#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
AP2A1	160	broad.mit.edu;hgsc.bcm.edu	37	19	50309986	50309986	+	Missense_Mutation	SNP	C	C	A	rs547032875		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr19:50309986C>A	ENST00000359032.5	+	24	2905	c.2905C>A	c.(2905-2907)Ctg>Atg	p.L969M	AC006942.4_ENST00000600669.1_RNA|AP2A1_ENST00000354293.5_Missense_Mutation_p.L947M	NM_014203.2	NP_055018.2	O95782	AP2A1_HUMAN	adaptor-related protein complex 2, alpha 1 subunit	969				ENFVGAGIIQTKALQVGCLLRLEPNAQAQMYRLTLRTSKEP VSRHLCELLAQQF -> GDREDTRVWGMPGTFLRPFVFLFL FICCCLHSGGLGGVPLPPFPPQAQRGEGPGKWMSPPLPPHP VVAPPTPSPSRGCVLL (in Ref. 4; AAH14214). {ECO:0000305}.	antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	AP-2 adaptor complex (GO:0030122)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)	p.L969M(2)		cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)	19		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0023)|GBM - Glioblastoma multiforme(134;0.0157)		CTCCCGTCACCTGTGTGAGCT	0.652																																																	2	Substitution - Missense(2)	kidney(2)											46.0	51.0	50.0					19																	50309986		1986	4173	6159	SO:0001583	missense	160			AA993745	CCDS46148.1, CCDS46149.1	19q13.3	2008-05-23				ENSG00000196961			561	protein-coding gene	gene with protein product		601026		CLAPA1, ADTAA		2564002	Standard	NM_014203		Approved		uc002ppn.3	O95782		ENST00000359032.5:c.2905C>A	19.37:g.50309986C>A	ENSP00000351926:p.Leu969Met	Somatic		WXS	Illumina HiSeq	Phase_I	Q96CI7|Q96PP6|Q96PP7|Q9H070	Missense_Mutation	SNP	ENST00000359032.5	37	CCDS46148.1	.	.	.	.	.	.	.	.	.	.	C	19.34	3.808974	0.70797	.	.	ENSG00000196961	ENST00000354293;ENST00000359032	T;T	0.27720	1.72;1.65	4.97	1.68	0.24146	Coatomer/calthrin adaptor appendage, C-terminal subdomain (1);Clathrin alpha-adaptin/coatomer adaptor, appendage, C-terminal subdomain (1);Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain (1);	0.099134	0.48767	D	0.000167	T	0.49830	0.1580	M	0.74467	2.265	0.41696	D	0.989373	D;P	0.89917	1.0;0.89	D;P	0.91635	0.999;0.648	T	0.42832	-0.9428	10	0.52906	T	0.07	.	8.5334	0.33349	0.0:0.736:0.0:0.264	.	947;969	O95782-2;O95782	.;AP2A1_HUMAN	M	947;969	ENSP00000346246:L947M;ENSP00000351926:L969M	ENSP00000346246:L947M	L	+	1	2	AP2A1	55001798	0.996000	0.38824	0.961000	0.40146	0.989000	0.77384	2.322000	0.43814	0.136000	0.18733	0.561000	0.74099	CTG		0.652	AP2A1-008	NOVEL	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465809.1			
APOBEC3H	164668	hgsc.bcm.edu	37	22	39496323	39496325	+	In_Frame_Del	DEL	AAC	AAC	-	rs140936762|rs139292|rs201177427	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr22:39496323_39496325delAAC	ENST00000401756.1	+	2	116_118	c.40_42delAAC	c.(40-42)aacdel	p.N15del	APOBEC3H_ENST00000348946.4_In_Frame_Del_p.N15del|APOBEC3H_ENST00000421988.2_In_Frame_Del_p.N15del|APOBEC3H_ENST00000442487.3_In_Frame_Del_p.N15del	NM_001166003.1	NP_001159475.1	Q6NTF7	ABC3H_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3H	15			Missing (decreases protein stability). {ECO:0000269|PubMed:15461802}.		cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|hematopoietic progenitor cell differentiation (GO:0002244)|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)|negative regulation of viral process (GO:0048525)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(8)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15	Melanoma(58;0.04)					CTTACAGTTTAACAACAAGCGCC	0.532														1590	0.317492	0.3071	0.2795	5008	,	,		17995	0.2579		0.339	False		,,,				2504	0.3978																0									,,,	1382,2882		240,902,990					,,,	-1.8	0.2		dbSNP_129	82	2684,5570		426,1832,1869	no	coding,coding,coding,coding	APOBEC3H	NM_181773.3,NM_001166004.1,NM_001166003.1,NM_001166002.1	,,,	666,2734,2859	A1A1,A1R,RR		32.5176,32.4109,32.4812	,,,	,,,		4066,8452				SO:0001651	inframe_deletion	164668			BC069023	CCDS13985.1, CCDS54530.1, CCDS54531.1, CCDS54532.1	22q13.1	2007-02-01			ENSG00000100298	ENSG00000100298		"""Apolipoprotein B mRNA editing enzymes"""	24100	protein-coding gene	gene with protein product		610976				16571802	Standard	NM_001166003		Approved	ARP10	uc021wpt.1	Q6NTF7	OTTHUMG00000151082	ENST00000401756.1:c.40_42delAAC	22.37:g.39496326_39496328delAAC	ENSP00000385741:p.Asn15del	Somatic		WXS	Illumina HiSeq	Phase_I	B0QYP0|B0QYP1|B7TQM5|E9PF38|Q5JYL9|Q6IC87	In_Frame_Del	DEL	ENST00000401756.1	37	CCDS54530.1																																																																																				0.532	APOBEC3H-002	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321230.1		NM_181773	
AQP7	364	hgsc.bcm.edu	37	9	33395108	33395108	+	Silent	SNP	G	G	A	rs2381003	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr9:33395108G>A	ENST00000539936.1	-	3	350	c.112C>T	c.(112-114)Ctg>Ttg	p.L38L	AQP7_ENST00000541274.1_5'UTR|AQP7_ENST00000377425.4_Intron|AQP7_ENST00000537089.1_5'UTR			O14520	AQP7_HUMAN	aquaporin 7	38			L -> V (in dbSNP:rs2381003).		excretion (GO:0007588)|generation of precursor metabolites and energy (GO:0006091)|glycerol transport (GO:0015793)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|water channel activity (GO:0015250)			NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(4)|skin(2)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		AACTCGGCCAGGAACTCTCGC	0.587																																																	0													129.0	86.0	101.0					9																	33395108		2203	4300	6503	SO:0001819	synonymous_variant	364			AB006190	CCDS6541.1	9p13	2008-02-05			ENSG00000165269	ENSG00000165269		"""Ion channels / Aquaporins"""	640	protein-coding gene	gene with protein product		602974		AQP7L		9252401	Standard	NM_001170		Approved	AQP9, AQPap	uc003zst.3	O14520	OTTHUMG00000019773	ENST00000539936.1:c.112C>T	9.37:g.33395108G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q08E94|Q5T5L9|Q8NHM3	Silent	SNP	ENST00000539936.1	37																																																																																					0.587	AQP7-203	KNOWN	basic	protein_coding	protein_coding			NM_001170	
ARFGEF2	10564	hgsc.bcm.edu;ucsc.edu	37	20	47601976	47601982	+	Frame_Shift_Del	DEL	CAAGGTT	CAAGGTT	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	CAAGGTT	CAAGGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr20:47601976_47601982delCAAGGTT	ENST00000371917.4	+	16	2102_2108	c.2102_2108delCAAGGTT	c.(2101-2109)gcaaggttcfs	p.ARF701fs		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	701	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			GGAGATAGCGCAAGGTTCAACAAGGAG	0.464																																					Esophageal Squamous(176;1738 1974 26285 33069 35354)												0																																										SO:0001589	frameshift_variant	10564			AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"""A-kinase anchor proteins"""	15853	protein-coding gene	gene with protein product	"""Brefeldin A-inhibited guanine nucleotide-exchange protein 2"""	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.2102_2108delCAAGGTT	20.37:g.47601976_47601982delCAAGGTT	ENSP00000360985:p.Ala701fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q5TFT9|Q9NTS1	Frame_Shift_Del	DEL	ENST00000371917.4	37	CCDS13411.1																																																																																				0.464	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1		NM_006420	
ARGFX	503582	broad.mit.edu;hgsc.bcm.edu	37	3	121305227	121305227	+	Missense_Mutation	SNP	C	C	G	rs540135129		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr3:121305227C>G	ENST00000334384.3	+	4	738	c.728C>G	c.(727-729)tCc>tGc	p.S243C		NM_001012659.1	NP_001012677.1	A6NJG6	ARGFX_HUMAN	arginine-fifty homeobox	243					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.S243C(1)		kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	15				GBM - Glioblastoma multiforme(114;0.152)		AATGAGATATCCAGCTCTTCT	0.473													C|||	1	0.000199681	0.0	0.0	5008	,	,		21967	0.001		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)											110.0	109.0	109.0					3																	121305227		2203	4298	6501	SO:0001583	missense	503582				CCDS33834.1	3q13.33	2011-06-20			ENSG00000186103	ENSG00000186103		"""Homeoboxes / PRD class"""	30146	protein-coding gene	gene with protein product		611164					Standard	XM_005247505		Approved		uc003eef.3	A6NJG6	OTTHUMG00000159395	ENST00000334384.3:c.728C>G	3.37:g.121305227C>G	ENSP00000335578:p.Ser243Cys	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000334384.3	37	CCDS33834.1	.	.	.	.	.	.	.	.	.	.	C	11.05	1.523597	0.27299	.	.	ENSG00000186103	ENST00000334384	D	0.90788	-2.73	3.47	3.47	0.39725	.	0.392698	0.18909	N	0.127804	D	0.88588	0.6477	N	0.19112	0.55	0.09310	N	1	D	0.76494	0.999	P	0.58454	0.839	T	0.80632	-0.1296	10	0.62326	D	0.03	-1.3429	10.7334	0.46111	0.0:1.0:0.0:0.0	.	243	A6NJG6	ARGFX_HUMAN	C	243	ENSP00000335578:S243C	ENSP00000335578:S243C	S	+	2	0	ARGFX	122787917	0.000000	0.05858	0.004000	0.12327	0.026000	0.11368	0.696000	0.25541	2.243000	0.73865	0.491000	0.48974	TCC		0.473	ARGFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355096.2		NM_001012659	
ATP5S	27109	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	50779730	50779730	+	5'UTR	SNP	C	C	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr14:50779730C>T	ENST00000311459.7	+	0	372				L2HGDH_ENST00000261699.4_5'Flank|L2HGDH_ENST00000556393.1_5'Flank|L2HGDH_ENST00000555423.1_5'Flank|L2HGDH_ENST00000267436.4_5'Flank|L2HGDH_ENST00000421284.3_5'Flank|L2HGDH_ENST00000555610.1_5'Flank|ATP5S_ENST00000245448.6_5'UTR|ATP5S_ENST00000426751.2_5'UTR|ATP5S_ENST00000554438.1_Intron	NM_001003803.2	NP_001003803.1	Q99766	ATP5S_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit s (factor B)						ATP biosynthetic process (GO:0006754)|hydrogen ion transmembrane transport (GO:1902600)|proton transport (GO:0015992)	mitochondrial inner membrane (GO:0005743)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|large_intestine(2)|liver(1)|lung(2)|ovary(1)|skin(2)|stomach(1)	12	all_epithelial(31;0.000636)|Breast(41;0.0102)			OV - Ovarian serous cystadenocarcinoma(311;0.0685)		AACCGAGATACAGTTTTAAAT	0.488																																																	0													122.0	110.0	114.0					14																	50779730		2203	4300	6503	SO:0001623	5_prime_UTR_variant	27109			U79253	CCDS32075.1, CCDS32076.1, CCDS45102.1	14q21.3	2011-04-13	2010-06-11			ENSG00000125375			18799	protein-coding gene	gene with protein product			"""ATP synthase, H+ transporting, mitochondrial F0 complex, subunit s (factor B)"""			11744738, 8619474	Standard	NM_015684		Approved	HSU79253, ATPW	uc001wxw.2	Q99766		ENST00000311459.7:c.-9C>T	14.37:g.50779730C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A8K1U3|D9N156|Q8WWX3|Q96F77	RNA	SNP	ENST00000311459.7	37	CCDS32075.1																																																																																				0.488	ATP5S-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410761.1		NM_015684	
ATRNL1	26033	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	116881513	116881513	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr10:116881513G>C	ENST00000355044.3	+	3	554	c.428G>C	c.(427-429)aGc>aCc	p.S143T	ATRNL1_ENST00000529665.1_3'UTR|ATRNL1_ENST00000527407.1_Missense_Mutation_p.S143T	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	143	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.S143T(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		ACAGAATGTAGCTGGGATCAT	0.289																																																	1	Substitution - Missense(1)	kidney(1)											110.0	113.0	112.0					10																	116881513		2203	4285	6488	SO:0001583	missense	26033			AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.428G>C	10.37:g.116881513G>C	ENSP00000347152:p.Ser143Thr	Somatic		WXS	Illumina HiSeq	Phase_I	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Missense_Mutation	SNP	ENST00000355044.3	37	CCDS7592.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.477390	0.84640	.	.	ENSG00000107518	ENST00000526946;ENST00000355044	T;T	0.50813	0.73;0.73	5.26	5.26	0.73747	CUB (5);	0.040777	0.85682	D	0.000000	T	0.62551	0.2437	L	0.49256	1.55	0.80722	D	1	D;D;D	0.71674	0.989;0.975;0.998	P;P;D	0.63488	0.87;0.85;0.915	T	0.59236	-0.7492	10	0.39692	T	0.17	-19.4284	19.2144	0.93770	0.0:0.0:1.0:0.0	.	76;143;143	E9PL90;Q5VV63;Q5VV63-2	.;ATRN1_HUMAN;.	T	76;143	ENSP00000431423:S76T;ENSP00000347152:S143T	ENSP00000347152:S143T	S	+	2	0	ATRNL1	116871503	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.751000	0.98889	2.616000	0.88540	0.563000	0.77884	AGC		0.289	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3		XM_049349	
B3GNT2	10678	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	62450134	62450134	+	Missense_Mutation	SNP	A	A	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr2:62450134A>G	ENST00000301998.4	+	2	1031	c.779A>G	c.(778-780)aAt>aGt	p.N260S	B3GNT2_ENST00000405767.1_Missense_Mutation_p.N260S	NM_006577.5	NP_006568.2	Q9NY97	B3GN2_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	260					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)	p.N260S(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)	18	Lung NSC(7;0.031)|all_lung(7;0.0634)		LUSC - Lung squamous cell carcinoma(7;3.55e-06)|Epithelial(17;0.0963)			AATTACTTGAATAGTTTATCC	0.433																																																	1	Substitution - Missense(1)	kidney(1)											118.0	113.0	114.0					2																	62450134		2203	4300	6503	SO:0001583	missense	10678			AB049584	CCDS1870.1	2p15	2013-02-19	2006-04-12	2006-04-12	ENSG00000170340	ENSG00000170340		"""Beta 3-glycosyltransferases"""	15629	protein-coding gene	gene with protein product		605581	"""UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1"""	B3GNT1		9892646, 11042166	Standard	NM_006577		Approved	B3GNT-2, BETA3GNT, B3GN-T2, B3GN-T1	uc002sbs.3	Q9NY97	OTTHUMG00000129444	ENST00000301998.4:c.779A>G	2.37:g.62450134A>G	ENSP00000305595:p.Asn260Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q54AC1|Q9NQQ9|Q9NQR0|Q9NUT9	Missense_Mutation	SNP	ENST00000301998.4	37	CCDS1870.1	.	.	.	.	.	.	.	.	.	.	A	9.300	1.052831	0.19907	.	.	ENSG00000170340	ENST00000301998;ENST00000405767	T;T	0.40476	1.03;1.03	5.74	5.74	0.90152	.	0.261816	0.44097	D	0.000482	T	0.28067	0.0692	N	0.17082	0.46	0.32399	N	0.55221	B	0.28350	0.208	B	0.30251	0.113	T	0.23297	-1.0192	10	0.09338	T	0.73	.	16.0546	0.80788	1.0:0.0:0.0:0.0	.	260	Q9NY97	B3GN2_HUMAN	S	260	ENSP00000305595:N260S;ENSP00000384692:N260S	ENSP00000305595:N260S	N	+	2	0	B3GNT2	62303638	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.400000	0.59709	2.191000	0.70037	0.528000	0.53228	AAT		0.433	B3GNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251606.2		NM_006577	
