSP00000392057:p.Glu181*	Somatic		WXS	Illumina HiSeq	Phase_I	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Nonsense_Mutation	SNP	ENST00000431530.3	37	CCDS45022.1	.	.	.	.	.	.	.	.	.	.	g	37	6.001039	0.97189	.	.	ENSG00000132938	ENST00000431530	.	.	.	5.18	5.18	0.71444	.	0.365223	0.23293	N	0.049767	.	.	.	.	.	.	0.25407	N	0.9884	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.0125	0.24871	0.0965:0.1778:0.7257:0.0	.	.	.	.	X	181	.	.	E	+	1	0	MTUS2	28497346	0.998000	0.40836	0.967000	0.41034	0.578000	0.36192	2.756000	0.47549	2.406000	0.81754	0.561000	0.74099	GAA		0.532	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3		XM_166270	
KAT7	11143	broad.mit.edu;hgsc.bcm.edu	37	17	47895315	47895315	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr17:47895315A>G	ENST00000259021.4	+	9	1377	c.1097A>G	c.(1096-1098)tAt>tGt	p.Y366C	KAT7_ENST00000435742.2_Missense_Mutation_p.Y180C|KAT7_ENST00000454930.2_Missense_Mutation_p.Y227C|KAT7_ENST00000424009.2_Missense_Mutation_p.Y336C|KAT7_ENST00000513980.1_Intron|KAT7_ENST00000510819.1_Missense_Mutation_p.Y197C|KAT7_ENST00000503935.2_Missense_Mutation_p.Y210C|KAT7_ENST00000509773.1_Missense_Mutation_p.Y256C	NM_007067.4	NP_008998.1	O95251	KAT7_HUMAN	K(lysine) acetyltransferase 7	366	MYST-type HAT.				chromatin organization (GO:0006325)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.Y366C(1)									GGACGTCTCTATATGTGTGAA	0.438																																																	1	Substitution - Missense(1)	kidney(1)											81.0	79.0	80.0					17																	47895315		2203	4300	6503	SO:0001583	missense	0			AF074606	CCDS11554.1, CCDS56035.1, CCDS56036.1, CCDS56037.1, CCDS56038.1	17q21.32	2013-01-10	2011-07-21	2011-07-21	ENSG00000136504	ENSG00000136504	2.3.1.48	"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"""	17016	protein-coding gene	gene with protein product	"""histone acetyltransferase binding to ORC1"""	609880	"""MYST histone acetyltransferase 2"""	MYST2		10438470, 10930412	Standard	NM_001199155		Approved	HBOA, HBO1, ZC2HC7	uc002ipm.3	O95251	OTTHUMG00000161770	ENST00000259021.4:c.1097A>G	17.37:g.47895315A>G	ENSP00000259021:p.Tyr366Cys	Somatic		WXS	Illumina HiSeq	Phase_I	B3KN74|B4DF85|B4DFB4|B4DFE0|B4DGY4|E7ER15|G5E9K7	Missense_Mutation	SNP	ENST00000259021.4	37	CCDS11554.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.349023	0.82132	.	.	ENSG00000136504	ENST00000259021;ENST00000454930;ENST00000509773;ENST00000510819;ENST00000424009;ENST00000503935;ENST00000435742	.	.	.	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	D	0.86108	0.5854	H	0.94698	3.57	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.75484	0.977;0.983;0.942;0.962;0.985;0.986	D	0.90092	0.4178	9	0.87932	D	0	-12.4492	14.338	0.66606	1.0:0.0:0.0:0.0	.	329;197;256;227;366;336	B4DGY4;B4DFE0;B4DFB4;E7ER15;O95251;G5E9K7	.;.;.;.;KAT7_HUMAN;.	C	366;227;256;197;336;210;180	.	ENSP00000259021:Y366C	Y	+	2	0	KAT7	45250314	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.417000	0.80156	1.874000	0.54306	0.460000	0.39030	TAT		0.438	KAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366032.1		NM_007067	
NAP1L3	4675	hgsc.bcm.edu	37	X	92928035	92928036	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chrX:92928035_92928036insC	ENST00000373079.3	-	1	531_532	c.268_269insG	c.(268-270)gccfs	p.A90fs	NAP1L3_ENST00000475430.2_Frame_Shift_Ins_p.A83fs|FAM133A_ENST00000355813.5_5'Flank|FAM133A_ENST00000322139.4_5'Flank|FAM133A_ENST00000332647.4_5'Flank|FAM133A_ENST00000538690.1_5'Flank	NM_004538.5	NP_004529.2	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	90					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	34						TCCCAACGGGGCCCGCCGCGCC	0.564																																																	0																																										SO:0001589	frameshift_variant	4675				CCDS14465.1	Xq21.3-q22	2008-08-01			ENSG00000186310	ENSG00000186310			7639	protein-coding gene	gene with protein product		300117				8976385	Standard	NM_004538		Approved	MB20, NPL3, MGC26312	uc004efq.3	Q99457	OTTHUMG00000021974	ENST00000373079.3:c.269dupG	X.37:g.92928038_92928038dupC	ENSP00000362171:p.Ala90fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2RCM0|O60788	Frame_Shift_Ins	INS	ENST00000373079.3	37	CCDS14465.1																																																																																				0.564	NAP1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057449.1		NM_004538	
NEURL1	9148	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	105330649	105330649	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr10:105330649C>A	ENST00000369780.4	+	2	515	c.106C>A	c.(106-108)Ccc>Acc	p.P36T	NEURL_ENST00000369777.2_Missense_Mutation_p.P19T	NM_004210.4	NP_004201.3	O76050	NEUL1_HUMAN		36					brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|lactation (GO:0007595)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Notch signaling pathway (GO:0045746)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse maturation (GO:0090129)|protein monoubiquitination (GO:0006513)|skeletal muscle tissue development (GO:0007519)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)	apical dendrite (GO:0097440)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|translation factor activity, non-nucleic acid binding (GO:0045183)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P36T(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	17				Epithelial(162;2.12e-09)|all cancers(201;6.99e-08)|BRCA - Breast invasive adenocarcinoma(275;0.125)		GGGCCCCTTCCCCGTCACTTC	0.652																																																	1	Substitution - Missense(1)	kidney(1)											109.0	128.0	122.0					10																	105330649		2203	4300	6503	SO:0001583	missense	9148																														ENST00000369780.4:c.106C>A	10.37:g.105330649C>A	ENSP00000358795:p.Pro36Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q5TDR2|Q5TDR3|Q8TAN0|Q9H463	Missense_Mutation	SNP	ENST00000369780.4	37	CCDS7551.1	.	.	.	.	.	.	.	.	.	.	C	18.50	3.637890	0.67130	.	.	ENSG00000107954	ENST00000369780;ENST00000437579;ENST00000369777	.	.	.	4.51	4.51	0.55191	.	0.000000	0.85682	D	0.000000	T	0.47600	0.1454	L	0.34521	1.04	0.58432	D	0.999999	D	0.55605	0.972	P	0.48304	0.573	T	0.44329	-0.9335	9	0.40728	T	0.16	-11.7665	12.8724	0.57972	0.0:0.9183:0.0:0.0817	.	36	O76050	NEU1A_HUMAN	T	36;19;19	.	ENSP00000358792:P19T	P	+	1	0	NEURL	105320639	0.999000	0.42202	0.996000	0.52242	0.633000	0.38033	4.445000	0.60007	2.317000	0.78254	0.561000	0.74099	CCC		0.652	NEURL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050170.1			
NPNT	255743	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	106819134	106819134	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr4:106819134C>T	ENST00000379987.2	+	2	364	c.148C>T	c.(148-150)Cgc>Tgc	p.R50C	NPNT_ENST00000506666.1_Missense_Mutation_p.R50C|NPNT_ENST00000427316.2_Missense_Mutation_p.R50C|NPNT_ENST00000453617.2_Missense_Mutation_p.R50C|NPNT_ENST00000514622.1_Missense_Mutation_p.R50C|NPNT_ENST00000305572.8_Missense_Mutation_p.R50C	NM_001033047.2	NP_001028219.1	Q6UXI9	NPNT_HUMAN	nephronectin	50					branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to tumor necrosis factor (GO:0071356)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|pilomotor reflex (GO:0097195)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|ureteric bud development (GO:0001657)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integrin alpha8-beta1 complex (GO:0034678)|proteinaceous extracellular matrix (GO:0005578)|smooth muscle contractile fiber (GO:0030485)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)	p.R50C(1)		kidney(5)|large_intestine(2)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	21		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)		GGGCTGGGCTCGCCAGTCTTG	0.522																																																	1	Substitution - Missense(1)	kidney(1)											113.0	102.0	105.0					4																	106819134		2203	4300	6503	SO:0001583	missense	255743				CCDS34046.1, CCDS54784.1, CCDS54785.1, CCDS54786.1, CCDS54787.1	4q25	2005-10-07							27405	protein-coding gene	gene with protein product		610306				15754038	Standard	NM_001033047		Approved	EGFL6L, POEM	uc011cfd.2	Q6UXI9		ENST00000379987.2:c.148C>T	4.37:g.106819134C>T	ENSP00000369323:p.Arg50Cys	Somatic		WXS	Illumina HiSeq	Phase_I	A6NFT9|A8K1W4|B4DIT4|B4DYK3|B4E2H7|B4E3H2|D6RCA1|E9PCK8|E9PCQ1|E9PE64|E9PF04	Missense_Mutation	SNP	ENST00000379987.2	37	CCDS34046.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.5|24.5	4.533819|4.533819	0.85812|0.85812	.|.	.|.	ENSG00000168743|ENSG00000168743	ENST00000379987;ENST00000453617;ENST00000427316;ENST00000514622;ENST00000305572;ENST00000506666;ENST00000503451|ENST00000514837	T;T;T;T;T;T;T|.	0.79352|.	-1.26;-1.26;-1.26;-1.26;-1.26;-1.26;-1.26|.	5.81|5.81	5.81|5.81	0.92471|0.92471	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.84745|0.84745	0.5540|0.5540	M|M	0.89214|0.89214	3.015|3.015	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	1.0;0.997;0.994;0.981;1.0;0.996|.	D;P;P;P;D;P|.	0.85130|.	0.984;0.816;0.816;0.726;0.997;0.724|.	D|D	0.86348|0.86348	0.1709|0.1709	10|5	0.45353|.	T|.	0.12|.	.|.	18.854|18.854	0.92244|0.92244	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	50;50;50;50;50;50|.	E9PF04;E9PE64;E9PCQ1;E9PCK8;Q6UXI9-2;Q6UXI9|.	.;.;.;.;.;NPNT_HUMAN|.	C|L	50|26	ENSP00000369323:R50C;ENSP00000402884:R50C;ENSP00000389252:R50C;ENSP00000422044:R50C;ENSP00000302557:R50C;ENSP00000422474:R50C;ENSP00000426146:R50C|.	ENSP00000302557:R50C|.	R|S	+|+	1|2	0|0	NPNT|NPNT	107038583|107038583	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.950000|0.950000	0.60333|0.60333	3.860000|3.860000	0.55995|0.55995	2.746000|2.746000	0.94184|0.94184	0.655000|0.655000	0.94253|0.94253	CGC|TCG		0.522	NPNT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364083.1		NM_198278	