C17orf104	284071	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	42745374	42745374	+	Missense_Mutation	SNP	T	T	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr17:42745374T>G	ENST00000409122.2	+	5	2237	c.2095T>G	c.(2095-2097)Tca>Gca	p.S699A	C17orf104_ENST00000359945.3_Missense_Mutation_p.S699A|C17orf104_ENST00000409464.1_Missense_Mutation_p.S533A	NM_001145080.2	NP_001138552.2	A2RUB1	CQ104_HUMAN	chromosome 17 open reading frame 104	699								p.S699A(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|skin(1)	24						ATTTGGCCATTCAGTTGTTCC	0.348																																																	1	Substitution - Missense(1)	kidney(1)											83.0	74.0	77.0					17																	42745374		2203	4300	6503	SO:0001583	missense	284071				CCDS45703.1, CCDS45703.2	17q21.31	2009-09-08			ENSG00000180336	ENSG00000180336			26670	protein-coding gene	gene with protein product							Standard	NM_001145080		Approved	FLJ35848	uc002iha.3	A2RUB1	OTTHUMG00000153039	ENST00000409122.2:c.2095T>G	17.37:g.42745374T>G	ENSP00000386452:p.Ser699Ala	Somatic		WXS	Illumina HiSeq	Phase_I	B4DXJ2|B5MD93|B9EGQ6|C4AM97|Q4G0Y1|Q8IVZ7|Q8NA45	Missense_Mutation	SNP	ENST00000409122.2	37	CCDS45703.2	.	.	.	.	.	.	.	.	.	.	T	5.124	0.208564	0.09757	.	.	ENSG00000180336	ENST00000359945;ENST00000409122;ENST00000409464	T;T;T	0.34275	1.37;1.39;1.38	5.76	2.08	0.27032	.	0.511495	0.17831	N	0.160553	T	0.17746	0.0426	L	0.27053	0.805	0.23249	N	0.998043	B;B;B	0.23377	0.047;0.084;0.047	B;B;B	0.18561	0.015;0.022;0.015	T	0.25882	-1.0119	10	0.07325	T	0.83	-26.1272	4.2473	0.10677	0.1146:0.0645:0.2384:0.5825	.	699;699;533	A2RUB1-5;A2RUB1;A2RUB1-1	.;CQ104_HUMAN;.	A	699;699;533	ENSP00000353028:S699A;ENSP00000386452:S699A;ENSP00000386586:S533A	ENSP00000353028:S699A	S	+	1	0	C17orf104	40100900	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	1.482000	0.35486	0.421000	0.25980	-0.346000	0.07831	TCA		0.348	C17orf104-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329171.2		NM_001145080	
C17orf99	100141515	broad.mit.edu;hgsc.bcm.edu	37	17	76157222	76157222	+	Missense_Mutation	SNP	A	A	T	rs554071901		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr17:76157222A>T	ENST00000340363.5	+	3	312	c.257A>T	c.(256-258)aAc>aTc	p.N86I	C17orf99_ENST00000451352.3_3'UTR	NM_001163075.1	NP_001156547.1	Q6UX52	CQ099_HUMAN	chromosome 17 open reading frame 99	86						extracellular region (GO:0005576)		p.N86I(1)									TTCAACCTCAACGTCACACTC	0.587																																																	1	Substitution - Missense(1)	kidney(1)											98.0	99.0	98.0					17																	76157222		692	1591	2283	SO:0001583	missense	100141515			AY358510	CCDS54171.1	17q25.3	2012-10-23			ENSG00000187997	ENSG00000187997			34490	protein-coding gene	gene with protein product							Standard	NM_001163075		Approved	GLPG464, UNQ464	uc002jus.4	Q6UX52	OTTHUMG00000153871	ENST00000340363.5:c.257A>T	17.37:g.76157222A>T	ENSP00000343493:p.Asn86Ile	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000340363.5	37	CCDS54171.1	.	.	.	.	.	.	.	.	.	.	A	13.81	2.349350	0.41599	.	.	ENSG00000187997	ENST00000340363;ENST00000451352	T	0.39406	1.08	4.41	-0.681	0.11342	.	0.328381	0.21759	N	0.069554	T	0.33498	0.0865	L	0.32530	0.975	0.09310	N	1	D;D	0.53745	0.962;0.962	P;P	0.51657	0.676;0.604	T	0.15521	-1.0434	10	0.59425	D	0.04	-28.4984	3.0854	0.06276	0.4786:0.0:0.3324:0.189	.	73;86	E7ESU9;Q6UX52	.;CQ099_HUMAN	I	86;73	ENSP00000343493:N86I	ENSP00000343493:N86I	N	+	2	0	C17orf99	73668817	0.311000	0.24536	0.025000	0.17156	0.001000	0.01503	1.128000	0.31369	0.183000	0.20059	-0.441000	0.05720	AAC		0.587	C17orf99-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332775.1		NM_001163075	
ERICH3	127254	broad.mit.edu;ucsc.edu	37	1	75102000	75102000	+	Silent	SNP	G	G	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr1:75102000G>T	ENST00000326665.5	-	6	785	c.567C>A	c.(565-567)acC>acA	p.T189T	C1orf173_ENST00000420661.2_5'Flank	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		189								p.T189T(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						CCAGCAATGAGGTTTTTGATC	0.348																																																	1	Substitution - coding silent(1)	kidney(1)											153.0	157.0	155.0					1																	75102000		2203	4300	6503	SO:0001819	synonymous_variant	127254																														ENST00000326665.5:c.567C>A	1.37:g.75102000G>T		Somatic		WXS	Illumina GAIIx	Phase_I	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Silent	SNP	ENST00000326665.5	37	CCDS30755.1																																																																																				0.348	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			
SPRTN	83932	broad.mit.edu;hgsc.bcm.edu	37	1	231489083	231489083	+	Silent	SNP	A	A	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr1:231489083A>G	ENST00000295050.7	+	5	1782	c.1446A>G	c.(1444-1446)aaA>aaG	p.K482K		NM_001010984.2|NM_032018.5	NP_001010984.1|NP_114407.3	Q9H040	SPRTN_HUMAN	SprT-like N-terminal domain	482					cellular response to DNA damage stimulus (GO:0006974)|positive regulation of protein ubiquitination (GO:0031398)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|K63-linked polyubiquitin binding (GO:0070530)|metal ion binding (GO:0046872)|ubiquitin binding (GO:0043130)	p.K482K(1)									ACAGCATCAAAGTCAAAAGCG	0.418																																																	1	Substitution - coding silent(1)	kidney(1)											37.0	37.0	37.0					1																	231489083		2203	4297	6500	SO:0001819	synonymous_variant	0			AL512744	CCDS1594.1, CCDS31054.1, CCDS58066.1	1q42.12-q43	2013-01-30	2012-06-18	2012-06-18	ENSG00000010072	ENSG00000010072			25356	protein-coding gene	gene with protein product	"""SprT-like domain at the N terminus"", ""DNA damage-targeting VCP (p97) adaptor"""		"""chromosome 1 open reading frame 124"""	C1orf124		22681887	Standard	NM_032018		Approved	DKFZP547N043, Spartan, DVC1	uc001hur.4	Q9H040	OTTHUMG00000038022	ENST00000295050.7:c.1446A>G	1.37:g.231489083A>G		Somatic		WXS	Illumina HiSeq	Phase_I	B1AKT0|B5MEF7|Q5TE78|Q6UWW6|Q96BC5|Q96KA0	Silent	SNP	ENST00000295050.7	37	CCDS1594.1																																																																																				0.418	SPRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092858.1		NM_032018	
C20orf194	25943	broad.mit.edu;hgsc.bcm.edu	37	20	3355713	3355713	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr20:3355713C>T	ENST00000252032.9	-	5	536	c.469G>A	c.(469-471)Gac>Aac	p.D157N		NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194	157								p.D157N(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						CTACTACAGTCTCGAACCATG	0.408																																																	1	Substitution - Missense(1)	kidney(1)											270.0	257.0	261.0					20																	3355713		1863	4096	5959	SO:0001583	missense	25943			AL110249	CCDS42851.1	20p13	2012-10-30			ENSG00000088854	ENSG00000088854			17721	protein-coding gene	gene with protein product		614146					Standard	NM_001009984		Approved	DKFZp434N061	uc002wii.3	Q5TEA3	OTTHUMG00000031742	ENST00000252032.9:c.469G>A	20.37:g.3355713C>T	ENSP00000252032:p.Asp157Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q66K86|Q6P2R9|Q9UFX9	Missense_Mutation	SNP	ENST00000252032.9	37	CCDS42851.1	.	.	.	.	.	.	.	.	.	.	C	33	5.254756	0.95336	.	.	ENSG00000088854	ENST00000252032	T	0.23348	1.91	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.51958	0.1705	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.38628	-0.9652	10	0.35671	T	0.21	.	18.6895	0.91578	0.0:1.0:0.0:0.0	.	157	Q5TEA3	CT194_HUMAN	N	157	ENSP00000252032:D157N	ENSP00000252032:D157N	D	-	1	0	C20orf194	3303713	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.304000	0.78882	2.706000	0.92434	0.650000	0.86243	GAC		0.408	C20orf194-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077734.1		NM_001009984	
CCDC171	203238	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	15724841	15724841	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr9:15724841G>A	ENST00000380701.3	+	14	1887	c.1559G>A	c.(1558-1560)cGa>cAa	p.R520Q	CCDC171_ENST00000297641.3_Missense_Mutation_p.R520Q	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	520								p.R520Q(2)									TGTGCAGACCGAGAGGCTTTA	0.393																																																	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)											122.0	134.0	130.0					9																	15724841		2203	4300	6503	SO:0001583	missense	0			AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"""myosin tail domain containing protein"""		"""chromosome 9 open reading frame 93"""	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.1559G>A	9.37:g.15724841G>A	ENSP00000370077:p.Arg520Gln	Somatic		WXS	Illumina HiSeq	Phase_I	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Missense_Mutation	SNP	ENST00000380701.3	37	CCDS6481.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.035823	0.75617	.	.	ENSG00000164989	ENST00000297641;ENST00000380701	T;T	0.50001	0.76;0.76	5.42	5.42	0.78866	.	0.327625	0.33401	N	0.004954	T	0.25791	0.0628	N	0.14661	0.345	0.80722	D	1	P;P;P	0.52463	0.953;0.953;0.953	B;B;B	0.39152	0.292;0.292;0.292	T	0.06023	-1.0850	10	0.12103	T	0.63	-11.2819	11.1066	0.48207	0.1433:0.0:0.8567:0.0	.	528;520;520	B7ZM22;Q6TFL3-3;Q6TFL3	.;.;CI093_HUMAN	Q	520	ENSP00000297641:R520Q;ENSP00000370077:R520Q	ENSP00000297641:R520Q	R	+	2	0	C9orf93	15714841	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.356000	0.44116	2.716000	0.92895	0.650000	0.86243	CGA		0.393	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4		NM_173550	
CDK5RAP2	55755	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	123205921	123205921	+	Missense_Mutation	SNP	T	T	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr9:123205921T>A	ENST00000349780.4	-	23	3304	c.3125A>T	c.(3124-3126)gAt>gTt	p.D1042V	CDK5RAP2_ENST00000360822.3_Missense_Mutation_p.D1010V|CDK5RAP2_ENST00000359309.3_Intron|CDK5RAP2_ENST00000360190.4_Missense_Mutation_p.D1042V	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	1042	Interaction with MAPRE1.				brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)	p.D1042V(1)		breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						TCTTTGCTGATCACTGTCCAT	0.473																																																	1	Substitution - Missense(1)	kidney(1)											256.0	226.0	236.0					9																	123205921		2203	4300	6503	SO:0001583	missense	55755			BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"""centrosomin"""	608201	"""microcephaly, primary autosomal recessive 3"""	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.3125A>T	9.37:g.123205921T>A	ENSP00000343818:p.Asp1042Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Missense_Mutation	SNP	ENST00000349780.4	37	CCDS6823.1	.	.	.	.	.	.	.	.	.	.	T	14.80	2.644994	0.47258	.	.	ENSG00000136861	ENST00000360822;ENST00000349780;ENST00000360190;ENST00000416449;ENST00000345313	T;T;T;T	0.23552	3.57;3.55;3.45;1.9	3.77	-0.00269	0.14028	.	1.528960	0.03973	N	0.291975	T	0.29491	0.0735	L	0.27053	0.805	0.23043	N	0.998387	P;P;D;P;B	0.54601	0.815;0.815;0.967;0.718;0.094	B;B;P;B;B	0.54372	0.39;0.39;0.75;0.218;0.051	T	0.23440	-1.0188	10	0.87932	D	0	.	6.2457	0.20815	0.0:0.3559:0.0:0.6441	.	811;1010;1042;1042;436	Q6MZT4;Q96SN8-2;Q96SN8-4;Q96SN8;B1AMJ5	.;.;.;CK5P2_HUMAN;.	V	1010;1042;1042;436;814	ENSP00000354065:D1010V;ENSP00000343818:D1042V;ENSP00000353317:D1042V;ENSP00000400395:D436V	ENSP00000341695:D814V	D	-	2	0	CDK5RAP2	122245742	0.498000	0.26075	0.097000	0.21041	0.856000	0.48823	0.515000	0.22801	-0.106000	0.12110	0.379000	0.24179	GAT		0.473	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1		NM_018249	
CDX4	1046	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	72673463	72673463	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chrX:72673463G>A	ENST00000373514.2	+	2	613	c.613G>A	c.(613-615)Gag>Aag	p.E205K		NM_005193.1	NP_005184.1	O14627	CDX4_HUMAN	caudal type homeobox 4	205					anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|labyrinthine layer development (GO:0060711)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	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)	p.E205K(1)		endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|skin(1)	18	Renal(35;0.156)					GAGAAAATCAGAGCTGGCAGT	0.393																																																	1	Substitution - Missense(1)	kidney(1)											73.0	62.0	66.0					X																	72673463		2203	4300	6503	SO:0001583	missense	1046			AF029879	CCDS14424.1	Xq13.2	2012-03-09	2007-07-09		ENSG00000131264	ENSG00000131264		"""Homeoboxes / ANTP class : HOXL subclass"""	1808	protein-coding gene	gene with protein product		300025	"""caudal type homeo box transcription factor 4"""			7655457	Standard	NM_005193		Approved		uc011mqk.2	O14627	OTTHUMG00000021831	ENST00000373514.2:c.613G>A	X.37:g.72673463G>A	ENSP00000362613:p.Glu205Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A1A513|Q5JS20	Missense_Mutation	SNP	ENST00000373514.2	37	CCDS14424.1	.	.	.	.	.	.	.	.	.	.	.	21.8	4.203993	0.79127	.	.	ENSG00000131264	ENST00000373514	D	0.96522	-4.04	3.63	2.76	0.32466	Homeobox, eukaryotic (1);Homeodomain-related (1);Helix-turn-helix motif, lambda-like repressor (1);Homeobox (3);Homeodomain-like (1);	0.200249	0.42053	N	0.000778	D	0.93953	0.8064	L	0.58925	1.835	0.80722	D	1	B	0.27559	0.181	B	0.30716	0.119	D	0.90563	0.4517	10	0.87932	D	0	-7.3264	8.3561	0.32331	0.1264:0.0:0.8736:0.0	.	205	O14627	CDX4_HUMAN	K	205	ENSP00000362613:E205K	ENSP00000362613:E205K	E	+	1	0	CDX4	72590188	1.000000	0.71417	1.000000	0.80357	0.821000	0.46438	6.784000	0.75084	0.498000	0.27948	0.436000	0.28706	GAG		0.393	CDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057229.2		NM_005193	
CES4A	283848	hgsc.bcm.edu	37	16	67029715	67029715	+	Silent	SNP	T	T	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr16:67029715T>C	ENST00000326686.5	+	2	243	c.243T>C	c.(241-243)gcT>gcC	p.A81A	CES4A_ENST00000541479.1_Silent_p.A104A|CES4A_ENST00000398354.1_Silent_p.A81A|CES4A_ENST00000338718.4_Silent_p.A104A|CES4A_ENST00000540947.2_Silent_p.A81A			Q5XG92	EST4A_HUMAN	carboxylesterase 4A	81						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			large_intestine(2)|liver(2)|lung(4)|ovary(1)	9						TCAGAGATGCTACCACCTACC	0.577																																																	0													60.0	63.0	62.0					16																	67029715		1906	4117	6023	SO:0001819	synonymous_variant	283848			AK094783	CCDS42174.1, CCDS42174.2, CCDS54024.1, CCDS54025.1, CCDS42174.3	16q22.1	2011-10-25	2010-10-12	2010-10-12	ENSG00000172824	ENSG00000172824		"""Carboxylesterases"""	26741	protein-coding gene	gene with protein product			"""carboxylesterase 8 (putative)"""	CES8		12975309, 17364878, 20931200	Standard	NM_001190201		Approved	FLJ37464	uc010vix.2	Q5XG92		ENST00000326686.5:c.243T>C	16.37:g.67029715T>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8KAJ6|B7Z349|B7Z3L2|B7Z6R3|Q6UX55|Q8N9F4	Silent	SNP	ENST00000326686.5	37																																																																																					0.577	CES4A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			NM_173815	
CFLAR	8837	broad.mit.edu;hgsc.bcm.edu	37	2	202025389	202025389	+	Missense_Mutation	SNP	A	A	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr2:202025389A>G	ENST00000309955.3	+	9	1543	c.1028A>G	c.(1027-1029)gAt>gGt	p.D343G	CFLAR_ENST00000341582.6_Missense_Mutation_p.D308G|CFLAR_ENST00000340870.5_Missense_Mutation_p.D343G|CFLAR-AS1_ENST00000415011.2_RNA|CFLAR_ENST00000423241.2_Missense_Mutation_p.D343G|CFLAR_ENST00000457277.1_Missense_Mutation_p.D343G|CFLAR_ENST00000443227.1_Missense_Mutation_p.D247G|CFLAR_ENST00000355558.4_Intron|CFLAR_ENST00000479953.2_Missense_Mutation_p.D247G	NM_001202515.1|NM_003879.5	NP_001189444.1|NP_003870.4	O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator	343	Caspase.|Interaction with TRAF1 and TRAF2.|Interaction with caspase-3.|Interaction with caspase-8 subunits p18 and p10.|Not proteolytically processed and involved in apoptosis inhibition.			D -> E (in Ref. 8; AAC15825). {ECO:0000305}.	apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of myoblast fusion (GO:1901740)|positive regulation of catalytic activity (GO:0043085)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of necroptotic process (GO:0060544)|regulation of satellite cell proliferation (GO:0014842)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|skeletal myofibril assembly (GO:0014866)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|ripoptosome (GO:0097342)	cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|enzyme activator activity (GO:0008047)|protease binding (GO:0002020)	p.D343G(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|stomach(1)	13						TTCATGGGAGATTCATGCCCT	0.532																																					Pancreas(16;548 657 22190 32864 42338)												1	Substitution - Missense(1)	kidney(1)											96.0	85.0	89.0					2																	202025389		2203	4300	6503	SO:0001583	missense	8837			AF005774	CCDS2337.1, CCDS46487.1, CCDS56157.1, CCDS56158.1, CCDS59436.1	2q33-q34	2014-01-30			ENSG00000003402	ENSG00000003402		"""Endogenous ligands"""	1876	protein-coding gene	gene with protein product		603599		CASP8AP1		9208847, 9217161	Standard	NM_003879		Approved	CASH, Casper, CLARP, FLAME, FLIP, I-FLICE, MRIT, c-FLIP	uc002uxb.4	O15519	OTTHUMG00000132819	ENST00000309955.3:c.1028A>G	2.37:g.202025389A>G	ENSP00000312455:p.Asp343Gly	Somatic		WXS	Illumina HiSeq	Phase_I	B4DJE0|B7Z9F9|O14673|O14674|O14675|O15137|O15138|O15356|O15510|O43618|O43619|O43620|O60458|O60459|Q53TS6|Q54AF1|Q96TE4|Q9UEW1	Missense_Mutation	SNP	ENST00000309955.3	37	CCDS2337.1	.	.	.	.	.	.	.	.	.	.	A	18.06	3.539654	0.65085	.	.	ENSG00000003402	ENST00000309955;ENST00000443227;ENST00000340870;ENST00000343375;ENST00000341582;ENST00000423241;ENST00000457277	T;T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0;2.0	5.62	5.62	0.85841	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (1);Peptidase C14, ICE, catalytic subunit p20 (1);	0.204781	0.50627	D	0.000102	T	0.50939	0.1645	M	0.86953	2.85	0.46874	D	0.999231	D;D;D;D	0.89917	0.986;1.0;1.0;1.0	D;D;D;D	0.83275	0.939;0.995;0.99;0.996	T	0.53308	-0.8457	10	0.24483	T	0.36	-21.9186	15.8114	0.78568	1.0:0.0:0.0:0.0	.	247;343;308;343	O15519-3;O15519-11;O15519-8;O15519	.;.;.;CFLAR_HUMAN	G	343;247;343;229;308;343;343	ENSP00000312455:D343G;ENSP00000413270:D247G;ENSP00000339326:D343G;ENSP00000345807:D308G;ENSP00000399420:D343G;ENSP00000411535:D343G	ENSP00000312455:D343G	D	+	2	0	CFLAR	201733634	1.000000	0.71417	0.892000	0.35008	0.410000	0.31052	6.026000	0.70873	2.137000	0.66172	0.454000	0.30748	GAT		0.532	CFLAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256276.3		NM_003879	
CHD3	1107	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	7797756	7797756	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr17:7797756G>A	ENST00000330494.7	+	8	1249	c.1099G>A	c.(1099-1101)Ggg>Agg	p.G367R	CHD3_ENST00000380358.4_Missense_Mutation_p.G426R|CHD3_ENST00000358181.4_Missense_Mutation_p.G367R	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	367					centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.G367R(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				TGCAGTGGCCGGGGAGGAGGA	0.587																																																	1	Substitution - Missense(1)	kidney(1)											97.0	78.0	85.0					17																	7797756		2203	4300	6503	SO:0001583	missense	1107			U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"""Zinc fingers, PHD-type"""	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.1099G>A	17.37:g.7797756G>A	ENSP00000332628:p.Gly367Arg	Somatic		WXS	Illumina HiSeq	Phase_I	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	37	CCDS32554.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.27|16.27	3.077209|3.077209	0.55753|0.55753	.|.	.|.	ENSG00000170004|ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494|ENST00000452447	D;D;D|.	0.94650|.	-3.48;-3.48;-3.48|.	4.47|4.47	4.47|4.47	0.54385|0.54385	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE/PHD-type (1);|.	0.000000|.	0.47093|.	D|.	0.000252|.	T|T	0.68081|0.68081	0.2962|0.2962	L|L	0.52573|0.52573	1.65|1.65	0.52501|0.52501	D|D	0.999953|0.999953	D;D;D|.	0.76494|.	0.998;0.999;0.999|.	P;P;P|.	0.59357|.	0.856;0.721;0.852|.	T|T	0.66504|0.66504	-0.5907|-0.5907	10|5	0.15066|.	T|.	0.55|.	-28.6676|-28.6676	16.0777|16.0777	0.80979|0.80979	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	367;367;426|.	Q12873-2;Q12873;E9PG89|.	.;CHD3_HUMAN;.|.	R|Q	426;367;367|237	ENSP00000369716:G426R;ENSP00000350907:G367R;ENSP00000332628:G367R|.	ENSP00000332628:G367R|.	G|R	+|+	1|2	0|0	CHD3|CHD3	7738481|7738481	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	5.136000|5.136000	0.64783|0.64783	2.315000|2.315000	0.78130|0.78130	0.557000|0.557000	0.71058|0.71058	GGG|CGG		0.587	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1		NM_001005273	
CHSY3	337876	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	129520692	129520692	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr5:129520692G>C	ENST00000305031.4	+	3	2215	c.1857G>C	c.(1855-1857)aaG>aaC	p.K619N		NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	619					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)	p.K619N(2)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		ACAATGAAAAGAAAGTACACA	0.348																																																	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)											62.0	63.0	63.0					5																	129520692		2203	4300	6503	SO:0001583	missense	337876			AB086062	CCDS34223.1	5q13	2013-02-19			ENSG00000198108	ENSG00000198108	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	24293	protein-coding gene	gene with protein product		609963				12907687	Standard	XM_005271982		Approved	CSS3, CHSY-2	uc003kvd.3	Q70JA7	OTTHUMG00000163043	ENST00000305031.4:c.1857G>C	5.37:g.129520692G>C	ENSP00000302629:p.Lys619Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B2RP97|Q76L22|Q86Y52	Missense_Mutation	SNP	ENST00000305031.4	37	CCDS34223.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.195538	0.38806	.	.	ENSG00000198108	ENST00000305031	T	0.34859	1.34	4.12	3.25	0.37280	.	0.000000	0.64402	D	0.000020	T	0.43077	0.1231	M	0.61703	1.905	0.45837	D	0.998702	P	0.47191	0.891	P	0.48738	0.588	T	0.38866	-0.9641	9	.	.	.	-7.9195	12.7885	0.57520	0.0811:0.0:0.9189:0.0	.	619	Q70JA7	CHSS3_HUMAN	N	619	ENSP00000302629:K619N	.	K	+	3	2	CHSY3	129548591	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.099000	0.41767	1.309000	0.44985	0.650000	0.86243	AAG		0.348	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1		NM_175856	
COL22A1	169044	broad.mit.edu;hgsc.bcm.edu	37	8	139824101	139824101	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr8:139824101C>T	ENST00000303045.6	-	9	1836	c.1390G>A	c.(1390-1392)Ggc>Agc	p.G464S	COL22A1_ENST00000435777.1_Missense_Mutation_p.G464S	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	464	Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.G464S(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TGTTCACTGCCTGGGGTGGGA	0.602										HNSCC(7;0.00092)																																							1	Substitution - Missense(1)	kidney(1)											38.0	33.0	35.0					8																	139824101		2203	4300	6503	SO:0001583	missense	169044			AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.1390G>A	8.37:g.139824101C>T	ENSP00000303153:p.Gly464Ser	Somatic		WXS	Illumina HiSeq	Phase_I	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	37	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	C	8.131	0.783128	0.16189	.	.	ENSG00000169436	ENST00000303045;ENST00000435777	D;D	0.88354	-2.37;-2.29	5.08	3.27	0.37495	.	0.139348	0.32459	U	0.006072	T	0.80486	0.4632	L	0.33485	1.01	0.34148	D	0.667135	B	0.24043	0.096	B	0.22386	0.039	T	0.77308	-0.2636	9	.	.	.	.	8.5535	0.33467	0.0:0.8223:0.0:0.1777	.	464	Q8NFW1	COMA1_HUMAN	S	464	ENSP00000303153:G464S;ENSP00000387655:G464S	.	G	-	1	0	COL22A1	139893283	0.997000	0.39634	0.955000	0.39395	0.920000	0.55202	2.223000	0.42936	1.144000	0.42321	-0.274000	0.10170	GGC		0.602	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2		XM_291257	
COL24A1	255631	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	86315055	86315055	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr1:86315055C>G	ENST00000370571.2	-	38	3701	c.3335G>C	c.(3334-3336)aGa>aCa	p.R1112T	COL24A1_ENST00000436319.1_Missense_Mutation_p.R1112T	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	1112	Collagen-like 10.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)	p.R1112T(1)		NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		TGGACGACCTCTTTGCCCTGG	0.338																																																	1	Substitution - Missense(1)	kidney(1)											95.0	91.0	92.0					1																	86315055		1814	4067	5881	SO:0001583	missense	255631			AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"""Collagens"""	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.3335G>C	1.37:g.86315055C>G	ENSP00000359603:p.Arg1112Thr	Somatic		WXS	Illumina HiSeq	Phase_I	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Missense_Mutation	SNP	ENST00000370571.2	37	CCDS41353.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.576373	0.28092	.	.	ENSG00000171502	ENST00000370571;ENST00000436319	D;D	0.96940	-4.18;-4.18	5.19	4.28	0.50868	.	0.000000	0.39146	N	0.001446	D	0.94315	0.8173	L	0.35341	1.055	0.51767	D	0.999935	P;D	0.61697	0.935;0.99	P;D	0.68483	0.74;0.958	D	0.92484	0.5995	10	0.19147	T	0.46	.	12.5369	0.56145	0.0:0.9172:0.0:0.0828	.	1112;1112	Q17RW2;Q17RW2-2	COOA1_HUMAN;.	T	1112	ENSP00000359603:R1112T;ENSP00000392531:R1112T	ENSP00000359603:R1112T	R	-	2	0	COL24A1	86087643	1.000000	0.71417	1.000000	0.80357	0.457000	0.32468	1.979000	0.40608	1.189000	0.43028	0.305000	0.20034	AGA		0.338	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4		NM_152890	
COL6A6	131873	broad.mit.edu;hgsc.bcm.edu	37	3	130380932	130380932	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr3:130380932C>G	ENST00000358511.6	+	34	6313	c.6282C>G	c.(6280-6282)agC>agG	p.S2094R	COL6A6_ENST00000453409.2_Missense_Mutation_p.S2094R	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	2094	Nonhelical region.|VWFA 9. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.S2094R(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GGGAAACCAGCCACTTAGATG	0.423																																																	1	Substitution - Missense(1)	kidney(1)											106.0	106.0	106.0					3																	130380932		1866	4105	5971	SO:0001583	missense	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.6282C>G	3.37:g.130380932C>G	ENSP00000351310:p.Ser2094Arg	Somatic		WXS	Illumina HiSeq	Phase_I	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	C	10.63	1.403529	0.25291	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	D;D	0.83837	-1.77;-1.77	5.88	-3.61	0.04556	von Willebrand factor, type A (3);	.	.	.	.	T	0.79907	0.4527	L	0.36672	1.1	0.19300	N	0.999972	P;B	0.50369	0.934;0.409	P;B	0.51170	0.661;0.255	T	0.71303	-0.4633	9	0.21014	T	0.42	.	15.8992	0.79359	0.0:0.7272:0.0:0.2728	.	2094;2094	A6NMZ7;F8W6Y7	CO6A6_HUMAN;.	R	2094	ENSP00000351310:S2094R;ENSP00000399236:S2094R	ENSP00000351310:S2094R	S	+	3	2	COL6A6	131863622	0.001000	0.12720	0.012000	0.15200	0.853000	0.48598	-0.372000	0.07504	-0.559000	0.06110	-0.367000	0.07326	AGC		0.423	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5		NM_001102608	