OAS1	4938	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	113346530	113346530	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr12:113346530C>A	ENST00000202917.5	+	2	633	c.370C>A	c.(370-372)Cca>Aca	p.P124T	RP1-71H24.1_ENST00000552784.1_RNA|OAS1_ENST00000445409.2_Missense_Mutation_p.P124T|OAS1_ENST00000452357.2_Missense_Mutation_p.P124T|OAS1_ENST00000553185.1_Missense_Mutation_p.P124T|OAS1_ENST00000551241.1_Missense_Mutation_p.P124T	NM_016816.2	NP_058132.2	P00973	OAS1_HUMAN	2'-5'-oligoadenylate synthetase 1, 40/46kDa	124					cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|protein oligomerization (GO:0051259)|purine nucleotide biosynthetic process (GO:0006164)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)	p.P124T(3)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)|skin(1)	16						GGTCCAGGCTCCACGCTGGGG	0.577																																																	3	Substitution - Missense(3)	kidney(3)											83.0	79.0	80.0					12																	113346530		2203	4300	6503	SO:0001583	missense	4938			X04371	CCDS31905.1, CCDS41838.1, CCDS44980.1	12q24.2	2014-05-21	2011-07-21				2.7.7.-		8086	protein-coding gene	gene with protein product		164350	"""2',5'-oligoadenylate synthetase 1 (40-46 kD)"""	OIAS		9344649, 9325053	Standard	XM_006719434		Approved	OIASI, IFI-4	uc001tud.3	P00973		ENST00000202917.5:c.370C>A	12.37:g.113346530C>A	ENSP00000202917:p.Pro124Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A8K4N8|P04820|P29080|P29081|P78485|P78486|Q16700|Q16701|Q1PG42|Q3ZM01|Q53GC5|Q53YA4|Q6A1Z3|Q6IPC6|Q6P7N9|Q96J61	Missense_Mutation	SNP	ENST00000202917.5	37	CCDS41838.1	.	.	.	.	.	.	.	.	.	.	C	3.348	-0.133143	0.06711	.	.	ENSG00000089127	ENST00000202917;ENST00000445409;ENST00000452357;ENST00000549820;ENST00000551241;ENST00000377508;ENST00000553185;ENST00000550689	T;T;T;T;T;T	0.07908	3.15;3.15;3.15;3.15;3.15;3.15	3.58	-0.663	0.11410	.	4.273350	0.00589	N	0.000355	T	0.05502	0.0145	N	0.16368	0.405	0.09310	N	1	B;B;B;B;B;B	0.15719	0.014;0.001;0.001;0.002;0.008;0.001	B;B;B;B;B;B	0.16722	0.016;0.004;0.001;0.006;0.005;0.004	T	0.33085	-0.9882	10	0.23302	T	0.38	2.0888	2.9683	0.05915	0.1938:0.4466:0.0:0.3596	.	124;124;124;124;124;124	B4DWE7;E7EMI9;F8VXY3;P00973;P00973-3;P00973-2	.;.;.;OAS1_HUMAN;.;.	T	124;124;124;124;124;124;124;120	ENSP00000202917:P124T;ENSP00000388001:P124T;ENSP00000415721:P124T;ENSP00000448790:P124T;ENSP00000448001:P124T;ENSP00000448348:P120T	ENSP00000202917:P124T	P	+	1	0	OAS1	111830913	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-3.441000	0.00470	-0.252000	0.09528	-0.463000	0.05309	CCA		0.577	OAS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405896.2			
PABPC1	26986	broad.mit.edu;hgsc.bcm.edu	37	8	101719135	101719135	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr8:101719135A>T	ENST00000318607.5	-	10	2555	c.1427T>A	c.(1426-1428)gTc>gAc	p.V476D	PABPC1_ENST00000519596.1_Intron|PABPC1_ENST00000519004.1_Missense_Mutation_p.V431D|PABPC1_ENST00000522387.1_Missense_Mutation_p.V444D|AP001205.1_ENST00000579868.1_RNA	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	476					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|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)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)	p.V476D(1)		breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			TGTTGACATGACTCGTGGAAC	0.393																																																	1	Substitution - Missense(1)	kidney(1)											78.0	74.0	75.0					8																	101719135		2203	4300	6503	SO:0001583	missense	26986			Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756		"""RNA binding motif (RRM) containing"""	8554	protein-coding gene	gene with protein product		604679	"""poly(A)-binding protein, cytoplasmic 2"""	PAB1, PABPC2		2885805	Standard	XM_005250861		Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.1427T>A	8.37:g.101719135A>T	ENSP00000313007:p.Val476Asp	Somatic		WXS	Illumina HiSeq	Phase_I	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	27.1|27.1	4.800090|4.800090	0.90538|0.90538	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000520868;ENST00000517403|ENST00000318607;ENST00000519004;ENST00000522387;ENST00000522658	.|T;T;T;T	.|0.46819	.|1.66;1.56;2.63;0.86	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	.|0.000000	.|0.56097	.|D	.|0.000021	T|T	0.45915|0.45915	0.1366|0.1366	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	.|B;B;B	.|0.23540	.|0.037;0.087;0.022	.|B;B;B	.|0.21546	.|0.017;0.035;0.028	T|T	0.34153|0.34153	-0.9840|-0.9840	5|10	.|0.36615	.|T	.|0.2	.|.	16.1251|16.1251	0.81386|0.81386	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|444;476;476	.|E7ERJ7;B3KT93;P11940	.|.;.;PABP1_HUMAN	T|D	9;129|476;431;444;23	.|ENSP00000313007:V476D;ENSP00000429594:V431D;ENSP00000429395:V444D;ENSP00000428840:V23D	.|ENSP00000313007:V476D	S|V	-|-	1|2	0|0	PABPC1|PABPC1	101788311|101788311	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	8.628000|8.628000	0.90979|0.90979	2.272000|2.272000	0.75746|0.75746	0.528000|0.528000	0.53228|0.53228	TCA|GTC		0.393	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1		NM_002568	
PAH	5053	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	103240687	103240687	+	Nonsense_Mutation	SNP	C	C	A	rs398123294		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr12:103240687C>A	ENST00000553106.1	-	9	1427	c.955G>T	c.(955-957)Gaa>Taa	p.E319*	PAH_ENST00000307000.2_Nonsense_Mutation_p.E314*	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	319					catecholamine biosynthetic process (GO:0042423)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|phenylalanine 4-monooxygenase activity (GO:0004505)	p.E319*(1)		endometrium(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(5)|skin(2)|urinary_tract(1)	27					Droxidopa(DB06262)|Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	GCGAGCTTTTCAATGTATTCA	0.488																																																	1	Substitution - Nonsense(1)	kidney(1)											137.0	124.0	128.0					12																	103240687		2203	4300	6503	SO:0001587	stop_gained	5053			U49897	CCDS9092.1	12q22-q24.2	2010-04-27				ENSG00000171759	1.14.16.1		8582	protein-coding gene	gene with protein product	"""phenylalanine 4-monooxygenase"""	612349				2063869	Standard	NM_000277		Approved	PH	uc001tjq.1	P00439		ENST00000553106.1:c.955G>T	12.37:g.103240687C>A	ENSP00000448059:p.Glu319*	Somatic		WXS	Illumina HiSeq	Phase_I	Q16717|Q8TC14	Nonsense_Mutation	SNP	ENST00000553106.1	37	CCDS9092.1	.	.	.	.	.	.	.	.	.	.	C	39	7.832619	0.98513	.	.	ENSG00000171759	ENST00000553106;ENST00000307000	.	.	.	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-26.4316	19.1358	0.93428	0.0:1.0:0.0:0.0	.	.	.	.	X	319;314	.	ENSP00000303500:E314X	E	-	1	0	PAH	101764817	1.000000	0.71417	0.985000	0.45067	0.145000	0.21501	4.550000	0.60733	2.523000	0.85059	0.650000	0.86243	GAA		0.488	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1			