CRTAC1	55118	hgsc.bcm.edu	37	10	99683108	99683108	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr10:99683108C>A	ENST00000370597.3	-	4	826	c.471G>T	c.(469-471)tgG>tgT	p.W157C	CRTAC1_ENST00000298819.4_Missense_Mutation_p.W157C|CRTAC1_ENST00000370591.2_Missense_Mutation_p.W157C	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	157						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(6)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	35		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		GGATGTCTTCCCACCGGTTAT	0.602																																																	0													115.0	86.0	96.0					10																	99683108		2203	4300	6503	SO:0001583	missense	55118			AJ276171	CCDS31266.1, CCDS55723.1	10q22	2007-12-03			ENSG00000095713	ENSG00000095713			14882	protein-coding gene	gene with protein product		606276				11139377	Standard	NM_018058		Approved	FLJ10320, CEP-68, ASPIC1	uc001kou.2	Q9NQ79	OTTHUMG00000018871	ENST00000370597.3:c.471G>T	10.37:g.99683108C>A	ENSP00000359629:p.Trp157Cys	Somatic		WXS	Illumina HiSeq	Phase_I	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Missense_Mutation	SNP	ENST00000370597.3	37	CCDS31266.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.184829	0.57909	.	.	ENSG00000095713	ENST00000413387;ENST00000370597;ENST00000298819;ENST00000309155;ENST00000370591	T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98	5.17	5.17	0.71159	.	0.123558	0.56097	D	0.000022	T	0.40932	0.1137	L	0.55990	1.75	0.80722	D	1	D;D	0.71674	0.998;0.985	P;P	0.61722	0.893;0.49	T	0.18023	-1.0350	10	0.56958	D	0.05	-13.9752	18.66	0.91469	0.0:1.0:0.0:0.0	.	157;157	Q9NQ79-2;Q9NQ79	.;CRAC1_HUMAN	C	53;157;157;149;157	ENSP00000408445:W53C;ENSP00000359629:W157C;ENSP00000298819:W157C;ENSP00000310810:W149C;ENSP00000359623:W157C	ENSP00000298819:W157C	W	-	3	0	CRTAC1	99673098	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	2.947000	0.49058	2.419000	0.82065	0.563000	0.77884	TGG		0.602	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1		NM_018058	
CSF1R	1436	broad.mit.edu;hgsc.bcm.edu	37	5	149449864	149449864	+	Splice_Site	SNP	G	G	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr5:149449864G>T	ENST00000286301.3	-	9	1491	c.1200C>A	c.(1198-1200)taC>taA	p.Y400*		NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	400					cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)	p.Y400*(2)		NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	CCTCTGGGGGGTCTGAGGAAG	0.592																																																	2	Substitution - Nonsense(2)	kidney(2)											76.0	77.0	77.0					5																	149449864		2203	4300	6503	SO:0001630	splice_region_variant	1436			U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	2433	protein-coding gene	gene with protein product		164770	"""McDonough feline sarcoma viral (v-fms) oncogene homolog"""	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.1199-1C>A	5.37:g.149449864G>T		Somatic		WXS	Illumina HiSeq	Phase_I	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Nonsense_Mutation	SNP	ENST00000286301.3	37	CCDS4302.1	.	.	.	.	.	.	.	.	.	.	G	34	5.349735	0.95830	.	.	ENSG00000182578	ENST00000286301;ENST00000394307	.	.	.	5.89	-1.62	0.08372	.	0.538685	0.16937	N	0.193439	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.7074	0.17915	0.4414:0.0:0.4345:0.1241	.	.	.	.	X	400;252	.	ENSP00000286301:Y400X	Y	-	3	2	CSF1R	149430057	0.969000	0.33509	0.970000	0.41538	0.855000	0.48748	-0.049000	0.11924	-0.361000	0.08125	0.561000	0.74099	TAC		0.592	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2		NM_005211	Nonsense_Mutation
CSMD1	64478	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	3253877	3253877	+	Missense_Mutation	SNP	G	G	A	rs373861459		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr8:3253877G>A	ENST00000520002.1	-	18	2990	c.2435C>T	c.(2434-2436)aCc>aTc	p.T812I	CSMD1_ENST00000542608.1_Missense_Mutation_p.T811I|CSMD1_ENST00000539096.1_Missense_Mutation_p.T811I|CSMD1_ENST00000602557.1_Missense_Mutation_p.T812I|CSMD1_ENST00000537824.1_Missense_Mutation_p.T811I|CSMD1_ENST00000602723.1_Missense_Mutation_p.T812I|CSMD1_ENST00000400186.3_Missense_Mutation_p.T812I			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	812	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)		p.T811I(1)|p.T540I(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)		GACCTCCAAGGTGTCATAATT	0.522																																																	2	Substitution - Missense(2)	kidney(2)						G	ILE/THR	1,4289		0,1,2144	49.0	61.0	57.0		2432	4.4	0.3	8		57	0,8526		0,0,4263	no	missense	CSMD1	NM_033225.5	89	0,1,6407	AA,AG,GG		0.0,0.0233,0.0078	possibly-damaging	811/3565	3253877	1,12815	2145	4263	6408	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.2435C>T	8.37:g.3253877G>A	ENSP00000430733:p.Thr812Ile	Somatic		WXS	Illumina HiSeq	Phase_I	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	G	0.006	-2.021559	0.00414	2.33E-4	0.0	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.59224	0.28;0.28;0.28;0.28;0.28	5.3	4.42	0.53409	CUB (5);	0.000000	0.85682	D	0.000000	T	0.50514	0.1620	N	0.05441	-0.05	0.42041	D	0.991071	P;B	0.38642	0.641;0.009	P;B	0.56788	0.806;0.05	T	0.48502	-0.9030	10	0.19590	T	0.45	.	9.446	0.38697	0.0748:0.1449:0.7802:0.0	.	812;812	E5RIG2;Q96PZ7	.;CSMD1_HUMAN	I	812;812;674;811;811;811	ENSP00000383047:T812I;ENSP00000430733:T812I;ENSP00000441462:T811I;ENSP00000446243:T811I;ENSP00000441675:T811I	ENSP00000320445:T674I	T	-	2	0	CSMD1	3241284	1.000000	0.71417	0.321000	0.25320	0.001000	0.01503	4.011000	0.57124	1.189000	0.43028	-0.175000	0.13238	ACC		0.522	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2		NM_033225	
CYP21A1P	1590	hgsc.bcm.edu	37	6	31974850	31974852	+	In_Frame_Del	DEL	GAG	GAG	-	rs200027963|rs386699253	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr6:31974850_31974852delGAG	ENST00000594256.1	-	1	29_31	c.30_32delCTC	c.(28-33)tcctcg>tcg	p.10_11SS>S	CYP21A1P_ENST00000342991.6_RNA																							GGACCACAACGAGGAGAAGCAGC	0.611														29	0.00579073	0.0	0.0173	5008	,	,		19361	0.001		0.0159	False		,,,				2504	0.0																0										17,4131		1,15,2058						-4.7	0.0			278	293,7673		52,189,3742	no	intergenic				53,204,5800	A1A1,A1R,RR		3.6781,0.4098,2.559				310,11804				SO:0001651	inframe_deletion	1589																														ENST00000594256.1:c.30_32delCTC	6.37:g.31974853_31974855delGAG	ENSP00000472615:p.Ser11del	Somatic		WXS	Illumina HiSeq	Phase_I		In_Frame_Del	DEL	ENST00000594256.1	37																																																																																					0.611	AL645922.1-201	NOVEL	basic|appris_principal	protein_coding	protein_coding				
DIP2C	22982	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	390776	390776	+	Silent	SNP	G	G	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr10:390776G>T	ENST00000280886.6	-	28	3513	c.3426C>A	c.(3424-3426)tcC>tcA	p.S1142S		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1142						nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.S1142S(1)		breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		TCCCAGTTGTGGACACGCTGA	0.587																																																	1	Substitution - coding silent(1)	kidney(1)											84.0	73.0	77.0					10																	390776		2203	4300	6503	SO:0001819	synonymous_variant	22982			BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"""KIAA0934"""	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.3426C>A	10.37:g.390776G>T		Somatic		WXS	Illumina HiSeq	Phase_I	B4DPI5|Q5SS78	Silent	SNP	ENST00000280886.6	37	CCDS7054.1																																																																																				0.587	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1		NM_014974	
DLL4	54567	broad.mit.edu;hgsc.bcm.edu	37	15	41223809	41223809	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr15:41223809G>A	ENST00000249749.5	+	4	779	c.503G>A	c.(502-504)cGc>cAc	p.R168H		NM_019074.3	NP_061947.1	Q9NR61	DLL4_HUMAN	delta-like 4 (Drosophila)	168					angiogenesis (GO:0001525)|blood circulation (GO:0008015)|blood vessel lumenization (GO:0072554)|blood vessel remodeling (GO:0001974)|cardiac atrium morphogenesis (GO:0003209)|cardiac ventricle morphogenesis (GO:0003208)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|dorsal aorta morphogenesis (GO:0035912)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|pericardium morphogenesis (GO:0003344)|positive regulation of neural precursor cell proliferation (GO:2000179)|regulation of neural retina development (GO:0061074)|regulation of neurogenesis (GO:0050767)|signal transduction (GO:0007165)|ventral spinal cord interneuron fate commitment (GO:0060579)|ventricular trabecula myocardium morphogenesis (GO:0003222)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|Notch binding (GO:0005112)	p.R168H(1)		breast(3)|large_intestine(1)	4		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)		ACAAGGCTGCGCTACTCTTAC	0.552																																																	1	Substitution - Missense(1)	kidney(1)											57.0	63.0	61.0					15																	41223809		2062	4206	6268	SO:0001583	missense	54567			AF253468	CCDS45232.1	15q14	2008-07-03	2001-12-03			ENSG00000128917			2910	protein-coding gene	gene with protein product		605185	"""delta-like 4 homolog (Drosophila)"""			10837024	Standard	NM_019074		Approved		uc001zng.2	Q9NR61		ENST00000249749.5:c.503G>A	15.37:g.41223809G>A	ENSP00000249749:p.Arg168His	Somatic		WXS	Illumina HiSeq	Phase_I	Q3KP23|Q9NQT9	Missense_Mutation	SNP	ENST00000249749.5	37	CCDS45232.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.320897	0.81469	.	.	ENSG00000128917	ENST00000249749	D	0.96041	-3.89	5.84	4.87	0.63330	Delta/Serrate/lag-2 (DSL) protein (2);	0.094831	0.64402	D	0.000001	D	0.93536	0.7937	L	0.48218	1.51	0.33767	D	0.622552	P	0.44690	0.841	P	0.47206	0.541	D	0.94424	0.7643	10	0.44086	T	0.13	.	9.1987	0.37244	0.0722:0.0:0.7812:0.1466	.	168	Q9NR61	DLL4_HUMAN	H	168	ENSP00000249749:R168H	ENSP00000249749:R168H	R	+	2	0	DLL4	39011101	0.881000	0.30235	1.000000	0.80357	0.989000	0.77384	2.500000	0.45381	2.768000	0.95171	0.561000	0.74099	CGC		0.552	DLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418859.1			
DMBT1	1755	hgsc.bcm.edu	37	10	124345866	124345866	+	Missense_Mutation	SNP	G	G	C	rs577720017	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr10:124345866G>C	ENST00000338354.3	+	16	1856	c.1750G>C	c.(1750-1752)Ggc>Cgc	p.G584R	DMBT1_ENST00000368956.2_Intron|DMBT1_ENST00000368909.3_Missense_Mutation_p.G584R|DMBT1_ENST00000344338.3_Missense_Mutation_p.G574R|DMBT1_ENST00000368955.3_Missense_Mutation_p.G574R|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000330163.4_Intron			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	584	SRCR 4. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CCATAACTGTGGCCATAGTGA	0.527													G|||	2	0.000399361	0.0	0.0	5008	,	,		18532	0.0		0.001	False		,,,				2504	0.001				Ovarian(182;93 2026 18125 22222 38972)												0													138.0	99.0	112.0					10																	124345866		1948	4089	6037	SO:0001583	missense	1755				CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.1750G>C	10.37:g.124345866G>C	ENSP00000342210:p.Gly584Arg	Somatic		WXS	Illumina HiSeq	Phase_I	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	37		.	.	.	.	.	.	.	.	.	.	G	3.393	-0.123997	0.06795	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000344338;ENST00000368909;ENST00000368955	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	4.5	-6.33	0.01988	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	.	.	.	.	T	0.17109	0.0411	L	0.37897	1.145	0.33680	D	0.612021	B;B;B	0.22909	0.063;0.063;0.077	B;B;B	0.19946	0.016;0.016;0.027	T	0.39143	-0.9628	9	0.13108	T	0.6	.	8.7636	0.34689	0.3162:0.4756:0.2082:0.0	.	584;574;584	Q9UGM3-6;Q9UGM3-3;Q9UGM3	.;.;DMBT1_HUMAN	R	584;584;584;584;584;584;574;584;574	ENSP00000342210:G584R;ENSP00000343175:G574R;ENSP00000357905:G584R;ENSP00000357951:G574R	ENSP00000342210:G584R	G	+	1	0	DMBT1	124335856	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.631000	0.00871	-0.964000	0.03595	-0.564000	0.04169	GGC		0.527	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2		NM_004406	
DOCK9	23348	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	99505670	99505670	+	Missense_Mutation	SNP	A	A	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr13:99505670A>T	ENST00000376460.1	-	35	4018	c.3938T>A	c.(3937-3939)aTg>aAg	p.M1313K	DOCK9_ENST00000448493.2_Missense_Mutation_p.M1325K|DOCK9_ENST00000339416.2_Missense_Mutation_p.M1314K	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	1314					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.M1314K(1)|p.M1325K(1)|p.M1313K(1)		breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					ACCATCAGACATGCTCTTTAA	0.368																																																	3	Substitution - Missense(3)	kidney(3)											191.0	185.0	187.0					13																	99505670		1859	4096	5955	SO:0001583	missense	23348			AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"""Pleckstrin homology (PH) domain containing"""	14132	protein-coding gene	gene with protein product	"""zizimin1"""	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.3938T>A	13.37:g.99505670A>T	ENSP00000365643:p.Met1313Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Missense_Mutation	SNP	ENST00000376460.1	37	CCDS45062.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.900440	0.92035	.	.	ENSG00000088387	ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000400220;ENST00000339416;ENST00000448493;ENST00000449796	T;T;T;T	0.20463	2.37;2.45;2.07;3.59	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.43055	0.1230	L	0.54323	1.7	0.80722	D	1	D;P;D	0.61697	0.99;0.759;0.959	D;B;B	0.69142	0.962;0.352;0.326	T	0.20874	-1.0262	10	0.72032	D	0.01	-32.1826	16.8061	0.85666	1.0:0.0:0.0:0.0	.	1314;1313;1314	A8MWZ5;Q9BZ29-5;Q9BZ29	.;.;DOCK9_HUMAN	K	1313;1314;1314;1314;1313;244;1314;1325;65	ENSP00000365643:M1313K;ENSP00000341086:M1314K;ENSP00000401958:M1325K;ENSP00000403528:M65K	ENSP00000341086:M1314K	M	-	2	0	DOCK9	98303671	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.900000	0.92551	2.367000	0.80283	0.528000	0.53228	ATG		0.368	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1		NM_015296	