PIK3C3	5289	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	39567803	39567803	+	Missense_Mutation	SNP	A	A	T	rs368043076		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr18:39567803A>T	ENST00000262039.4	+	5	645	c.559A>T	c.(559-561)Atg>Ttg	p.M187L	PIK3C3_ENST00000398870.3_Missense_Mutation_p.M124L	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3	187					autophagic vacuole assembly (GO:0000045)|cytokinesis (GO:0000910)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein processing (GO:0016485)|regulation of protein secretion (GO:0050708)|response to leucine (GO:0043201)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)|midbody (GO:0030496)|phagocytic vesicle (GO:0045335)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|protein kinase activity (GO:0004672)	p.M187L(1)		breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(25)|ovary(1)|skin(2)|urinary_tract(1)	49						ACAAGGACACATGGTGAAAGT	0.318										TSP Lung(28;0.18)																											NSCLC(37;552 1060 2683 16430 37914)												1	Substitution - Missense(1)	kidney(1)											105.0	106.0	106.0					18																	39567803		2203	4300	6503	SO:0001583	missense	5289			Z46973	CCDS11920.1	18q12.3	2012-07-13	2012-07-13		ENSG00000078142	ENSG00000078142	2.7.1.137		8974	protein-coding gene	gene with protein product		602609	"""phosphoinositide-3-kinase, class 3"""			7628435	Standard	NM_002647		Approved	Vps34	uc002lap.3	Q8NEB9	OTTHUMG00000132593	ENST00000262039.4:c.559A>T	18.37:g.39567803A>T	ENSP00000262039:p.Met187Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q15134	Missense_Mutation	SNP	ENST00000262039.4	37	CCDS11920.1	.	.	.	.	.	.	.	.	.	.	A	14.86	2.662546	0.47572	.	.	ENSG00000078142	ENST00000262039;ENST00000398870	T;T	0.76186	-1.0;-1.0	5.66	5.66	0.87406	Phosphoinositide 3-kinase, C2 (1);	0.000000	0.85682	D	0.000000	T	0.62159	0.2405	N	0.24115	0.695	0.80722	D	1	B;B	0.09022	0.001;0.002	B;B	0.14023	0.01;0.01	T	0.57021	-0.7882	9	.	.	.	.	16.1819	0.81915	1.0:0.0:0.0:0.0	.	124;187	A8MYT4;Q8NEB9	.;PK3C3_HUMAN	L	187;124	ENSP00000262039:M187L;ENSP00000381845:M124L	.	M	+	1	0	PIK3C3	37821801	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.436000	0.80404	2.279000	0.76181	0.533000	0.62120	ATG		0.318	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255804.1		NM_002647	
PIP5K1C	23396	broad.mit.edu;hgsc.bcm.edu	37	19	3651895	3651895	+	Silent	SNP	C	C	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr19:3651895C>A	ENST00000335312.3	-	8	1144	c.1056G>T	c.(1054-1056)gcG>gcT	p.A352A	PIP5K1C_ENST00000587482.1_5'UTR|PIP5K1C_ENST00000589578.1_Silent_p.A352A|PIP5K1C_ENST00000539785.1_Silent_p.A352A|PIP5K1C_ENST00000537021.1_Silent_p.A352A	NM_001195733.1|NM_012398.2	NP_001182662.1|NP_036530.1	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, gamma	352	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				actin cytoskeleton organization (GO:0030036)|adherens junction assembly (GO:0034333)|axon guidance (GO:0007411)|clathrin-mediated endocytosis (GO:0072583)|cytoskeletal anchoring at plasma membrane (GO:0007016)|neutrophil chemotaxis (GO:0030593)|phagocytosis (GO:0006909)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet aggregation (GO:0070527)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle exocytosis (GO:0016079)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)	p.A352A(1)		large_intestine(3)|ovary(1)|skin(3)|stomach(2)	9		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		TGGAGTAGAGCGCCTTCTGGC	0.706																																					Esophageal Squamous(135;99 1744 12852 27186 39851)												1	Substitution - coding silent(1)	kidney(1)											38.0	38.0	38.0					19																	3651895		2202	4296	6498	SO:0001819	synonymous_variant	23396			AB011161	CCDS32872.1, CCDS56074.1, CCDS74257.1	19p13.3	2012-10-02			ENSG00000186111	ENSG00000186111			8996	protein-coding gene	gene with protein product		606102				9535851	Standard	NM_001195733		Approved	PIP5Kgamma, KIAA0589, LCCS3	uc002lyj.2	O60331	OTTHUMG00000180870	ENST00000335312.3:c.1056G>T	19.37:g.3651895C>A		Somatic		WXS	Illumina HiSeq	Phase_I	B7Z9E7|C6GIJ7|C6GIJ8|Q7LE07	Silent	SNP	ENST00000335312.3	37	CCDS32872.1																																																																																				0.706	PIP5K1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453432.2		NM_012398	
PLEKHH2	130271	hgsc.bcm.edu;ucsc.edu	37	2	43939458	43939458	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr2:43939458delA	ENST00000282406.4	+	15	2506	c.2396delA	c.(2395-2397)caafs	p.Q799fs		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	799					negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				CTTCGAGTACAAGCTGCCAAC	0.463																																																	0													121.0	107.0	112.0					2																	43939458		2203	4300	6503	SO:0001589	frameshift_variant	130271			AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"""Pleckstrin homology (PH) domain containing"""	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.2396delA	2.37:g.43939458delA	ENSP00000282406:p.Gln799fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q5JPJ6|Q6P4Q1|Q8N3Q3	Frame_Shift_Del	DEL	ENST00000282406.4	37	CCDS1812.1																																																																																				0.463	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1		NM_172069	
PLEKHM2	23207	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	16058448	16058448	+	Missense_Mutation	SNP	A	A	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr1:16058448A>C	ENST00000375799.3	+	17	2757	c.2530A>C	c.(2530-2532)Att>Ctt	p.I844L	PLEKHM2_ENST00000477849.1_3'UTR|RP11-288I21.1_ENST00000453804.1_RNA|PLEKHM2_ENST00000375793.2_Missense_Mutation_p.I824L	NM_015164.2	NP_055979.2	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 2	844	Interaction with sifA.|PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				Golgi organization (GO:0007030)	cytoplasm (GO:0005737)	kinesin binding (GO:0019894)	p.I844L(1)|p.I947L(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		CTTCCAGGTCATTCTCTCCGA	0.667																																																	2	Substitution - Missense(2)	kidney(2)											23.0	31.0	28.0					1																	16058448		2095	4195	6290	SO:0001583	missense	23207			AB020649	CCDS44063.1	1p36.13	2013-01-10			ENSG00000116786	ENSG00000116786		"""Pleckstrin homology (PH) domain containing"""	29131	protein-coding gene	gene with protein product		609613				10048485	Standard	NM_015164		Approved	KIAA0842	uc010obo.2	Q8IWE5	OTTHUMG00000003062	ENST00000375799.3:c.2530A>C	1.37:g.16058448A>C	ENSP00000364956:p.Ile844Leu	Somatic		WXS	Illumina HiSeq	Phase_I	O94928|Q5VT65|Q6NUH9|Q7L8G1|Q8IVT7|Q8N2T4|Q96AY0|Q9NTF7	Missense_Mutation	SNP	ENST00000375799.3	37	CCDS44063.1	.	.	.	.	.	.	.	.	.	.	A	17.79	3.476875	0.63849	.	.	ENSG00000116786	ENST00000375799;ENST00000375793	T;T	0.74947	-0.89;-0.89	5.27	2.93	0.34026	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.060042	0.64402	D	0.000003	T	0.65386	0.2686	L	0.33485	1.01	0.53005	D	0.999966	B	0.34241	0.444	B	0.42625	0.393	T	0.52946	-0.8507	10	0.17369	T	0.5	-10.2524	9.2979	0.37827	0.8526:0.0:0.1474:0.0	.	844	Q8IWE5	PKHM2_HUMAN	L	844;824	ENSP00000364956:I844L;ENSP00000364950:I824L	ENSP00000364950:I824L	I	+	1	0	PLEKHM2	15931035	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.830000	0.39131	0.323000	0.23307	0.459000	0.35465	ATT		0.667	PLEKHM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008463.1		NM_015164	
PPFIBP2	8495	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	7663540	7663540	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr11:7663540C>T	ENST00000299492.4	+	17	1917	c.1529C>T	c.(1528-1530)aCt>aTt	p.T510I	PPFIBP2_ENST00000533792.1_Missense_Mutation_p.T352I|PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000530181.1_Missense_Mutation_p.T367I|PPFIBP2_ENST00000528883.1_Missense_Mutation_p.T398I	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	510					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)	p.T510I(1)		breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		ATCCGAAGAACTCAGTCAGGA	0.542																																																	1	Substitution - Missense(1)	kidney(1)											71.0	66.0	68.0					11																	7663540		2201	4296	6497	SO:0001583	missense	8495			AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"""Sterile alpha motif (SAM) domain containing"""	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.1529C>T	11.37:g.7663540C>T	ENSP00000299492:p.Thr510Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	37	CCDS31419.1	.	.	.	.	.	.	.	.	.	.	C	19.89	3.910927	0.72983	.	.	ENSG00000166387	ENST00000299492;ENST00000533792;ENST00000537467;ENST00000541115;ENST00000528883;ENST00000530181;ENST00000530081	T;T;T;T	0.33654	1.83;1.41;1.83;1.4	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.59376	0.2189	M	0.63843	1.955	0.52099	D	0.999946	D;D;D;D;D;D	0.89917	0.998;1.0;1.0;0.999;0.999;0.998	D;D;D;D;D;D	0.85130	0.965;0.986;0.989;0.997;0.997;0.953	T	0.56890	-0.7904	10	0.54805	T	0.06	-15.7796	17.7725	0.88497	0.0:1.0:0.0:0.0	.	398;398;433;352;367;510	E9PK77;B7Z433;F5GWB0;E9PP16;E9PMU1;Q8ND30	.;.;.;.;.;LIPB2_HUMAN	I	510;352;352;433;398;367;171	ENSP00000299492:T510I;ENSP00000436498:T352I;ENSP00000435469:T398I;ENSP00000437321:T367I	ENSP00000299492:T510I	T	+	2	0	PPFIBP2	7620116	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	4.288000	0.59007	2.798000	0.96311	0.650000	0.86243	ACT		0.542	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2		NM_003621	