DOK3	79930	hgsc.bcm.edu	37	5	176930172	176930174	+	IGR	DEL	GAG	GAG	-	rs376911686|rs370427653|rs79945738|rs138153794	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr5:176930172_176930174delGAG	ENST00000357198.4	-	0	1729				DOK3_ENST00000377112.4_In_Frame_Del_p.L187del|DOK3_ENST00000312943.6_In_Frame_Del_p.L289del|RP11-1334A24.6_ENST00000506025.1_RNA	NM_024872.2	NP_079148.2	Q7L591	DOK3_HUMAN	docking protein 3						Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|lung(7)	13	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.191)			AGCAGGAGCAGAGGAGGGAACGC	0.631														2674	0.533946	0.4425	0.4741	5008	,	,		19022	0.6121		0.5318	False		,,,				2504	0.6217																0									,	1477,1699		465,547,576					,	1.2	0.0		dbSNP_126	47	2974,2754		1007,960,897	no	coding,coding	DOK3	NM_001144876.1,NM_001144875.1	,	1472,1507,1473	A1A1,A1R,RR		48.0796,46.505,49.9888	,	,		4451,4453				SO:0001628	intergenic_variant	79930			AK026223	CCDS4426.1, CCDS47349.1, CCDS47350.1	5q35	2008-02-05			ENSG00000146094	ENSG00000146094			24583	protein-coding gene	gene with protein product		611435				10733577, 12595900	Standard	NM_024872		Approved	FLJ22570	uc003mhk.3	Q7L591	OTTHUMG00000130850		5.37:g.176930175_176930177delGAG		Somatic		WXS	Illumina HiSeq	Phase_I	E9PAT0|H7BXS0|Q8N864|Q9BQB3|Q9H666	In_Frame_Del	DEL	ENST00000357198.4	37	CCDS4426.1																																																																																				0.631	DOK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253420.4		NM_024872	
EMILIN2	84034	broad.mit.edu;hgsc.bcm.edu	37	18	2891708	2891708	+	Nonsense_Mutation	SNP	C	C	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr18:2891708C>G	ENST00000254528.3	+	4	1742	c.1583C>G	c.(1582-1584)tCa>tGa	p.S528*		NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	528					cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)	p.S528*(1)		breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		CCAGGAGTGTCAGGGTCAGGA	0.532																																																	1	Substitution - Nonsense(1)	kidney(1)											67.0	70.0	69.0					18																	2891708		2203	4300	6503	SO:0001587	stop_gained	84034			AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"""EMI domain containing"""	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.1583C>G	18.37:g.2891708C>G	ENSP00000254528:p.Ser528*	Somatic		WXS	Illumina HiSeq	Phase_I	B2RMY3|Q8NBH3|Q96JQ4	Nonsense_Mutation	SNP	ENST00000254528.3	37	CCDS11828.1	.	.	.	.	.	.	.	.	.	.	C	36	5.930559	0.97116	.	.	ENSG00000132205	ENST00000254528	.	.	.	4.51	2.69	0.31865	.	0.716429	0.12527	N	0.461129	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	-1.2327	9.4094	0.38482	0.1442:0.7791:0.0:0.0767	.	.	.	.	X	528	.	ENSP00000254528:S528X	S	+	2	0	EMILIN2	2881708	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.087000	0.11215	0.585000	0.29608	0.563000	0.77884	TCA		0.532	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2		NM_032048	
EMR3	84658	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	14758037	14758037	+	Missense_Mutation	SNP	C	C	T	rs200966967		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr19:14758037C>T	ENST00000253673.5	-	8	938	c.838G>A	c.(838-840)Gtg>Atg	p.V280M	EMR3_ENST00000443157.2_Missense_Mutation_p.V154M|EMR3_ENST00000599900.1_Missense_Mutation_p.V65M|EMR3_ENST00000344373.4_Missense_Mutation_p.V228M	NM_032571.3	NP_115960.2	Q9BY15	EMR3_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 3	280					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.V280M(1)		NS(1)|autonomic_ganglia(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(14)|ovary(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	50						GAGAGAGACACGTTCCTTTTG	0.448																																																	1	Substitution - Missense(1)	kidney(1)											252.0	206.0	221.0					19																	14758037		2203	4300	6503	SO:0001583	missense	84658			AF239764	CCDS12315.1, CCDS74296.1, CCDS74297.1	19p13.1	2014-08-08				ENSG00000131355		"""-"", ""GPCR / Class B : Orphans"""	23647	protein-coding gene	gene with protein product		606101				11279179, 12975309	Standard	XM_005260118		Approved		uc002mzi.4	Q9BY15		ENST00000253673.5:c.838G>A	19.37:g.14758037C>T	ENSP00000253673:p.Val280Met	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000253673.5	37	CCDS12315.1	.	.	.	.	.	.	.	.	.	.	C	6.869	0.529670	0.13127	.	.	ENSG00000131355	ENST00000443157;ENST00000253673;ENST00000344373	T;T;T	0.58358	0.95;0.34;1.03	3.94	-1.8	0.07907	.	.	.	.	.	T	0.36853	0.0982	L	0.32530	0.975	0.09310	N	1	B;B;B	0.25850	0.037;0.136;0.037	B;B;B	0.22753	0.041;0.024;0.018	T	0.23119	-1.0197	9	0.45353	T	0.12	.	8.1844	0.31330	0.0:0.4614:0.0:0.5386	.	154;228;280	E7EW83;Q9BY15-2;Q9BY15	.;.;EMR3_HUMAN	M	154;280;228	ENSP00000396208:V154M;ENSP00000253673:V280M;ENSP00000340758:V228M	ENSP00000253673:V280M	V	-	1	0	EMR3	14619037	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.214000	0.09292	-0.363000	0.08101	-0.824000	0.03097	GTG		0.448	EMR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466488.1		NM_032571	
FBXO34	55030	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	55817459	55817459	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr14:55817459G>T	ENST00000313833.4	+	2	596	c.351G>T	c.(349-351)aaG>aaT	p.K117N	FBXO34_ENST00000440021.1_Missense_Mutation_p.K117N|FBXO34_ENST00000555087.1_3'UTR	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	117								p.K117N(1)		breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						GAAATACCAAGGAAAAAATTG	0.408																																																	1	Substitution - Missense(1)	kidney(1)											58.0	62.0	60.0					14																	55817459		2203	4300	6503	SO:0001583	missense	55030			AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"""F-boxes /  ""other"""""	20201	protein-coding gene	gene with protein product		609104	"""F-box only protein 34"""				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.351G>T	14.37:g.55817459G>T	ENSP00000313159:p.Lys117Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	37	CCDS32086.1	.	.	.	.	.	.	.	.	.	.	G	16.68	3.189709	0.57909	.	.	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.29397	1.57;1.57	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.58075	0.2097	M	0.74258	2.255	0.58432	D	0.999996	D	0.89917	1.0	D	0.81914	0.995	T	0.61734	-0.7002	10	0.87932	D	0	-17.2291	18.7952	0.91991	0.0:0.0:1.0:0.0	.	117	Q9NWN3	FBX34_HUMAN	N	117	ENSP00000313159:K117N;ENSP00000394117:K117N	ENSP00000313159:K117N	K	+	3	2	FBXO34	54887212	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.969000	0.49232	2.675000	0.91044	0.655000	0.94253	AAG		0.408	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1			
FNIP1	96459	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	131042127	131042127	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr5:131042127C>G	ENST00000510461.1	-	9	986	c.891G>C	c.(889-891)ttG>ttC	p.L297F	FNIP1_ENST00000307954.8_Missense_Mutation_p.L252F|CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000511848.1_Missense_Mutation_p.L297F|FNIP1_ENST00000307968.7_Missense_Mutation_p.L269F	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	297					cellular response to starvation (GO:0009267)|immature B cell differentiation (GO:0002327)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of GTPase activity (GO:0043547)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.L297F(1)		NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		CCCCATTTTCCAAACTTGTTG	0.433																																																	1	Substitution - Missense(1)	kidney(1)											97.0	94.0	95.0					5																	131042127		2203	4300	6503	SO:0001583	missense	96459			DQ145719	CCDS34226.1, CCDS34227.1	5q23.3	2014-01-28				ENSG00000217128			29418	protein-coding gene	gene with protein product		610594				11853319, 17028174	Standard	NM_001008738		Approved	KIAA1961		Q8TF40		ENST00000510461.1:c.891G>C	5.37:g.131042127C>G	ENSP00000421985:p.Leu297Phe	Somatic		WXS	Illumina HiSeq	Phase_I	D6RJH5|Q86T47|Q9BUT0	Missense_Mutation	SNP	ENST00000510461.1	37	CCDS34227.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.228513	0.79576	.	.	ENSG00000217128	ENST00000307968;ENST00000307954;ENST00000544351;ENST00000510461;ENST00000511848	T;T;T;T	0.34472	2.2;2.15;2.09;1.36	5.6	1.86	0.25419	.	.	.	.	.	T	0.49712	0.1573	L	0.52126	1.63	0.58432	D	0.999998	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.997;0.999;0.997	T	0.42275	-0.9461	9	0.54805	T	0.06	-4.1067	10.1562	0.42825	0.0:0.7315:0.0:0.2685	.	297;297;269;297	A8K8V8;Q8TF40-2;Q8TF40-3;Q8TF40	.;.;.;FNIP1_HUMAN	F	269;252;57;297;297	ENSP00000309266:L269F;ENSP00000310453:L252F;ENSP00000421985:L297F;ENSP00000425619:L297F	ENSP00000310453:L252F	L	-	3	2	FNIP1	131070026	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.207000	0.42788	0.422000	0.26005	0.591000	0.81541	TTG		0.433	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1		NM_133372	
FRYL	285527	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	48525026	48525026	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr4:48525026G>C	ENST00000503238.1	-	51	7412	c.7413C>G	c.(7411-7413)tgC>tgG	p.C2471W	FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000507873.2_5'UTR|FRYL_ENST00000358350.4_Missense_Mutation_p.C2471W|FRYL_ENST00000537810.1_Missense_Mutation_p.C2471W			O94915	FRYL_HUMAN	FRY-like	2471					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)			p.C2471W(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						TGCTACTAGAGCACTGGTACT	0.532																																																	1	Substitution - Missense(1)	kidney(1)											166.0	166.0	166.0					4																	48525026		1959	4145	6104	SO:0001583	missense	285527			AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"""KIAA0826"", ""furry homolog-like (Drosophila)"""	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.7413C>G	4.37:g.48525026G>C	ENSP00000426064:p.Cys2471Trp	Somatic		WXS	Illumina HiSeq	Phase_I	O95640|Q8WTZ5|Q9NT40	Missense_Mutation	SNP	ENST00000503238.1	37	CCDS43227.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.47|12.47	1.947796|1.947796	0.34377|0.34377	.|.	.|.	ENSG00000075539|ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810|ENST00000514617	T;T;T|.	0.21932|.	1.98;1.98;1.98|.	5.62|5.62	-1.76|-1.76	0.08006|0.08006	.|.	0.117006|.	0.64402|.	D|.	0.000012|.	T|T	0.36138|0.36138	0.0956|0.0956	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	D|D	1|1	B;B;B|.	0.30709|.	0.291;0.043;0.127|.	B;B;B|.	0.35770|.	0.064;0.104;0.21|.	T|T	0.07309|0.07309	-1.0779|-1.0779	10|5	0.39692|.	T|.	0.17|.	.|.	12.1184|12.1184	0.53878|0.53878	0.5067:0.0:0.4933:0.0|0.5067:0.0:0.4933:0.0	.|.	1301;2471;2471|.	Q6ZR29;O94915;F5GX82|.	.;FRYL_HUMAN;.|.	W|V	2471|1341	ENSP00000426064:C2471W;ENSP00000351113:C2471W;ENSP00000441114:C2471W|.	ENSP00000351113:C2471W|.	C|L	-|-	3|1	2|0	FRYL|FRYL	48219783|48219783	1.000000|1.000000	0.71417|0.71417	0.935000|0.935000	0.37517|0.37517	0.915000|0.915000	0.54546|0.54546	0.975000|0.975000	0.29449|0.29449	-0.836000|-0.836000	0.04229|0.04229	-0.384000|-0.384000	0.06662|0.06662	TGC|CTC		0.532	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			
GLYAT	10249	broad.mit.edu;ucsc.edu	37	11	58477555	58477555	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr11:58477555C>A	ENST00000344743.3	-	6	716	c.575G>T	c.(574-576)aGg>aTg	p.R192M	GLYAT_ENST00000529732.1_Missense_Mutation_p.R192M|GLYAT_ENST00000278400.3_Intron	NM_201648.2	NP_964011.2	Q6IB77	GLYAT_HUMAN	glycine-N-acyltransferase	192					acyl-CoA metabolic process (GO:0006637)|glycine metabolic process (GO:0006544)|monocarboxylic acid metabolic process (GO:0032787)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)|glycine N-benzoyltransferase activity (GO:0047962)|transferase activity, transferring acyl groups (GO:0016746)	p.R192M(1)		NS(1)|autonomic_ganglia(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16		Breast(21;0.0044)|all_epithelial(135;0.0157)			Glycine(DB00145)	TCTCTGGCTCCTCTCATTACC	0.502																																																	1	Substitution - Missense(1)	kidney(1)											74.0	74.0	74.0					11																	58477555		2201	4295	6496	SO:0001583	missense	10249			AF023466	CCDS7970.1, CCDS7971.1	11q12.1	2008-03-11					2.3.1.13		13734	protein-coding gene	gene with protein product		607424					Standard	NM_201648		Approved	GAT, ACGNAT	uc001nnb.3	Q6IB77		ENST00000344743.3:c.575G>T	11.37:g.58477555C>A	ENSP00000340200:p.Arg192Met	Somatic		WXS	Illumina GAIIx	Phase_I	O14833|Q96QK7	Missense_Mutation	SNP	ENST00000344743.3	37	CCDS7970.1	.	.	.	.	.	.	.	.	.	.	C	13.17	2.156772	0.38119	.	.	ENSG00000149124	ENST00000344743;ENST00000529732	T;T	0.19532	2.14;2.14	6.06	1.98	0.26296	Acyl-CoA N-acyltransferase (2);Glycine N-acyltransferase, N-terminal (1);	0.378676	0.30374	N	0.009779	T	0.46034	0.1372	M	0.90759	3.145	0.80722	D	1	D	0.60575	0.988	D	0.63488	0.915	T	0.46735	-0.9170	10	0.87932	D	0	-18.0766	8.1332	0.31039	0.0:0.6553:0.0:0.3447	.	192	Q6IB77	GLYAT_HUMAN	M	192	ENSP00000340200:R192M;ENSP00000431688:R192M	ENSP00000340200:R192M	R	-	2	0	GLYAT	58234131	0.097000	0.21791	0.991000	0.47740	0.028000	0.11728	0.130000	0.15850	0.400000	0.25396	-0.355000	0.07637	AGG		0.502	GLYAT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394593.1			
GOLGB1	2804	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	121412704	121412704	+	Silent	SNP	A	A	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr3:121412704A>G	ENST00000340645.5	-	13	6776	c.6651T>C	c.(6649-6651)gaT>gaC	p.D2217D	GOLGB1_ENST00000393667.3_Silent_p.D2222D	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2217					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.D2217D(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		TTTGAATCGCATCACTAAACT	0.403																																																	1	Substitution - coding silent(1)	kidney(1)											239.0	214.0	223.0					3																	121412704		2203	4300	6503	SO:0001819	synonymous_variant	2804			X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.6651T>C	3.37:g.121412704A>G		Somatic		WXS	Illumina HiSeq	Phase_I	B2ZZ91|D3DN92|E7EP74|Q14398	Silent	SNP	ENST00000340645.5	37	CCDS3004.1																																																																																				0.403	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1		NM_004487	