PREX1	57580	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	47258752	47258752	+	Silent	SNP	C	C	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr20:47258752C>A	ENST00000371941.3	-	29	3751	c.3729G>T	c.(3727-3729)cgG>cgT	p.R1243R	PREX1_ENST00000396220.1_Silent_p.R1243R|PREX1_ENST00000496915.1_5'UTR	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1243					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R1243R(2)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CTTCGAAAGCCCGGCTCATGA	0.577																																																	2	Substitution - coding silent(2)	kidney(2)											102.0	94.0	97.0					20																	47258752		2203	4300	6503	SO:0001819	synonymous_variant	57580			AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.3729G>T	20.37:g.47258752C>A		Somatic		WXS	Illumina HiSeq	Phase_I	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	CCDS13410.1																																																																																				0.577	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1		NM_020820	
PSKH2	85481	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	87060713	87060713	+	Nonsense_Mutation	SNP	G	G	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr8:87060713G>T	ENST00000276616.2	-	3	1210	c.1136C>A	c.(1135-1137)tCg>tAg	p.S379*		NM_033126.1	NP_149117.1	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	379							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.S379*(1)		NS(1)|breast(1)|kidney(11)|large_intestine(2)|lung(26)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(1)	47			STAD - Stomach adenocarcinoma(118;0.129)			AGACAGTGGCGATTCTACTAT	0.433																																																	1	Substitution - Nonsense(1)	kidney(1)											105.0	106.0	106.0					8																	87060713		2203	4300	6503	SO:0001587	stop_gained	85481			AY037806	CCDS6240.1	8q21.13	2004-06-03				ENSG00000147613			18997	protein-coding gene	gene with protein product							Standard	NM_033126		Approved		uc011lfy.2	Q96QS6		ENST00000276616.2:c.1136C>A	8.37:g.87060713G>T	ENSP00000276616:p.Ser379*	Somatic		WXS	Illumina HiSeq	Phase_I	A0AV22	Nonsense_Mutation	SNP	ENST00000276616.2	37	CCDS6240.1	.	.	.	.	.	.	.	.	.	.	G	17.15	3.315796	0.60524	.	.	ENSG00000147613	ENST00000276616	.	.	.	4.17	2.33	0.28932	.	.	.	.	.	.	.	.	.	.	.	0.21553	N	0.999642	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.5709	0.27907	0.2188:0.0:0.7812:0.0	.	.	.	.	X	379	.	ENSP00000276616:S379X	S	-	2	0	PSKH2	87129829	0.989000	0.36119	0.035000	0.18076	0.187000	0.23431	2.021000	0.41020	1.038000	0.40049	0.591000	0.81541	TCG		0.433	PSKH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374628.1		NM_033126	
PTPRN2	5799	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	157985057	157985057	+	Missense_Mutation	SNP	C	C	T	rs137877535	byFrequency	TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr7:157985057C>T	ENST00000389418.4	-	5	520	c.511G>A	c.(511-513)Gcc>Acc	p.A171T	PTPRN2_ENST00000389413.3_Missense_Mutation_p.A171T|PTPRN2_ENST00000389416.4_Missense_Mutation_p.A154T|PTPRN2_ENST00000404321.2_Missense_Mutation_p.A194T|PTPRN2_ENST00000409483.1_Missense_Mutation_p.A133T	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	171					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.A171T(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		TGGGTCCTGGCGAGCACGTCT	0.697													C|||	8	0.00159744	0.0	0.0072	5008	,	,		14951	0.0		0.0	False		,,,				2504	0.0031																1	Substitution - Missense(1)	kidney(1)							THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	38.0	44.0	42.0		511,460,511	-1.2	0.0	7	dbSNP_134	42	2,8596	2.2+/-6.3	0,2,4297	yes	missense,missense,missense	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	58,58,58	0,2,6500	TT,TC,CC		0.0233,0.0,0.0154	benign,benign,benign	171/1016,154/999,171/987	157985057	2,13002	2203	4299	6502	SO:0001583	missense	5799			AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.511G>A	7.37:g.157985057C>T	ENSP00000374069:p.Ala171Thr	Somatic		WXS	Illumina HiSeq	Phase_I	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	C	11.79	1.742541	0.30865	0.0	2.33E-4	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.03272	4.0;3.99;4.01;4.0;4.0	4.17	-1.21	0.09524	.	.	.	.	.	T	0.01489	0.0048	N	0.24115	0.695	0.09310	N	1	B;B;B;B;B	0.10296	0.003;0.001;0.001;0.001;0.001	B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001	T	0.48536	-0.9027	9	0.20046	T	0.44	.	1.9952	0.03455	0.1803:0.2879:0.3897:0.1421	.	194;133;171;154;171	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	T	133;171;154;171;194	ENSP00000387114:A133T;ENSP00000374064:A171T;ENSP00000374067:A154T;ENSP00000374069:A171T;ENSP00000385464:A194T	ENSP00000374064:A171T	A	-	1	0	PTPRN2	157677818	0.001000	0.12720	0.002000	0.10522	0.003000	0.03518	0.596000	0.24044	-0.399000	0.07668	-1.297000	0.01338	GCC		0.697	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			
PTPRS	5802	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	5219380	5219380	+	Silent	SNP	C	C	G	rs371702194		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr19:5219380C>G	ENST00000587303.1	-	22	3963	c.3864G>C	c.(3862-3864)ggG>ggC	p.G1288G	PTPRS_ENST00000353284.2_Silent_p.G857G|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000592099.1_Silent_p.G857G|PTPRS_ENST00000262963.6_Silent_p.G1284G|PTPRS_ENST00000372412.4_Silent_p.G1289G|PTPRS_ENST00000357368.4_Silent_p.G1288G|PTPRS_ENST00000588012.1_Silent_p.G1266G|PTPRS_ENST00000348075.2_Silent_p.G1266G			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	1288					cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.G1288G(1)		NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	CCAGCACAGGCCCGATCACCC	0.572																																																	1	Substitution - coding silent(1)	kidney(1)											70.0	70.0	70.0					19																	5219380		2203	4300	6503	SO:0001819	synonymous_variant	5802			U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.3864G>C	19.37:g.5219380C>G		Somatic		WXS	Illumina HiSeq	Phase_I	O75255|O75870|Q15718|Q16341|Q2M3R7	Silent	SNP	ENST00000587303.1	37	CCDS45930.1																																																																																				0.572	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2			
RPL18	6141	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	49119434	49119434	+	Missense_Mutation	SNP	C	C	T	rs559300689		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr19:49119434C>T	ENST00000549920.1	-	5	715	c.323G>A	c.(322-324)cGg>cAg	p.R108Q	RPL18_ENST00000552588.1_Missense_Mutation_p.R79Q|RPL18_ENST00000549273.1_Missense_Mutation_p.R108Q|FAM83E_ENST00000263266.3_5'Flank|FAM83E_ENST00000595110.1_5'Flank|RPL18_ENST00000550645.1_Intron	NM_000979.3	NP_000970.1	Q07020	RL18_HUMAN	ribosomal protein L18	108					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)	p.R108Q(1)		cervix(1)|kidney(2)	3		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;9.89e-05)|all cancers(93;0.00011)|GBM - Glioblastoma multiforme(486;0.0061)|Epithelial(262;0.0154)		GCTGCGGGCCCGGCTGGTCAC	0.672																																																	1	Substitution - Missense(1)	kidney(1)											50.0	51.0	50.0					19																	49119434		2203	4300	6503	SO:0001583	missense	6141			L11566	CCDS12726.1, CCDS58669.1	19q13	2011-04-06				ENSG00000063177		"""L ribosomal proteins"""	10310	protein-coding gene	gene with protein product	"""60S ribosomal protein L18"""	604179				8218404	Standard	NM_000979		Approved	L18	uc002pjq.2	Q07020	OTTHUMG00000169760	ENST00000549920.1:c.323G>A	19.37:g.49119434C>T	ENSP00000447001:p.Arg108Gln	Somatic		WXS	Illumina HiSeq	Phase_I	F8VWC5|Q8WTZ6	Missense_Mutation	SNP	ENST00000549920.1	37	CCDS12726.1	.	.	.	.	.	.	.	.	.	.	C	17.88	3.497973	0.64186	.	.	ENSG00000063177	ENST00000549920;ENST00000552588;ENST00000549273;ENST00000550973	.	.	.	4.99	3.93	0.45458	Ribosomal protein L18e/L15P (2);	0.253774	0.39146	N	0.001454	T	0.59335	0.2186	M	0.73319	2.225	0.41091	D	0.985594	B	0.12013	0.005	B	0.16722	0.016	T	0.58679	-0.7594	9	0.33141	T	0.24	-8.5114	12.0361	0.53425	0.0:0.9085:0.0:0.0915	.	108	Q07020	RL18_HUMAN	Q	108;79;108;56	.	ENSP00000449610:R108Q	R	-	2	0	RPL18	53811246	1.000000	0.71417	0.995000	0.50966	0.854000	0.48673	5.188000	0.65093	2.478000	0.83669	0.467000	0.42956	CGG		0.672	RPL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405732.2		NM_000979	