GRWD1	83743	broad.mit.edu;hgsc.bcm.edu	37	19	48954349	48954349	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr19:48954349C>T	ENST00000253237.5	+	6	1117	c.884C>T	c.(883-885)cCc>cTc	p.P295L		NM_031485.3	NP_113673.3	Q9BQ67	GRWD1_HUMAN	glutamate-rich WD repeat containing 1	295						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.P295L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|stomach(1)	19		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000206)|all cancers(93;0.000207)|Epithelial(262;0.0125)|GBM - Glioblastoma multiforme(486;0.0222)		CGGGCAGCCCCCAGCAAGGCC	0.667																																																	1	Substitution - Missense(1)	kidney(1)											55.0	57.0	57.0					19																	48954349		2203	4300	6503	SO:0001583	missense	83743			AF337808	CCDS12720.1	19q13.33	2013-05-21				ENSG00000105447		"""WD repeat domain containing"""	21270	protein-coding gene	gene with protein product	regulator of ribosome biogenesis 1 homolog (S. cerevisiae)	610597				15885502	Standard	NM_031485		Approved	WDR28, GRWD, RRB1	uc002pjd.2	Q9BQ67		ENST00000253237.5:c.884C>T	19.37:g.48954349C>T	ENSP00000253237:p.Pro295Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q8TF59	Missense_Mutation	SNP	ENST00000253237.5	37	CCDS12720.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.429888	0.83776	.	.	ENSG00000105447	ENST00000253237	T	0.69685	-0.42	3.84	3.84	0.44239	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.059646	0.64402	D	0.000002	T	0.60104	0.2243	N	0.25332	0.735	0.80722	D	1	P	0.46142	0.873	P	0.46975	0.533	T	0.64580	-0.6374	10	0.48119	T	0.1	-20.582	15.0469	0.71835	0.0:1.0:0.0:0.0	.	295	Q9BQ67	GRWD1_HUMAN	L	295	ENSP00000253237:P295L	ENSP00000253237:P295L	P	+	2	0	GRWD1	53646161	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	6.630000	0.74272	2.168000	0.68352	0.561000	0.74099	CCC		0.667	GRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466122.1		NM_031485	
GPR32	2854	hgsc.bcm.edu	37	19	51274851	51274851	+	Missense_Mutation	SNP	A	A	C	rs201404376		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr19:51274851A>C	ENST00000270590.4	+	1	1131	c.994A>C	c.(994-996)Act>Cct	p.T332P		NM_001506.1	NP_001497.1	O75388	GPR32_HUMAN	G protein-coupled receptor 32	332					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(4)|endometrium(4)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	29		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		CCAGTCTTTGACTTCTGCCCT	0.552																																					Esophageal Squamous(113;152 1581 5732 15840 44398)												0													66.0	71.0	69.0					19																	51274851		2203	4298	6501	SO:0001583	missense	2854			AF045764	CCDS12801.1	19q13.33	2012-08-20			ENSG00000142511	ENSG00000142511		"""GPCR / Class A : Resolvin receptors"""	4487	protein-coding gene	gene with protein product	"""resolvin D1 receptor"""	603195				9653656	Standard	NM_001506		Approved	RVDR1	uc010ycf.3	O75388		ENST00000270590.4:c.994A>C	19.37:g.51274851A>C	ENSP00000270590:p.Thr332Pro	Somatic		WXS	Illumina HiSeq	Phase_I	Q502U7|Q6NWS5	Missense_Mutation	SNP	ENST00000270590.4	37	CCDS12801.1	.	.	.	.	.	.	.	.	.	.	a	0.006	-2.066505	0.00382	.	.	ENSG00000142511	ENST00000270590	T	0.36699	1.24	2.71	-0.781	0.10965	.	.	.	.	.	T	0.12518	0.0304	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31138	-0.9954	9	0.02654	T	1	.	3.6506	0.08202	0.205:0.5623:0.0:0.2327	.	332	O75388	GPR32_HUMAN	P	332	ENSP00000270590:T332P	ENSP00000270590:T332P	T	+	1	0	GPR32	55966663	0.000000	0.05858	0.025000	0.17156	0.653000	0.38743	0.089000	0.15002	-0.262000	0.09392	-0.755000	0.03482	ACT		0.552	GPR32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465016.1			
HIRIP3	8479	broad.mit.edu;hgsc.bcm.edu	37	16	30006027	30006027	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr16:30006027G>A	ENST00000279392.3	-	4	1269	c.439C>T	c.(439-441)Cgg>Tgg	p.R147W	INO80E_ENST00000304516.7_5'Flank|INO80E_ENST00000567705.1_5'Flank|INO80E_ENST00000563197.1_5'Flank|INO80E_ENST00000567254.1_5'Flank|HIRIP3_ENST00000566471.1_5'Flank|HIRIP3_ENST00000564026.1_Intron	NM_003609.4	NP_003600.2	Q9BW71	HIRP3_HUMAN	HIRA interacting protein 3	147	Glu-rich.				chromatin assembly or disassembly (GO:0006333)	nucleus (GO:0005634)		p.R147W(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(9)	17						TCCCTCTGCCGTTCCTCATCA	0.567																																																	1	Substitution - Missense(1)	kidney(1)											166.0	175.0	172.0					16																	30006027		2197	4300	6497	SO:0001583	missense	8479			AJ223351	CCDS10664.1, CCDS58449.1	16p12.1	2008-02-05	2001-11-29		ENSG00000149929	ENSG00000149929			4917	protein-coding gene	gene with protein product		603365	"""HIRA-interacting protein 3"""			9710638	Standard	NM_003609		Approved		uc002dve.3	Q9BW71	OTTHUMG00000132118	ENST00000279392.3:c.439C>T	16.37:g.30006027G>A	ENSP00000279392:p.Arg147Trp	Somatic		WXS	Illumina HiSeq	Phase_I	H3BSR3|O75707|O75708	Missense_Mutation	SNP	ENST00000279392.3	37	CCDS10664.1	.	.	.	.	.	.	.	.	.	.	G	8.276	0.814414	0.16607	.	.	ENSG00000149929	ENST00000279392	T	0.38077	1.16	4.25	-1.65	0.08291	.	1.510760	0.04083	N	0.310030	T	0.17280	0.0415	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25363	-1.0134	10	0.72032	D	0.01	-1.1669	0.9598	0.01393	0.2776:0.2861:0.2903:0.146	.	147	Q9BW71	HIRP3_HUMAN	W	147	ENSP00000279392:R147W	ENSP00000279392:R147W	R	-	1	2	HIRIP3	29913528	0.005000	0.15991	0.001000	0.08648	0.017000	0.09413	0.169000	0.16641	-0.048000	0.13401	-0.229000	0.12294	CGG		0.567	HIRIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255160.2		NM_003609	
HOGA1	112817	broad.mit.edu;hgsc.bcm.edu	37	10	99344532	99344532	+	Silent	SNP	C	C	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr10:99344532C>T	ENST00000370646.4	+	1	433	c.72C>T	c.(70-72)gtC>gtT	p.V24V	PI4K2A_ENST00000555577.1_Silent_p.V24V|PI4K2A_ENST00000370649.3_Silent_p.V24V|HOGA1_ENST00000370647.4_Silent_p.V24V	NM_138413.3	NP_612422.2	Q86XE5	HOGA1_HUMAN	4-hydroxy-2-oxoglutarate aldolase 1	24					4-hydroxyproline catabolic process (GO:0019470)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|oxalate metabolic process (GO:0033609)|pyruvate biosynthetic process (GO:0042866)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	4-hydroxy-2-oxoglutarate aldolase activity (GO:0008700)|protein homodimerization activity (GO:0042803)	p.V24V(2)		breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|stomach(1)	14						ATGTGGGGGTCTGGGCCTCAG	0.597																																																	2	Substitution - coding silent(2)	kidney(2)											102.0	106.0	105.0					10																	99344532		2203	4300	6503	SO:0001819	synonymous_variant	112817			BC011916	CCDS7467.1, CCDS44469.1	10q24.1	2010-12-19	2010-12-19	2010-12-19	ENSG00000241935	ENSG00000241935			25155	protein-coding gene	gene with protein product	"""dihydrodipicolinate synthetase homolog 2 (E. coli)"", ""N-acetylneuraminate pyruvate lyase 2 (putative)"""	613597	"""chromosome 10 open reading frame 65"", ""dihydrodipicolinate synthase-like, mitochondrial"""	C10orf65, DHDPSL		20797690	Standard	NM_001134670		Approved	FLJ37472, DHDPS2, NPL2		Q86XE5	OTTHUMG00000018859	ENST00000370646.4:c.72C>T	10.37:g.99344532C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A8K075|Q5T680|Q5T684|Q711P0|Q8N9F2|Q96EV5	Silent	SNP	ENST00000370646.4	37	CCDS7467.1																																																																																				0.597	HOGA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049726.1		NM_138413	
IL33	90865	broad.mit.edu;ucsc.edu	37	9	6252967	6252967	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr9:6252967G>C	ENST00000381434.3	+	4	458	c.445G>C	c.(445-447)Gac>Cac	p.D149H	IL33_ENST00000417746.2_Intron|IL33_ENST00000456383.2_Intron	NM_033439.3	NP_254274.1	O95760	IL33_HUMAN	interleukin 33	149					extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of immunoglobulin secretion (GO:0051025)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type 2 immune response (GO:0002830)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|nucleus (GO:0005634)	cytokine activity (GO:0005125)	p.D149H(1)		breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|stomach(1)|urinary_tract(1)	16		Acute lymphoblastic leukemia(23;0.158)|Prostate(43;0.167)		GBM - Glioblastoma multiforme(50;0.0161)|Lung(218;0.105)		ATATGTTGAAGACTTGAAAAA	0.259																																																	1	Substitution - Missense(1)	kidney(1)											51.0	52.0	52.0					9																	6252967		2203	4298	6501	SO:0001583	missense	90865			AB024518	CCDS6468.1, CCDS56563.1, CCDS56564.1	9p24.1	2014-01-28	2006-11-20	2006-11-20	ENSG00000137033	ENSG00000137033		"""Interleukins and interleukin receptors"""	16028	protein-coding gene	gene with protein product	"""DVS27-related protein"", ""nuclear factor for high endothelial venules"", ""interleukin-1 family, member 11"""	608678	"""chromosome 9 open reading frame 26 (NF-HEV)"""	C9orf26		10566975, 12819012	Standard	NM_033439		Approved	DVS27, DKFZp586H0523, NF-HEV, IL1F11	uc003zjt.3	O95760	OTTHUMG00000019516	ENST00000381434.3:c.445G>C	9.37:g.6252967G>C	ENSP00000370842:p.Asp149His	Somatic		WXS	Illumina GAIIx	Phase_I	B2R8L1|B4DJ35|B4E1Q9|D3DRI5|E7EAX4|Q2YEJ5	Missense_Mutation	SNP	ENST00000381434.3	37	CCDS6468.1	.	.	.	.	.	.	.	.	.	.	G	12.43	1.934699	0.34189	.	.	ENSG00000137033	ENST00000381434	T	0.61040	0.14	5.15	4.25	0.50352	.	0.412070	0.20881	N	0.083992	T	0.49677	0.1571	L	0.47190	1.495	0.80722	D	1	P	0.45011	0.848	B	0.39152	0.292	T	0.56625	-0.7948	10	0.87932	D	0	-13.4406	11.9662	0.53035	0.0:0.1737:0.8263:0.0	.	149	O95760	IL33_HUMAN	H	149	ENSP00000370842:D149H	ENSP00000370842:D149H	D	+	1	0	IL33	6242967	0.998000	0.40836	0.295000	0.24960	0.221000	0.24807	1.783000	0.38664	1.528000	0.49103	0.650000	0.86243	GAC		0.259	IL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051655.1		NM_033439	
KCNJ12	3768	hgsc.bcm.edu	37	17	21319716	21319716	+	Silent	SNP	G	G	A	rs78135255	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr17:21319716G>A	ENST00000583088.1	+	3	1957	c.1062G>A	c.(1060-1062)acG>acA	p.T354T	KCNJ12_ENST00000331718.5_Silent_p.T354T	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	354					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)	p.T354T(1)		NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	TGCCCTCTACGCCCCGCTGCA	0.577										Prostate(3;0.18)																																							1	Substitution - coding silent(1)	stomach(1)											115.0	114.0	114.0					17																	21319716		2203	4300	6503	SO:0001819	synonymous_variant	3768			L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.1062G>A	17.37:g.21319716G>A		Somatic		WXS	Illumina HiSeq	Phase_I	O43401|Q15756|Q8NG63	Silent	SNP	ENST00000583088.1	37	CCDS11219.1																																																																																				0.577	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2		NM_021012	
KDR	3791	broad.mit.edu;hgsc.bcm.edu	37	4	55973949	55973949	+	Missense_Mutation	SNP	A	A	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr4:55973949A>C	ENST00000263923.4	-	10	1662	c.1367T>G	c.(1366-1368)aTc>aGc	p.I456S		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	456	Ig-like C2-type 5.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.I456S(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ATACCAGTGGATGTGATGCGG	0.512			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)																														Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	1	Substitution - Missense(1)	kidney(1)											204.0	173.0	183.0					4																	55973949		2203	4300	6503	SO:0001583	missense	3791			AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.1367T>G	4.37:g.55973949A>C	ENSP00000263923:p.Ile456Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	.	.	.	.	.	.	.	.	.	.	A	17.14	3.314454	0.60524	.	.	ENSG00000128052	ENST00000263923	T	0.13420	2.59	5.29	5.29	0.74685	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.530991	0.21343	N	0.076095	T	0.37293	0.0998	M	0.82823	2.61	0.28306	N	0.922896	D;D	0.55172	0.97;0.957	P;P	0.58577	0.714;0.841	T	0.36601	-0.9741	10	0.87932	D	0	.	15.2002	0.73130	1.0:0.0:0.0:0.0	.	456;456	P35968-2;P35968	.;VGFR2_HUMAN	S	456	ENSP00000263923:I456S	ENSP00000263923:I456S	I	-	2	0	KDR	55668706	0.999000	0.42202	0.058000	0.19502	0.260000	0.26232	8.696000	0.91302	2.004000	0.58718	0.260000	0.18958	ATC		0.512	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			
LILRB4	11006	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	55177763	55177763	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr19:55177763G>A	ENST00000391736.1	+	10	1262	c.947G>A	c.(946-948)aGg>aAg	p.R316K	LILRB4_ENST00000430952.2_Missense_Mutation_p.R316K|LILRB4_ENST00000391734.3_Missense_Mutation_p.R316K|LILRB4_ENST00000270452.2_Missense_Mutation_p.R316K|LILRB4_ENST00000391733.3_Missense_Mutation_p.R316K	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	316					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)	p.R316K(1)		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)		GGCCTACAGAGGAGGTAATTC	0.617																																																	1	Substitution - Missense(1)	kidney(1)											118.0	104.0	108.0					19																	55177763		2203	4300	6503	SO:0001583	missense	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.947G>A	19.37:g.55177763G>A	ENSP00000375616:p.Arg316Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.605715	0.00842	.	.	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733;ENST00000434286	T;T;T;T;T;T	0.00460	7.37;7.37;7.37;7.3;7.39;7.27	1.86	-3.73	0.04398	.	.	.	.	.	T	0.00241	0.0007	L	0.35644	1.08	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.0;0.001;0.0	T	0.45906	-0.9229	9	0.05351	T	0.99	.	2.7192	0.05196	0.4277:0.0:0.2576:0.3147	.	316;315;316;316;316	A8MUE1;C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;.;LIRB4_HUMAN	K	316;316;316;316;316;315	ENSP00000375616:R316K;ENSP00000270452:R316K;ENSP00000408995:R316K;ENSP00000375614:R316K;ENSP00000375613:R316K;ENSP00000401962:R315K	ENSP00000270452:R316K	R	+	2	0	LILRB4	59869575	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-2.071000	0.01378	-1.624000	0.01556	-0.481000	0.04817	AGG		0.617	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3			
LRP2	4036	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	170028541	170028541	+	Silent	SNP	T	T	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr2:170028541T>C	ENST00000263816.3	-	58	11532	c.11247A>G	c.(11245-11247)tcA>tcG	p.S3749S		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3749	LDL-receptor class A 31. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.S3749S(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	TTTCCTCATCTGAGTTATCTC	0.453																																																	1	Substitution - coding silent(1)	kidney(1)											152.0	134.0	140.0					2																	170028541		2203	4300	6503	SO:0001819	synonymous_variant	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.11247A>G	2.37:g.170028541T>C		Somatic		WXS	Illumina HiSeq	Phase_I	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																				0.453	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2		NM_004525	
LRRC4	64101	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	127669258	127669258	+	Missense_Mutation	SNP	G	G	A	rs531914482		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr7:127669258G>A	ENST00000249363.3	-	2	1693	c.1436C>T	c.(1435-1437)aCg>aTg	p.T479M	SND1_ENST00000354725.3_Intron	NM_022143.4	NP_071426.1	Q9HBW1	LRRC4_HUMAN	leucine rich repeat containing 4	479	Thr-rich.				postsynaptic density protein 95 clustering (GO:0097119)|regulation of synapse organization (GO:0050807)|synapse organization (GO:0050808)	cell junction (GO:0030054)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.T479M(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(6)|lung(4)|pancreas(1)|skin(2)	26				Lung(243;0.124)		ACCAGTGGACGTGGTAGGAAC	0.552													G|||	1	0.000199681	0.0	0.0014	5008	,	,		20602	0.0		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)											167.0	132.0	144.0					7																	127669258		2203	4300	6503	SO:0001583	missense	64101			AF196976	CCDS5799.1	7q31	2013-01-14	2003-11-19		ENSG00000128594	ENSG00000128594		"""Immunoglobulin superfamily / I-set domain containing"""	15586	protein-coding gene	gene with protein product		610486	"""leucine-rich repeat-containing 4"""			12969517	Standard	NM_022143		Approved	NAG14	uc003vmk.3	Q9HBW1	OTTHUMG00000157563	ENST00000249363.3:c.1436C>T	7.37:g.127669258G>A	ENSP00000249363:p.Thr479Met	Somatic		WXS	Illumina HiSeq	Phase_I	A4D0Y9|Q14DU9|Q6ZMI8|Q96A85	Missense_Mutation	SNP	ENST00000249363.3	37	CCDS5799.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.903056	0.52227	.	.	ENSG00000128594	ENST00000249363	T	0.27890	1.64	4.8	4.8	0.61643	.	0.354305	0.23993	N	0.042560	T	0.35219	0.0924	L	0.52011	1.625	0.43099	D	0.994784	D	0.54397	0.966	P	0.46320	0.512	T	0.19877	-1.0292	10	0.54805	T	0.06	.	15.4005	0.74838	0.0:0.0:1.0:0.0	.	479	Q9HBW1	LRRC4_HUMAN	M	479	ENSP00000249363:T479M	ENSP00000249363:T479M	T	-	2	0	LRRC4	127456494	1.000000	0.71417	0.848000	0.33437	0.982000	0.71751	7.627000	0.83176	2.494000	0.84150	0.561000	0.74099	ACG		0.552	LRRC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349170.1		NM_022143	
MAP2K3	5606	hgsc.bcm.edu	37	17	21204192	21204192	+	Missense_Mutation	SNP	C	C	T	rs56216806	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr17:21204192C>T	ENST00000342679.4	+	5	535	c.286C>T	c.(286-288)Cgg>Tgg	p.R96W	MAP2K3_ENST00000361818.5_Missense_Mutation_p.R67W|MAP2K3_ENST00000316920.6_Missense_Mutation_p.R67W	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	96	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> W (in dbSNP:rs56216806). {ECO:0000269|PubMed:17344846}.		activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)								COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		GCAGCGGATCCGGGCCACCGT	0.622																																																	0																																										SO:0001583	missense	5606			L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152		"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6843	protein-coding gene	gene with protein product	"""MAPK/ERK kinase 3"", ""MAP kinase kinase 3"", ""dual specificity mitogen activated protein kinase kinase 3"""	602315		PRKMK3		9465908	Standard	NM_145109		Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.286C>T	17.37:g.21204192C>T	ENSP00000345083:p.Arg96Trp	Somatic		WXS	Illumina HiSeq	Phase_I	B3KSK7|Q99441|Q9UE71|Q9UE72	Missense_Mutation	SNP	ENST00000342679.4	37	CCDS11217.1	1092	0.5	246	0.5	181	0.5	286	0.5	379	0.5	C	14.98	2.698443	0.48307	.	.	ENSG00000034152	ENST00000342679;ENST00000395491;ENST00000361818;ENST00000526076;ENST00000316920	T;T;T	0.66815	-0.23;-0.23;-0.23	5.08	5.08	0.68730	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000006	T	0.00012	0.0000	M	0.77486	2.375	0.58432	D	0.999999	D	0.89917	1.0	D	0.80764	0.994	T	0.42565	-0.9444	10	0.72032	D	0.01	-27.0478	13.4514	0.61174	0.1566:0.8434:0.0:0.0	rs56216806	96	P46734	MP2K3_HUMAN	W	96;67;67;67;100	ENSP00000345083:R96W;ENSP00000355081:R67W;ENSP00000434068:R67W	ENSP00000319139:R100W	R	+	1	2	MAP2K3	21144785	0.986000	0.35501	1.000000	0.80357	0.876000	0.50452	2.458000	0.45014	2.359000	0.80004	0.655000	0.94253	CGG		0.622	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2		NM_145109	
MRPL32	64983	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	42974658	42974658	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr7:42974658G>A	ENST00000223324.2	+	2	422	c.235G>A	c.(235-237)Gca>Aca	p.A79T	PSMA2_ENST00000442788.1_5'Flank|PSMA2_ENST00000223321.4_5'Flank|MRPL32_ENST00000496564.1_3'UTR|PSMA2_ENST00000445517.1_5'Flank|PSMA2_ENST00000538645.1_5'Flank	NM_031903.2	NP_114109.1	Q9BYC8	RM32_HUMAN	mitochondrial ribosomal protein L32	79					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.A79T(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(6)	10						CTTTTGGATGGCAGCTCCCAA	0.428																																																	1	Substitution - Missense(1)	kidney(1)											101.0	92.0	95.0					7																	42974658		2203	4300	6503	SO:0001583	missense	64983			AB051343	CCDS5468.1	7p14	2012-09-13			ENSG00000106591	ENSG00000106591		"""Mitochondrial ribosomal proteins / large subunits"""	14035	protein-coding gene	gene with protein product		611839				11543634	Standard	NM_031903		Approved	HSPC283, L32mt, MRP-L32, bMRP-59b	uc003tia.3	Q9BYC8	OTTHUMG00000155180	ENST00000223324.2:c.235G>A	7.37:g.42974658G>A	ENSP00000223324:p.Ala79Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q96Q68|Q9P098	Missense_Mutation	SNP	ENST00000223324.2	37	CCDS5468.1	.	.	.	.	.	.	.	.	.	.	G	31	5.082823	0.94050	.	.	ENSG00000106591	ENST00000223324	.	.	.	5.35	4.48	0.54585	.	0.000000	0.85682	D	0.000000	D	0.86900	0.6044	H	0.96239	3.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90644	0.4577	9	0.87932	D	0	-16.2803	13.8769	0.63657	0.0731:0.0:0.9269:0.0	.	79	Q9BYC8	RM32_HUMAN	T	79	.	ENSP00000223324:A79T	A	+	1	0	MRPL32	42941183	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.855000	0.99526	1.259000	0.44117	0.650000	0.86243	GCA		0.428	MRPL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338669.1		NM_031903	
MS4A6E	245802	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	60102420	60102420	+	Missense_Mutation	SNP	G	G	C	rs200264244		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr11:60102420G>C	ENST00000300182.4	+	1	117	c.52G>C	c.(52-54)Gtc>Ctc	p.V18L		NM_139249.2	NP_640342.1	Q96DS6	M4A6E_HUMAN	membrane-spanning 4-domains, subfamily A, member 6E	18						integral component of membrane (GO:0016021)		p.V18L(1)		endometrium(2)|kidney(1)|lung(9)|stomach(1)	13						CCCATCAAATGTCATCAACTT	0.418																																																	1	Substitution - Missense(1)	kidney(1)											166.0	147.0	153.0					11																	60102420		2203	4300	6503	SO:0001583	missense	245802			AF354931	CCDS7984.1	11q12	2008-03-25				ENSG00000166926			14285	protein-coding gene	gene with protein product		608402				11486273	Standard	NM_139249		Approved		uc001npd.3	Q96DS6		ENST00000300182.4:c.52G>C	11.37:g.60102420G>C	ENSP00000300182:p.Val18Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q3MIL2|Q8NE56|Q96PG4|Q96PG5	Missense_Mutation	SNP	ENST00000300182.4	37	CCDS7984.1	.	.	.	.	.	.	.	.	.	.	G	9.993	1.231224	0.22626	.	.	ENSG00000166926	ENST00000300182	T	0.09723	2.95	2.4	2.4	0.29515	.	1.001370	0.08053	N	0.996871	T	0.08133	0.0203	N	0.22421	0.69	0.09310	N	1	B	0.22003	0.063	B	0.11329	0.006	T	0.28681	-1.0036	10	0.41790	T	0.15	.	8.2277	0.31579	0.0:0.0:1.0:0.0	.	18	Q96DS6	M4A6E_HUMAN	L	18	ENSP00000300182:V18L	ENSP00000300182:V18L	V	+	1	0	MS4A6E	59858996	0.032000	0.19561	0.008000	0.14137	0.199000	0.23934	2.213000	0.42844	1.317000	0.45149	0.305000	0.20034	GTC		0.418	MS4A6E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394296.1			
MTA2	9219	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	62362921	62362921	+	Missense_Mutation	SNP	C	C	T	rs139421444		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr11:62362921C>T	ENST00000278823.2	-	14	1687	c.1298G>A	c.(1297-1299)aGt>aAt	p.S433N	MTA2_ENST00000527204.1_Missense_Mutation_p.S260N|MTA2_ENST00000524902.1_Missense_Mutation_p.S260N	NM_004739.3	NP_004730.2	O94776	MTA2_HUMAN	metastasis associated 1 family, member 2	433					ATP-dependent chromatin remodeling (GO:0043044)|chromatin assembly or disassembly (GO:0006333)|DNA methylation (GO:0006306)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	histone deacetylase complex (GO:0000118)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|histone deacetylase activity (GO:0004407)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.S433N(1)		endometrium(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	26						AGGAGAGAGACTTTGAGCTTC	0.502																																																	1	Substitution - Missense(1)	kidney(1)						C	ASN/SER	0,4404		0,0,2202	163.0	147.0	152.0		1298	5.2	1.0	11	dbSNP_134	152	1,8597	1.2+/-3.3	0,1,4298	yes	missense	MTA2	NM_004739.3	46	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	benign	433/669	62362921	1,13001	2202	4299	6501	SO:0001583	missense	9219			AB016591	CCDS8022.1	11q12-q13.1	2013-01-25	2004-12-15	2003-12-17	ENSG00000149480	ENSG00000149480		"""GATA zinc finger domain containing"""	7411	protein-coding gene	gene with protein product		603947	"""metastasis associated gene family, member 2"""	MTA1L1		9929979	Standard	NM_004739		Approved	MTA1-L1	uc001ntq.2	O94776	OTTHUMG00000167684	ENST00000278823.2:c.1298G>A	11.37:g.62362921C>T	ENSP00000278823:p.Ser433Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q68DB1|Q9UQB5	Missense_Mutation	SNP	ENST00000278823.2	37	CCDS8022.1	.	.	.	.	.	.	.	.	.	.	C	8.355	0.831871	0.16820	0.0	1.16E-4	ENSG00000149480	ENST00000278823;ENST00000524902;ENST00000527204	T;T;T	0.44482	1.51;0.92;0.92	5.19	5.19	0.71726	.	0.235594	0.50627	D	0.000119	T	0.27419	0.0673	N	0.17082	0.46	0.50467	D	0.999876	B	0.25105	0.118	B	0.21151	0.033	T	0.07986	-1.0744	10	0.14656	T	0.56	-7.8749	16.1912	0.81989	0.0:1.0:0.0:0.0	.	433	O94776	MTA2_HUMAN	N	433;260;260	ENSP00000278823:S433N;ENSP00000431346:S260N;ENSP00000431797:S260N	ENSP00000278823:S433N	S	-	2	0	MTA2	62119497	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	3.065000	0.49994	2.419000	0.82065	0.655000	0.94253	AGT		0.502	MTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395578.1		NM_004739	
MYLK	4638	broad.mit.edu;hgsc.bcm.edu	37	3	123418999	123418999	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr3:123418999C>T	ENST00000475616.1	-	15	3315	c.3316G>A	c.(3316-3318)Gat>Aat	p.D1106N	MYLK_ENST00000360304.3_Missense_Mutation_p.D1106N|MYLK_ENST00000346322.5_Missense_Mutation_p.D1037N|MYLK_ENST00000359169.1_Missense_Mutation_p.D1106N|MYLK_ENST00000510775.1_5'Flank|MYLK_ENST00000360772.3_Missense_Mutation_p.D1106N			Q15746	MYLK_HUMAN	myosin light chain kinase	1106	Actin-binding (calcium/calmodulin- insensitive). {ECO:0000250}.|Ig-like C2-type 7.				actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)	p.D1106N(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		ACATGAACATCTTGCAGCTTC	0.547																																																	1	Substitution - Missense(1)	kidney(1)											111.0	109.0	110.0					3																	123418999		2203	4300	6503	SO:0001583	missense	4638			X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7590	protein-coding gene	gene with protein product	"""smooth muscle myosin light chain kinase"""	600922	"""myosin, light polypeptide kinase"""			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.3316G>A	3.37:g.123418999C>T	ENSP00000418335:p.Asp1106Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Missense_Mutation	SNP	ENST00000475616.1	37	CCDS46896.1	.	.	.	.	.	.	.	.	.	.	C	17.51	3.408573	0.62399	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616	T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94	5.76	5.76	0.90799	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.56863	0.2014	L	0.37507	1.11	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	0.97110	0.999;0.997;0.999;1.0;0.999;1.0	T	0.47328	-0.9126	9	0.30854	T	0.27	.	19.9663	0.97271	0.0:1.0:0.0:0.0	.	1106;184;1037;1106;1037;1106	Q15746-6;Q15746-7;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;.;MYLK_HUMAN	N	1106;1106;1106;1037;1106	ENSP00000354004:D1106N;ENSP00000353452:D1106N;ENSP00000352088:D1106N;ENSP00000320622:D1037N;ENSP00000418335:D1106N	ENSP00000320622:D1037N	D	-	1	0	MYLK	124901689	1.000000	0.71417	0.427000	0.26684	0.070000	0.16714	6.025000	0.70864	2.727000	0.93392	0.555000	0.69702	GAT		0.547	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1		NM_053025	