RYR3	6263	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	34137144	34137144	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr15:34137144G>A	ENST00000389232.4	+	93	13448	c.13378G>A	c.(13378-13380)Gcg>Acg	p.A4460T	RYR3_ENST00000415757.3_Missense_Mutation_p.A4455T	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4460					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.A4459T(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		AGAGGAAGAAGCGATGGTATT	0.473																																																	1	Substitution - Missense(1)	kidney(1)											142.0	134.0	137.0					15																	34137144		1959	4153	6112	SO:0001583	missense	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.13378G>A	15.37:g.34137144G>A	ENSP00000373884:p.Ala4460Thr	Somatic		WXS	Illumina HiSeq	Phase_I	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	16.48	3.136296	0.56936	.	.	ENSG00000198838	ENST00000389232;ENST00000361728	D	0.93659	-3.26	5.24	5.24	0.73138	Ryanodine Receptor TM 4-6 (1);	0.232351	0.36167	N	0.002747	D	0.91164	0.7217	L	0.46157	1.445	0.46317	D	0.998986	B;P	0.35107	0.277;0.484	B;B	0.37989	0.061;0.262	D	0.88123	0.2833	10	0.13853	T	0.58	.	19.3787	0.94523	0.0:0.0:1.0:0.0	.	4455;4460	Q15413-2;Q15413	.;RYR3_HUMAN	T	4460;4456	ENSP00000373884:A4460T	ENSP00000354735:A4456T	A	+	1	0	RYR3	31924436	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.899000	0.56288	2.884000	0.98904	0.655000	0.94253	GCG		0.473	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			
STK10	6793	broad.mit.edu;hgsc.bcm.edu	37	5	171481605	171481605	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr5:171481605C>G	ENST00000176763.5	-	17	2963	c.2620G>C	c.(2620-2622)Gag>Cag	p.E874Q		NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	874	Gln-rich.				cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)	p.E874Q(1)		breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ATGTTGCTCTCACACTGCGCC	0.627																																																	1	Substitution - Missense(1)	kidney(1)											115.0	97.0	103.0					5																	171481605		2203	4300	6503	SO:0001583	missense	6793			AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.2620G>C	5.37:g.171481605C>G	ENSP00000176763:p.Glu874Gln	Somatic		WXS	Illumina HiSeq	Phase_I	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Missense_Mutation	SNP	ENST00000176763.5	37	CCDS34290.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.265341	0.80358	.	.	ENSG00000072786	ENST00000176763;ENST00000545839	T	0.33438	1.41	4.75	4.75	0.60458	.	0.251645	0.38605	N	0.001625	T	0.50939	0.1645	L	0.58428	1.81	0.45607	D	0.998549	D	0.67145	0.996	D	0.69142	0.962	T	0.54153	-0.8336	10	0.87932	D	0	.	15.619	0.76790	0.0:1.0:0.0:0.0	.	874	O94804	STK10_HUMAN	Q	874	ENSP00000176763:E874Q	ENSP00000176763:E874Q	E	-	1	0	STK10	171414210	1.000000	0.71417	0.958000	0.39756	0.711000	0.40976	7.771000	0.85420	2.340000	0.79590	0.561000	0.74099	GAG		0.627	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2		NM_005990	
STRN3	29966	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	31376115	31376115	+	Nonsense_Mutation	SNP	A	A	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr14:31376115A>T	ENST00000357479.5	-	14	2052	c.1856T>A	c.(1855-1857)tTg>tAg	p.L619*	STRN3_ENST00000355683.5_Nonsense_Mutation_p.L535*	NM_001083893.1	NP_001077362.1	Q13033	STRN3_HUMAN	striatin, calmodulin binding protein 3	619					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|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)|response to estradiol (GO:0032355)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L535*(1)|p.L619*(1)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.0124)		AATACATGGCAATTTTTCTTG	0.323																																																	2	Substitution - Nonsense(2)	kidney(2)											98.0	96.0	97.0					14																	31376115		2203	4300	6503	SO:0001587	stop_gained	29966				CCDS9641.1, CCDS41938.1	14q13-q21	2013-01-10			ENSG00000196792	ENSG00000196792		"""WD repeat domain containing"""	15720	protein-coding gene	gene with protein product	"""cell cycle S/G2 nuclear autoantigen"""	614766				7864889, 10681496	Standard	NM_014574		Approved	SG2NA	uc001wqu.2	Q13033	OTTHUMG00000140201	ENST00000357479.5:c.1856T>A	14.37:g.31376115A>T	ENSP00000350071:p.Leu619*	Somatic		WXS	Illumina HiSeq	Phase_I	A2RTX7|A6NHZ7|Q9NRA5	Nonsense_Mutation	SNP	ENST00000357479.5	37	CCDS41938.1	.	.	.	.	.	.	.	.	.	.	A	38	7.150070	0.98096	.	.	ENSG00000196792	ENST00000355683;ENST00000357479	.	.	.	5.73	4.56	0.56223	.	0.490128	0.23012	N	0.052956	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	-1.1221	5.7875	0.18340	0.6694:0.0:0.0695:0.2611	.	.	.	.	X	535;619	.	ENSP00000347909:L535X	L	-	2	0	STRN3	30445866	0.938000	0.31826	1.000000	0.80357	0.990000	0.78478	1.751000	0.38339	0.958000	0.37956	0.460000	0.39030	TTG		0.323	STRN3-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409713.1		NM_014574	
STT3B	201595	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	31658488	31658488	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr3:31658488G>C	ENST00000295770.2	+	7	1253	c.1044G>C	c.(1042-1044)gaG>gaC	p.E348D	STT3B_ENST00000453168.1_3'UTR	NM_178862.1	NP_849193.1	Q8TCJ2	STT3B_HUMAN	STT3B, subunit of the oligosaccharyltransferase complex (catalytic)	348					co-translational protein modification (GO:0043686)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)	p.E348D(1)		autonomic_ganglia(1)|biliary_tract(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	19						CAAAACAAGAGTTCCAGACCC	0.398																																																	1	Substitution - Missense(1)	kidney(1)											212.0	214.0	213.0					3																	31658488		2203	4300	6503	SO:0001583	missense	201595			AK027789	CCDS2650.1	3p24.1	2013-03-06	2013-03-06		ENSG00000163527	ENSG00000163527	2.4.99.18		30611	protein-coding gene	gene with protein product	"""source of immunodominant MHC associated peptides"", ""dolichyl-diphosphooligosaccharide protein glycotransferase"""	608605	"""STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)"""			12887896, 12439619	Standard	XM_006713017		Approved	SIMP, FLJ90106, STT3-B	uc011axe.2	Q8TCJ2	OTTHUMG00000130673	ENST00000295770.2:c.1044G>C	3.37:g.31658488G>C	ENSP00000295770:p.Glu348Asp	Somatic		WXS	Illumina HiSeq	Phase_I	Q96JZ4|Q96KY7	Missense_Mutation	SNP	ENST00000295770.2	37	CCDS2650.1	.	.	.	.	.	.	.	.	.	.	G	13.05	2.121478	0.37436	.	.	ENSG00000163527	ENST00000295770	.	.	.	5.44	0.157	0.14915	.	0.000000	0.85682	D	0.000000	T	0.40040	0.1101	L	0.31845	0.965	0.51767	D	0.999935	B	0.12013	0.005	B	0.18561	0.022	T	0.06862	-1.0803	9	0.36615	T	0.2	-14.109	6.7845	0.23665	0.5292:0.0:0.3519:0.1189	.	348	Q8TCJ2	STT3B_HUMAN	D	348	.	ENSP00000295770:E348D	E	+	3	2	STT3B	31633492	1.000000	0.71417	0.991000	0.47740	0.870000	0.49936	0.994000	0.29693	-0.280000	0.09154	-1.199000	0.01669	GAG		0.398	STT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253166.2		NM_178862	
SULT4A1	25830	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	44237743	44237743	+	Missense_Mutation	SNP	A	A	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr22:44237743A>C	ENST00000330884.4	-	2	359	c.239T>G	c.(238-240)aTg>aGg	p.M80R	SULT4A1_ENST00000249130.5_Missense_Mutation_p.M80R|SULT4A1_ENST00000540422.1_Intron	NM_014351.3	NP_055166.1	Q9BR01	ST4A1_HUMAN	sulfotransferase family 4A, member 1	80					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	sulfotransferase activity (GO:0008146)	p.M80R(1)		kidney(1)|large_intestine(3)|lung(4)|ovary(1)	9		Ovarian(80;0.024)|all_neural(38;0.0416)		Colorectal(1;0.00242)|READ - Rectum adenocarcinoma(1;0.0419)		GTCGATGTTCATCAAGCCGAT	0.637																																																	1	Substitution - Missense(1)	kidney(1)											60.0	58.0	59.0					22																	44237743		2203	4300	6503	SO:0001583	missense	25830			AF188698	CCDS14051.1	22q13.2	2012-11-05			ENSG00000130540	ENSG00000130540		"""Sulfotransferases, cytosolic"""	14903	protein-coding gene	gene with protein product		608359				10698717	Standard	NM_014351		Approved	SULTX3, hBR-STL-1	uc003bee.1	Q9BR01	OTTHUMG00000141314	ENST00000330884.4:c.239T>G	22.37:g.44237743A>C	ENSP00000332565:p.Met80Arg	Somatic		WXS	Illumina HiSeq	Phase_I	B2R7N3|O43728	Missense_Mutation	SNP	ENST00000330884.4	37	CCDS14051.1	.	.	.	.	.	.	.	.	.	.	A	10.82	1.457391	0.26161	.	.	ENSG00000130540	ENST00000330884;ENST00000249130	D;D	0.82255	-1.59;-1.59	4.4	4.4	0.53042	Sulfotransferase domain (1);	0.039181	0.85682	D	0.000000	T	0.69815	0.3153	N	0.12637	0.245	0.80722	D	1	B	0.20368	0.044	B	0.26094	0.066	T	0.64922	-0.6293	10	0.29301	T	0.29	.	12.7883	0.57518	1.0:0.0:0.0:0.0	.	80	Q9BR01	ST4A1_HUMAN	R	80	ENSP00000332565:M80R;ENSP00000249130:M80R	ENSP00000249130:M80R	M	-	2	0	SULT4A1	42569076	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	8.586000	0.90806	1.626000	0.50381	0.528000	0.53228	ATG		0.637	SULT4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280660.2		NM_014351	
TAS1R3	83756	broad.mit.edu;hgsc.bcm.edu	37	1	1267928	1267928	+	Silent	SNP	G	G	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr1:1267928G>A	ENST00000339381.5	+	3	1049	c.1017G>A	c.(1015-1017)aaG>aaA	p.K339K		NM_152228.1	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3	339					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)	p.K339K(1)		kidney(2)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.88e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.146)		AGTACGTGAAGACGCACCTGG	0.697																																																	1	Substitution - coding silent(1)	kidney(1)											34.0	36.0	35.0					1																	1267928		2199	4292	6491	SO:0001819	synonymous_variant	83756			AC026283	CCDS30556.1	1p36	2012-08-22			ENSG00000169962	ENSG00000169962		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	15661	protein-coding gene	gene with protein product		605865				11319557	Standard	XM_006710939		Approved	T1R3	uc010nyk.2	Q7RTX0	OTTHUMG00000003071	ENST00000339381.5:c.1017G>A	1.37:g.1267928G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q5TA49|Q8NGW9	Silent	SNP	ENST00000339381.5	37	CCDS30556.1																																																																																				0.697	TAS1R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008493.1			
THSD7B	80731	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	138033572	138033572	+	Missense_Mutation	SNP	T	T	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr2:138033572T>A	ENST00000409968.1	+	12	2654	c.2476T>A	c.(2476-2478)Tgt>Agt	p.C826S	THSD7B_ENST00000413152.2_Missense_Mutation_p.C795S|THSD7B_ENST00000272643.3_Missense_Mutation_p.C826S|THSD7B_ENST00000543459.1_Intron			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	826	TSP type-1 10. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)		p.C826S(1)|p.C795S(1)		NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		CAGTGAAGCCTGTGGAAAGGG	0.398																																																	2	Substitution - Missense(2)	kidney(2)											94.0	101.0	99.0					2																	138033572		1868	4101	5969	SO:0001583	missense	80731					2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.2476T>A	2.37:g.138033572T>A	ENSP00000387145:p.Cys826Ser	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000409968.1	37		.	.	.	.	.	.	.	.	.	.	T	23.5	4.419104	0.83559	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	T;T;T	0.79033	-1.23;-1.23;-1.23	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	D	0.89139	0.6630	M	0.85041	2.73	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.90736	0.4646	10	0.87932	D	0	.	15.307	0.74001	0.0:0.0:0.0:1.0	.	826;795	Q9C0I4;C9JKN6	THS7B_HUMAN;.	S	826;826;795	ENSP00000387145:C826S;ENSP00000272643:C826S;ENSP00000413841:C795S	ENSP00000272643:C826S	C	+	1	0	THSD7B	137750042	1.000000	0.71417	1.000000	0.80357	0.794000	0.44872	7.081000	0.76844	2.254000	0.74563	0.460000	0.39030	TGT		0.398	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2		XM_046570.9	
TTN	7273	broad.mit.edu;hgsc.bcm.edu	37	2	179558720	179558720	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr2:179558720G>T	ENST00000591111.1	-	116	30715	c.30491C>A	c.(30490-30492)aCa>aAa	p.T10164K	TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.T10481K|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T9237K			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.T9237K(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CATCTTCTTTGTATGCACAGC	0.373																																																	1	Substitution - Missense(1)	kidney(1)											107.0	93.0	97.0					2																	179558720		1855	4096	5951	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.30491C>A	2.37:g.179558720G>T	ENSP00000465570:p.Thr10164Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	14.83	2.652524	0.47362	.	.	ENSG00000155657	ENST00000342992;ENST00000414766	T	0.66815	-0.23	6.16	6.16	0.99307	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.55593	0.1930	N	0.14661	0.345	0.80722	D	1	B;P	0.49783	0.048;0.928	B;B	0.44085	0.031;0.44	T	0.62798	-0.6778	9	0.87932	D	0	.	16.3599	0.83257	0.0:0.0:1.0:0.0	.	10164;10164	Q8WZ42;Q8WZ42-5	TITIN_HUMAN;.	K	9237;359	ENSP00000343764:T9237K	ENSP00000343764:T9237K	T	-	2	0	TTN	179266965	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.484000	0.60271	2.937000	0.99478	0.650000	0.86243	ACA		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1		NM_133378	
UBE3C	9690	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	157049683	157049683	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr7:157049683G>A	ENST00000348165.5	+	22	3386	c.3026G>A	c.(3025-3027)cGc>cAc	p.R1009H		NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	1009	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R1009H(2)		central_nervous_system(2)|endometrium(3)|kidney(16)|large_intestine(13)|lung(25)|ovary(2)|prostate(1)|urinary_tract(1)	63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		GAAGAAAAGCGCAAACTGCTG	0.423																																																	2	Substitution - Missense(2)	urinary_tract(1)|kidney(1)											168.0	160.0	163.0					7																	157049683		2203	4300	6503	SO:0001583	missense	9690			AK127280	CCDS34789.1	7q36.3	2004-05-04			ENSG00000009335	ENSG00000009335			16803	protein-coding gene	gene with protein product		614454				7584026, 11278995	Standard	NM_014671		Approved	KIAA0010, KIAA10	uc010lqs.3	Q15386	OTTHUMG00000157239	ENST00000348165.5:c.3026G>A	7.37:g.157049683G>A	ENSP00000309198:p.Arg1009His	Somatic		WXS	Illumina HiSeq	Phase_I	A4D235|A6NCP3|Q8TC15|Q96CR4|Q9UDU3	Missense_Mutation	SNP	ENST00000348165.5	37	CCDS34789.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.106411	0.77096	.	.	ENSG00000009335	ENST00000348165	T	0.60299	0.2	5.67	5.67	0.87782	HECT (4);	0.000000	0.85682	D	0.000000	T	0.80444	0.4624	M	0.88310	2.945	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.987	T	0.79478	-0.1787	10	0.33141	T	0.24	.	19.7785	0.96405	0.0:0.0:1.0:0.0	.	1009;862	Q15386;B4DHJ9	UBE3C_HUMAN;.	H	1009	ENSP00000309198:R1009H	ENSP00000309198:R1009H	R	+	2	0	UBE3C	156742444	1.000000	0.71417	1.000000	0.80357	0.052000	0.14988	9.261000	0.95576	2.667000	0.90743	0.563000	0.77884	CGC		0.423	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1		NM_014671	
ZC3H18	124245	broad.mit.edu;hgsc.bcm.edu	37	16	88697620	88697620	+	Silent	SNP	G	G	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr16:88697620G>A	ENST00000301011.5	+	18	2975	c.2775G>A	c.(2773-2775)ctG>ctA	p.L925L	ZC3H18_ENST00000452588.2_Silent_p.L949L	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	925						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.L925L(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		CCAGCACGCTGTCTCGGCGGG	0.652																																					Ovarian(121;375 2276 20373 38669)												1	Substitution - coding silent(1)	kidney(1)											34.0	34.0	34.0					16																	88697620		2197	4300	6497	SO:0001819	synonymous_variant	124245			BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"""Zinc fingers, CCCH-type domain containing"""	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.2775G>A	16.37:g.88697620G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q96DG4|Q96MP7	Silent	SNP	ENST00000301011.5	37	CCDS10967.1	.	.	.	.	.	.	.	.	.	.	G	6.268	0.417611	0.11870	.	.	ENSG00000158545	ENST00000289509	.	.	.	5.61	1.44	0.22558	.	.	.	.	.	T	0.62804	0.2458	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64118	-0.6482	5	0.87932	D	0	-20.9204	7.8469	0.29431	0.178:0.219:0.6031:0.0	.	.	.	.	Y	751	.	ENSP00000289509:C751Y	C	+	2	0	ZC3H18	87225121	1.000000	0.71417	0.872000	0.34217	0.534000	0.34807	1.920000	0.40025	0.723000	0.32274	0.561000	0.74099	TGT		0.652	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1		NM_144604	
ZCCHC9	84240	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	80600797	80600797	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr5:80600797G>T	ENST00000254037.2	+	1	3376	c.221G>T	c.(220-222)gGa>gTa	p.G74V	ZCCHC9_ENST00000407610.3_Missense_Mutation_p.G74V|ZCCHC9_ENST00000506458.1_Intron|ZCCHC9_ENST00000380199.5_Missense_Mutation_p.G74V|ZCCHC9_ENST00000438268.2_Missense_Mutation_p.G74V			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	74					negative regulation of phosphatase activity (GO:0010923)		poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.G74V(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)	13		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;8.18e-45)|Epithelial(54;2.72e-39)|all cancers(79;7.33e-34)		GATGTGAATGGATTCATGGAA	0.363																																																	1	Substitution - Missense(1)	kidney(1)											82.0	82.0	82.0					5																	80600797		2203	4300	6503	SO:0001583	missense	84240			BC014841	CCDS4054.1	5q14.1	2013-01-09			ENSG00000131732	ENSG00000131732		"""Zinc fingers, CCHC domain containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25424	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 41"""					12477932	Standard	NM_032280		Approved	DKFZp761J139, PPP1R41	uc003khi.3	Q8N567	OTTHUMG00000119014	ENST00000254037.2:c.221G>T	5.37:g.80600797G>T	ENSP00000254037:p.Gly74Val	Somatic		WXS	Illumina HiSeq	Phase_I	B2RAE7|Q9H027	Missense_Mutation	SNP	ENST00000254037.2	37	CCDS4054.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.500352	0.85176	.	.	ENSG00000131732	ENST00000254037;ENST00000407610;ENST00000380199;ENST00000438268	T;T;T;T	0.54479	0.57;0.57;0.57;0.57	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.69940	0.3167	M	0.68593	2.085	0.80722	D	1	D	0.76494	0.999	P	0.61658	0.892	T	0.72988	-0.4124	10	0.87932	D	0	-18.8778	18.9545	0.92653	0.0:0.0:1.0:0.0	.	74	Q8N567	ZCHC9_HUMAN	V	74	ENSP00000254037:G74V;ENSP00000385047:G74V;ENSP00000369546:G74V;ENSP00000412637:G74V	ENSP00000254037:G74V	G	+	2	0	ZCCHC9	80636553	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	8.754000	0.91642	2.544000	0.85801	0.655000	0.94253	GGA		0.363	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239213.1		NM_032280	
RBFOX1	54715	broad.mit.edu	37	16	7703894	7703894	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr16:7703894G>A	ENST00000550418.1	+	12	1823	c.835G>A	c.(835-837)Gtg>Atg	p.V279M	RBFOX1_ENST00000553186.1_Missense_Mutation_p.V252M|RBFOX1_ENST00000422070.4_Missense_Mutation_p.V322M|RBFOX1_ENST00000355637.4_Missense_Mutation_p.V299M|RBFOX1_ENST00000535565.2_Missense_Mutation_p.V236M|RBFOX1_ENST00000436368.2_Missense_Mutation_p.V299M|RBFOX1_ENST00000552089.1_Missense_Mutation_p.V296M|RBFOX1_ENST00000547372.1_Missense_Mutation_p.V322M|RBFOX1_ENST00000340209.4_Missense_Mutation_p.V284M|RBFOX1_ENST00000311745.5_Missense_Mutation_p.V299M|RBFOX1_ENST00000547338.1_Missense_Mutation_p.V279M	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	279					mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)	p.V299M(2)|p.V279M(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						CGGTCGCACCGTGTACAACAC	0.741																																					Ovarian(157;934 2567 15163 39509)												3	Substitution - Missense(3)	kidney(3)											11.0	14.0	13.0					16																	7703894		1886	3889	5775	SO:0001583	missense	0			AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"""RNA binding motif (RRM) containing"""	18222	protein-coding gene	gene with protein product	"""ataxin 2-binding protein 1"", ""hexaribonucleotide binding protein 1"""	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.835G>A	16.37:g.7703894G>A	ENSP00000450031:p.Val279Met	Somatic		WXS	Illumina GAIIx	Phase_I	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Missense_Mutation	SNP	ENST00000550418.1	37	CCDS55983.1	.	.	.	.	.	.	.	.	.	.	g	27.2	4.811473	0.90707	.	.	ENSG00000078328	ENST00000550418;ENST00000553186;ENST00000547372;ENST00000422070;ENST00000535565;ENST00000552089;ENST00000547338;ENST00000436368;ENST00000311745;ENST00000355637;ENST00000352951;ENST00000340209	T;T;T;T;T;T;T;T;T	0.37411	1.2;1.56;1.53;1.49;1.2;1.36;1.52;1.57;1.2	4.25	4.25	0.50352	.	0.206066	0.40385	N	0.001117	T	0.57417	0.2052	M	0.64997	1.995	0.50813	D	0.999893	D;D;D;P;P;D;D;D;D	0.89917	1.0;1.0;1.0;0.746;0.884;1.0;1.0;1.0;1.0	D;D;D;B;P;D;D;D;D	0.87578	0.968;0.998;0.997;0.14;0.618;0.996;0.992;0.994;0.993	T	0.58934	-0.7548	9	.	.	.	-7.8987	17.0189	0.86428	0.0:0.0:1.0:0.0	.	272;236;322;299;299;299;252;279;322	F8WAC5;F5H0M1;B7Z1U7;Q9NWB1-2;Q9NWB1-4;Q9NWB1-5;Q9NWB1-3;Q9NWB1;F8VZG9	.;.;.;.;.;.;.;RFOX1_HUMAN;.	M	279;252;322;322;236;296;279;299;299;299;272;284	ENSP00000450031:V279M;ENSP00000447753:V252M;ENSP00000446842:V322M;ENSP00000391269:V322M;ENSP00000447717:V279M;ENSP00000402745:V299M;ENSP00000309117:V299M;ENSP00000347855:V299M;ENSP00000344196:V284M	.	V	+	1	0	RBFOX1	7643895	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.439000	0.97543	2.076000	0.62316	0.401000	0.26515	GTG		0.741	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2		NM_145891	
ATF6B	1388	broad.mit.edu	37	6	32095464	32095464	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr6:32095464G>C	ENST00000375203.3	-	2	187	c.155C>G	c.(154-156)cCg>cGg	p.P52R	ATF6B_ENST00000468502.1_5'UTR|ATF6B_ENST00000375201.4_Missense_Mutation_p.P49R	NM_001136153.1|NM_004381.4	NP_001129625.1|NP_004372.3	Q99941	ATF6B_HUMAN	activating transcription factor 6 beta	52	Transcription activation.				response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P52R(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	22						ATCCTGCTCCGGGCAACGGAA	0.572																																																	1	Substitution - Missense(1)	kidney(1)											87.0	88.0	88.0					6																	32095464		2203	4300	6503	SO:0001583	missense	1388				CCDS47408.1, CCDS4737.1	6p21.3	2013-01-10	2008-10-21	2008-10-21	ENSG00000213676	ENSG00000213676		"""basic leucine zipper proteins"""	2349	protein-coding gene	gene with protein product		600984	"""cAMP responsive element binding protein-like 1"""	CREBL1		11256944, 14973138	Standard	NM_004381		Approved	G13	uc003nzn.3	Q99941	OTTHUMG00000031296	ENST00000375203.3:c.155C>G	6.37:g.32095464G>C	ENSP00000364349:p.Pro52Arg	Somatic		WXS	Illumina GAIIx	Phase_I	B0UYX6|Q13269|Q14343|Q14345|Q5SSW7|Q99635|Q99637|Q9H3V9|Q9H3W1|Q9NPL0	Missense_Mutation	SNP	ENST00000375203.3	37	CCDS4737.1	.	.	.	.	.	.	.	.	.	.	G	12.86	2.065965	0.36470	.	.	ENSG00000213676	ENST00000375192;ENST00000375203;ENST00000375201	T;T	0.57752	0.38;1.14	4.76	-0.249	0.13011	.	0.760810	0.11305	U	0.577804	T	0.37544	0.1007	L	0.53249	1.67	0.09310	N	0.999991	D;B;P	0.58620	0.983;0.302;0.64	P;B;B	0.61132	0.884;0.223;0.238	T	0.13282	-1.0515	10	0.23891	T	0.37	-0.4784	3.2125	0.06687	0.5533:0.0:0.2287:0.218	.	52;49;52	Q96QL7;Q99941-2;Q99941	.;.;ATF6B_HUMAN	R	52;52;49	ENSP00000364349:P52R;ENSP00000364347:P49R	ENSP00000364338:P52R	P	-	2	0	ATF6B	32203442	0.126000	0.22350	0.570000	0.28473	0.934000	0.57294	0.218000	0.17622	0.058000	0.16222	-0.274000	0.10170	CCG		0.572	ATF6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076638.2			
FLJ36000	284124	broad.mit.edu	37	17	21904083	21904083	+	lincRNA	SNP	C	C	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr17:21904083C>A	ENST00000581223.2	+	0	0					NR_027084.1																						ctgacctctccacggggtcca	0.677																																																	0																																												284124																															17.37:g.21904083C>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000581223.2	37																																																																																					0.677	RP11-744K17.9-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000451067.1			
OSBPL5	114879	broad.mit.edu	37	11	3109495	3109495	+	Silent	SNP	G	G	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr11:3109495G>A	ENST00000263650.7	-	22	2739	c.2580C>T	c.(2578-2580)tcC>tcT	p.S860S	OSBPL5_ENST00000542243.1_Silent_p.S491S|OSBPL5_ENST00000478260.1_Silent_p.S314S|OSBPL5_ENST00000348039.5_Silent_p.S792S|OSBPL5_ENST00000525498.1_Silent_p.S771S|OSBPL5_ENST00000389989.3_Silent_p.S792S	NM_020896.3	NP_065947.1	Q9H0X9	OSBL5_HUMAN	oxysterol binding protein-like 5	860					cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|Golgi to plasma membrane transport (GO:0006893)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|oxysterol binding (GO:0008142)	p.S860S(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	25		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		GCAGGAACCAGGATCGGGGGC	0.642																																																	1	Substitution - coding silent(1)	kidney(1)											54.0	56.0	55.0					11																	3109495		2202	4298	6500	SO:0001819	synonymous_variant	114879			AF392453	CCDS31343.1, CCDS31344.1	11p15.4	2013-01-10			ENSG00000021762	ENSG00000021762		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16392	protein-coding gene	gene with protein product		606733					Standard	NM_145638		Approved	KIAA1534, ORP5	uc001lxk.2	Q9H0X9	OTTHUMG00000011702	ENST00000263650.7:c.2580C>T	11.37:g.3109495G>A		Somatic		WXS	Illumina GAIIx	Phase_I	A6NDP0|A6NJS8|Q54A90|Q8N596|Q9BZB0|Q9P1Z4	Silent	SNP	ENST00000263650.7	37	CCDS31344.1																																																																																				0.642	OSBPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032332.2			
S1PR4	8698	broad.mit.edu	37	19	3179921	3179921	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr19:3179921C>A	ENST00000246115.3	+	1	1186	c.1131C>A	c.(1129-1131)agC>agA	p.S377R		NM_003775.3	NP_003766.1	O95977	S1PR4_HUMAN	sphingosine-1-phosphate receptor 4	377					activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)	p.S377R(2)		breast(1)|kidney(2)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	13						CCCTGTCCAGCATCTCCAGCG	0.647																																					GBM(82;318 1638 33279 49708)												2	Substitution - Missense(2)	kidney(2)											51.0	60.0	57.0					19																	3179921		2146	4184	6330	SO:0001583	missense	8698			AJ000479	CCDS12105.1	19p13.3	2012-08-08	2008-04-30	2008-04-30		ENSG00000125910		"""GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"""	3170	protein-coding gene	gene with protein product		603751	"""endothelial differentiation, G-protein-coupled receptor 6"", ""endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 6"""	EDG6		9790765	Standard	NM_003775		Approved		uc002lxg.3	O95977		ENST00000246115.3:c.1131C>A	19.37:g.3179921C>A	ENSP00000246115:p.Ser377Arg	Somatic		WXS	Illumina GAIIx	Phase_I	D6W612	Missense_Mutation	SNP	ENST00000246115.3	37	CCDS12105.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.158885	0.57368	.	.	ENSG00000125910	ENST00000246115	D	0.82893	-1.66	3.85	0.267	0.15622	.	0.414587	0.23309	N	0.049598	T	0.79930	0.4531	L	0.29908	0.895	0.35277	D	0.781006	D	0.59357	0.985	P	0.58077	0.832	T	0.80254	-0.1459	10	0.87932	D	0	.	7.0012	0.24811	0.0:0.5706:0.0:0.4294	.	377	O95977	S1PR4_HUMAN	R	377	ENSP00000246115:S377R	ENSP00000246115:S377R	S	+	3	2	S1PR4	3130921	0.254000	0.23992	0.965000	0.40720	0.963000	0.63663	0.504000	0.22626	-0.028000	0.13850	-0.339000	0.08088	AGC		0.647	S1PR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452517.1		NM_003775	
RN7SL417P	0	broad.mit.edu	37	15	84946555	84946556	+	RNA	INS	-	-	TT	rs71453238		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr15:84946555_84946556insTT	ENST00000459938.2	+	0	0									RNA, 7SL, cytoplasmic 417, pseudogene																		CGAAGGGAGGAttttttttttt	0.515																																																	0																																												0					15q25.2	2013-04-02			ENSG00000244056	ENSG00000244056		"""ncRNAs / Small cytoplasmic RNAs"""	46433	pseudogene	RNA, pseudogene							Standard			Approved						15.37:g.84946564_84946565dupTT		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	INS	ENST00000459938.2	37																																																																																					0.515	RN7SL417P-201	KNOWN	basic	misc_RNA	misc_RNA				
MTOR	2475	broad.mit.edu	37	1	11217230	11217230	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454	.		Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr1:11217230C>A	ENST00000361445.4	-	30	4524	c.4448G>T	c.(4447-4449)tGc>tTc	p.C1483F		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1483	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.C1483F(2)|p.C1483Y(1)		breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	GGCCTCGAGGCAGCGCATGCG	0.527																																						.											3	Substitution - Missense(3)	kidney(3)											191.0	177.0	182.0					1																	11217230		2203	4300	6503	SO:0001583	missense	2475			L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.4448G>T	1.37:g.11217230C>A	ENSP00000354558:p.Cys1483Phe	Somatic		WXS	Illumina GAIIx	Phase_I	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	37	CCDS127.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.600766	0.87055	.	.	ENSG00000198793	ENST00000361445;ENST00000539766	T	0.69806	-0.43	5.32	5.32	0.75619	PIK-related kinase (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.82047	0.4952	M	0.91920	3.255	0.80722	D	1	D	0.59357	0.985	P	0.52627	0.704	D	0.86849	0.2022	10	0.87932	D	0	-11.9694	19.0009	0.92834	0.0:1.0:0.0:0.0	.	1483	P42345	MTOR_HUMAN	F	1483	ENSP00000354558:C1483F	ENSP00000354558:C1483F	C	-	2	0	MTOR	11139817	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	7.414000	0.80117	2.486000	0.83907	0.655000	0.94253	TGC		0.527	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1		NM_004958	
EPHA8	2046	broad.mit.edu	37	1	22902868	22902868	+	Silent	SNP	C	C	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454	.		Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr1:22902868C>T	ENST00000166244.3	+	3	390	c.318C>T	c.(316-318)cgC>cgT	p.R106R	EPHA8_ENST00000538803.1_Silent_p.R106R|EPHA8_ENST00000374644.4_Silent_p.R106R	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	106	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.R106R(2)		breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TTACCCTGCGCGACTGCAACA	0.622																																						.											2	Substitution - coding silent(2)	kidney(2)											60.0	59.0	59.0					1																	22902868		2203	4300	6503	SO:0001819	synonymous_variant	2046			BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3391	protein-coding gene	gene with protein product		176945	"""EphA8"""	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.318C>T	1.37:g.22902868C>T		Somatic		WXS	Illumina GAIIx	Phase_I	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Silent	SNP	ENST00000166244.3	37	CCDS225.1																																																																																				0.622	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1		NM_020526	
CSMD1	64478	broad.mit.edu	37	8	3216686	3216686	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454	.		Illumina GAIIx	7c69fcb9-4b94-478a-bcb3-6ebd162d9482	37409a95-7e2f-42ee-ad41-b3f5b32c7236	g.chr8:3216686G>A	ENST00000520002.1	-	22	3850	c.3295C>T	c.(3295-3297)Cca>Tca	p.P1099S	CSMD1_ENST00000537824.1_Missense_Mutation_p.P1098S|CSMD1_ENST00000602723.1_Missense_Mutation_p.P1099S|CSMD1_ENST00000400186.3_Missense_Mutation_p.P1099S|CSMD1_ENST00000542608.1_Missense_Mutation_p.P1098S|CSMD1_ENST00000602557.1_Missense_Mutation_p.P1099S|CSMD1_ENST00000539096.1_Missense_Mutation_p.P1098S			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1099	Sushi 6. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.P827S(1)|p.P1098S(1)		breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		ACACACCTTGGCAGAGGTGCA	0.592																																						.											2	Substitution - Missense(2)	kidney(2)											68.0	71.0	70.0					8																	3216686		2203	4300	6503	SO:0001583	missense	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.3295C>T	8.37:g.3216686G>A	ENSP00000430733:p.Pro1099Ser	Somatic		WXS	Illumina GAIIx	Phase_I	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	29.1|29.1	4.974930|4.974930	0.92919|0.92919	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000335551|ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	.|T;T;T;T;T	.|0.76968	.|-1.06;-1.06;-1.06;-1.06;-1.06	5.34|5.34	5.34|5.34	0.76211|0.76211	.|Complement control module (2);Sushi/SCR/CCP (3);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.93739|0.93739	0.7999|0.7999	H|H	0.99169|0.99169	4.455|4.455	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|0.999;0.999;1.0	.|D;D;D	.|0.97110	.|0.998;1.0;1.0	D|D	0.96422|0.96422	0.9312|0.9312	5|10	.|0.87932	.|D	.|0	.|.	19.067|19.067	0.93116|0.93116	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1099;1099;1099	.|E5RIG2;Q96PZ7;Q96PZ7-4	.|.;CSMD1_HUMAN;.	V|S	578|1099;1099;961;1098;1098;1098	.|ENSP00000383047:P1099S;ENSP00000430733:P1099S;ENSP00000441462:P1098S;ENSP00000446243:P1098S;ENSP00000441675:P1098S	.|ENSP00000320445:P961S	A|P	-|-	2|1	0|0	CSMD1|CSMD1	3204093|3204093	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.601000|9.601000	0.98297|0.98297	2.489000|2.489000	0.83994|0.83994	0.550000|0.550000	0.68814|0.68814	GCC|CCA		0.592	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2		NM_033225	