MUC20	200958	hgsc.bcm.edu	37	3	195452960	195452960	+	Missense_Mutation	SNP	G	G	A	rs4093817	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr3:195452960G>A	ENST00000447234.2	+	2	1612	c.1486G>A	c.(1486-1488)Gtt>Att	p.V496I	MUC20_ENST00000436408.1_Missense_Mutation_p.V496I|MUC20_ENST00000445522.2_Missense_Mutation_p.V461I|MUC20_ENST00000320736.6_Missense_Mutation_p.V325I	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	496	Involved in oligomerization.		Missing. {ECO:0000269|PubMed:14702039}.	V -> I (in Ref. 5; AAH29267). {ECO:0000305}.	activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		TGATGCCACGGTTGGGACCCC	0.597																																																	0													57.0	51.0	53.0					3																	195452960		2183	4280	6463	SO:0001583	missense	200958			AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1486G>A	3.37:g.195452960G>A	ENSP00000414350:p.Val496Ile	Somatic		WXS	Illumina HiSeq	Phase_I	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		.	.	.	.	.	.	.	.	.	.	G	9.647	1.140515	0.21205	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.15718	2.82;2.84;2.99;2.4	3.86	-0.128	0.13506	.	0.860472	0.09679	N	0.770091	T	0.10981	0.0268	L	0.32530	0.975	0.09310	N	1	B	0.23891	0.093	B	0.17433	0.018	T	0.36359	-0.9751	10	0.27785	T	0.31	0.7218	5.1463	0.14987	0.2242:0.4104:0.3653:0.0	rs4093817	325	E9PH32	.	I	496;325;496;461	ENSP00000414350:V496I;ENSP00000325431:V325I;ENSP00000396774:V496I;ENSP00000405629:V461I	ENSP00000325431:V325I	V	+	1	0	MUC20	196938631	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.098000	0.15189	-0.151000	0.11176	-0.351000	0.07748	GTT		0.597	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1		NM_152673	
NCL	4691	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	232322358	232322358	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr2:232322358C>G	ENST00000322723.4	-	9	1683	c.1443G>C	c.(1441-1443)tgG>tgC	p.W481C	SNORD20_ENST00000384550.1_RNA|SNORA75_ENST00000384158.1_RNA|SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	481					angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)	p.W481C(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		TCTTACCACTCCAAGTGCTAT	0.368																																																	1	Substitution - Missense(1)	kidney(1)											143.0	145.0	145.0					2																	232322358		2202	4299	6501	SO:0001583	missense	4691				CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"""RNA binding motif (RRM) containing"""	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.1443G>C	2.37:g.232322358C>G	ENSP00000318195:p.Trp481Cys	Somatic		WXS	Illumina HiSeq	Phase_I	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Missense_Mutation	SNP	ENST00000322723.4	37	CCDS33397.1	.	.	.	.	.	.	.	.	.	.	C	16.49	3.137925	0.56936	.	.	ENSG00000115053	ENST00000322723;ENST00000392033;ENST00000322732;ENST00000356936	D;T	0.83837	-1.77;-0.81	5.76	3.95	0.45737	Nucleotide-binding, alpha-beta plait (1);	0.319059	0.35615	N	0.003084	D	0.82958	0.5150	L	0.40543	1.245	0.50313	D	0.999865	D	0.56968	0.978	P	0.55749	0.783	T	0.82299	-0.0526	10	0.56958	D	0.05	-1.5288	10.6995	0.45918	0.0:0.8432:0.0:0.1568	.	481	P19338	NUCL_HUMAN	C	481;373;253;82	ENSP00000318195:W481C;ENSP00000349410:W82C	ENSP00000318195:W481C	W	-	3	0	NCL	232030602	0.998000	0.40836	1.000000	0.80357	0.982000	0.71751	0.632000	0.24583	0.777000	0.33496	0.558000	0.71614	TGG		0.368	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1		NM_005381	
NLRC5	84166	hgsc.bcm.edu;ucsc.edu	37	16	57065327	57065327	+	Missense_Mutation	SNP	T	T	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr16:57065327T>G	ENST00000262510.6	+	11	2654	c.2429T>G	c.(2428-2430)cTc>cGc	p.L810R	NLRC5_ENST00000539144.1_Missense_Mutation_p.L810R|NLRC5_ENST00000436936.1_Missense_Mutation_p.L810R|NLRC5_ENST00000308149.7_Missense_Mutation_p.L810R	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	810				ADL -> RTI (in Ref. 1; AAO59377 and 2; ABO40479). {ECO:0000305}.	defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				GAGGCGGACCTCATCTTCCTT	0.557																																																	0													138.0	114.0	122.0					16																	57065327		2198	4300	6498	SO:0001583	missense	84166			AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.2429T>G	16.37:g.57065327T>G	ENSP00000262510:p.Leu810Arg	Somatic		WXS	Illumina HiSeq	Phase_I	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	37	CCDS10773.1	.	.	.	.	.	.	.	.	.	.	T	16.90	3.249274	0.59103	.	.	ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000327982;ENST00000539144;ENST00000538110;ENST00000543030	T;T;T;T;T;T	0.74947	-0.7;-0.72;-0.89;-0.72;2.28;0.24	4.18	4.18	0.49190	.	.	.	.	.	T	0.76535	0.4001	L	0.29908	0.895	0.33480	D	0.587286	D;D;D;D	0.71674	0.998;0.998;0.998;0.995	D;D;D;D	0.70487	0.935;0.969;0.966;0.931	T	0.80703	-0.1264	9	0.56958	D	0.05	.	9.9174	0.41444	0.0:0.0:0.0:1.0	.	810;810;810;810	Q86WI3-5;Q86WI3-4;Q86WI3-6;Q86WI3	.;.;.;NLRC5_HUMAN	R	810;810;810;284;810;317;109	ENSP00000262510:L810R;ENSP00000308886:L810R;ENSP00000389739:L810R;ENSP00000441727:L810R;ENSP00000441597:L317R;ENSP00000440153:L109R	ENSP00000262510:L810R	L	+	2	0	NLRC5	55622828	0.173000	0.23056	0.997000	0.53966	0.787000	0.44495	3.042000	0.49815	2.127000	0.65507	0.459000	0.35465	CTC		0.557	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1		NM_032206	
NNMT	4837	broad.mit.edu;hgsc.bcm.edu	37	11	114183068	114183068	+	Missense_Mutation	SNP	G	G	C	rs201804258		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr11:114183068G>C	ENST00000535401.1	+	5	928	c.664G>C	c.(664-666)Gag>Cag	p.E222Q	NNMT_ENST00000542647.1_Missense_Mutation_p.E27Q|NNMT_ENST00000299964.3_Missense_Mutation_p.E222Q|NNMT_ENST00000545255.1_Missense_Mutation_p.E27Q|NNMT_ENST00000541754.1_Missense_Mutation_p.E27Q|RP11-64D24.2_ENST00000544925.1_RNA			P40261	NNMT_HUMAN	nicotinamide N-methyltransferase	222					methylation (GO:0032259)|organ regeneration (GO:0031100)|response to drug (GO:0042493)|response to organonitrogen compound (GO:0010243)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	nicotinamide N-methyltransferase activity (GO:0008112)	p.E222Q(1)		kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(61;4.83e-16)|all_epithelial(67;7.28e-09)|all_hematologic(158;0.000135)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;2.79e-06)|Epithelial(105;1.32e-05)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.128)	Niacin(DB00627)	GGAGGCAGTAGAGGCTGCTGT	0.542																																																	1	Substitution - Missense(1)	kidney(1)											62.0	66.0	65.0					11																	114183068		2201	4296	6497	SO:0001583	missense	4837			U08021	CCDS8368.1	11q23.1	2007-08-15					2.1.1.1		7861	protein-coding gene	gene with protein product		600008				8575745	Standard	NM_006169		Approved		uc001pos.1	P40261		ENST00000535401.1:c.664G>C	11.37:g.114183068G>C	ENSP00000441434:p.Glu222Gln	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000535401.1	37	CCDS8368.1	.	.	.	.	.	.	.	.	.	.	G	7.740	0.701011	0.15172	.	.	ENSG00000166741	ENST00000535401;ENST00000299964;ENST00000541754;ENST00000542647;ENST00000545255	T;T;T;T;T	0.10382	2.88;2.88;2.88;2.88;2.88	5.06	-0.323	0.12709	.	0.414156	0.23483	N	0.047689	T	0.06005	0.0156	L	0.33485	1.01	0.09310	N	1	P	0.39044	0.656	B	0.36922	0.236	T	0.38478	-0.9659	10	0.17832	T	0.49	-5.6098	4.6744	0.12705	0.3433:0.2998:0.3569:0.0	.	222	P40261	NNMT_HUMAN	Q	222;222;27;27;27	ENSP00000441434:E222Q;ENSP00000299964:E222Q;ENSP00000445680:E27Q;ENSP00000445994:E27Q;ENSP00000445248:E27Q	ENSP00000299964:E222Q	E	+	1	0	NNMT	113688278	0.027000	0.19231	0.001000	0.08648	0.079000	0.17450	0.262000	0.18460	-0.354000	0.08212	-0.136000	0.14681	GAG		0.542	NNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398951.1		NM_006169	
NRBF2	29982	hgsc.bcm.edu	37	10	64913306	64913306	+	Frame_Shift_Del	DEL	T	T	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr10:64913306delT	ENST00000277746.6	+	4	373	c.192delT	c.(190-192)catfs	p.H64fs	NRBF2_ENST00000435510.2_Frame_Shift_Del_p.H54fs	NM_030759.3	NP_110386.2	Q96F24	NRBF2_HUMAN	nuclear receptor binding factor 2	64					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)				large_intestine(2)|lung(3)|skin(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)					GGGATAGCCATATGAAACAGC	0.413																																																	0													43.0	46.0	45.0					10																	64913306		2203	4300	6503	SO:0001589	frameshift_variant	29982			D82519	CCDS7268.1, CCDS60537.1	10q22.1	2012-11-01			ENSG00000148572	ENSG00000148572			19692	protein-coding gene	gene with protein product	"""comodulator of PPAR and RXR 1"", ""comodulator of PPAR and RXR 2"""					10786636	Standard	NM_001282405		Approved	DKFZp564C1664, FLJ30395, COPR1, COPR2	uc001jmj.4	Q96F24	OTTHUMG00000018309	ENST00000277746.6:c.192delT	10.37:g.64913306delT	ENSP00000277746:p.His64fs	Somatic		WXS	Illumina HiSeq	Phase_I	A6PW36|B4DWS0|Q86UR2|Q96NP6|Q9H0S9|Q9H2I2	Frame_Shift_Del	DEL	ENST00000277746.6	37	CCDS7268.1																																																																																				0.413	NRBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048247.1		NM_030759	
NSD1	64324	broad.mit.edu;ucsc.edu	37	5	176636690	176636690	+	Silent	SNP	G	G	A	rs535674820		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr5:176636690G>A	ENST00000439151.2	+	5	1335	c.1290G>A	c.(1288-1290)caG>caA	p.Q430Q	NSD1_ENST00000354179.4_Silent_p.Q161Q|NSD1_ENST00000361032.4_Silent_p.Q327Q|NSD1_ENST00000347982.4_Silent_p.Q161Q	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	430					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.Q430Q(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		TTGCAGAACAGTATGATGTTC	0.373			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)			G|||	1	0.000199681	0.0008	0.0	5008	,	,		16581	0.0		0.0	False		,,,				2504	0.0							Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	2	Substitution - coding silent(2)	kidney(2)											76.0	73.0	74.0					5																	176636690		2203	4300	6503	SO:0001819	synonymous_variant	64324	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.1290G>A	5.37:g.176636690G>A		Somatic		WXS	Illumina GAIIx	Phase_I	Q96PD8|Q96RN7	Silent	SNP	ENST00000439151.2	37	CCDS4412.1																																																																																				0.373	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2		NM_172349	
NT5DC3	51559	broad.mit.edu;hgsc.bcm.edu	37	12	104208888	104208888	+	Missense_Mutation	SNP	A	A	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr12:104208888A>C	ENST00000392876.3	-	2	260	c.220T>G	c.(220-222)Tcc>Gcc	p.S74A		NM_001031701.2	NP_001026871.1	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	74						cytosol (GO:0005829)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.S74A(1)		NS(1)|breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|ovary(2)|skin(1)|stomach(2)	30						CTCATAATGGAAGGAACCAAT	0.303																																																	1	Substitution - Missense(1)	kidney(1)											56.0	52.0	53.0					12																	104208888		2203	4300	6503	SO:0001583	missense	51559			AB032786	CCDS41824.1	12q22-q23.1	2006-02-03			ENSG00000111696	ENSG00000111696			30826	protein-coding gene	gene with protein product		611076					Standard	NM_001031701		Approved	TU12B1-TY, FLJ11266	uc010swe.1	Q86UY8	OTTHUMG00000157017	ENST00000392876.3:c.220T>G	12.37:g.104208888A>C	ENSP00000376615:p.Ser74Ala	Somatic		WXS	Illumina HiSeq	Phase_I	Q9NUM7|Q9P2T2|Q9P2T3	Missense_Mutation	SNP	ENST00000392876.3	37	CCDS41824.1	.	.	.	.	.	.	.	.	.	.	A	13.36	2.215365	0.39102	.	.	ENSG00000111696	ENST00000392876	T	0.21932	1.98	5.87	5.87	0.94306	.	0.339432	0.27851	U	0.017584	T	0.16896	0.0406	L	0.29908	0.895	0.40947	D	0.984517	B	0.06786	0.001	B	0.06405	0.002	T	0.09574	-1.0668	10	0.13853	T	0.58	-12.7682	16.5764	0.84681	1.0:0.0:0.0:0.0	.	74	Q86UY8	NT5D3_HUMAN	A	74	ENSP00000376615:S74A	ENSP00000376615:S74A	S	-	1	0	NT5DC3	102733018	1.000000	0.71417	0.570000	0.28473	0.992000	0.81027	3.578000	0.53892	2.371000	0.80710	0.533000	0.62120	TCC		0.303	NT5DC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347118.2		NM_016575	
OR1I1	126370	hgsc.bcm.edu;ucsc.edu	37	19	15198241	15198241	+	Missense_Mutation	SNP	G	G	A	rs75278395	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr19:15198241G>A	ENST00000209540.2	+	1	451	c.365G>A	c.(364-366)cGc>cAc	p.R122H		NM_001004713.1	NP_001004713.1	O60431	OR1I1_HUMAN	olfactory receptor, family 1, subfamily I, member 1	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(3)|ovary(2)|stomach(2)	20						GCCATCGACCGCTTCGTGGCC	0.577													G|||	117	0.0233626	0.0825	0.0115	5008	,	,		21078	0.0		0.0	False		,,,				2504	0.0																0								G	HIS/ARG	269,4137	152.2+/-185.9	8,253,1942	87.0	72.0	77.0		365	-1.0	0.0	19	dbSNP_131	77	2,8598	2.2+/-6.3	0,2,4298	yes	missense	OR1I1	NM_001004713.1	29	8,255,6240	AA,AG,GG		0.0233,6.1053,2.0837	probably-damaging	122/356	15198241	271,12735	2203	4300	6503	SO:0001583	missense	126370			AC004794	CCDS32937.1	19p13.1	2012-08-09				ENSG00000094661		"""GPCR / Class A : Olfactory receptors"""	8207	protein-coding gene	gene with protein product							Standard	NM_001004713		Approved	OR1I1P, OR19-20, OR1I1Q	uc010xoe.2	O60431		ENST00000209540.2:c.365G>A	19.37:g.15198241G>A	ENSP00000209540:p.Arg122His	Somatic		WXS	Illumina HiSeq	Phase_I	Q96R92	Missense_Mutation	SNP	ENST00000209540.2	37	CCDS32937.1	51	0.023351648351648352	49	0.09959349593495935	2	0.0055248618784530384	0	0.0	0	0.0	g	12.43	1.935489	0.34189	0.061053	2.33E-4	ENSG00000094661	ENST00000209540	T	0.77489	-1.1	4.9	-1.05	0.10036	GPCR, rhodopsin-like superfamily (1);	0.000000	0.30093	U	0.010421	T	0.17450	0.0419	M	0.88704	2.975	0.25671	N	0.985897	D	0.89917	1.0	D	0.97110	1.0	T	0.56553	-0.7960	10	0.72032	D	0.01	.	5.1436	0.14973	0.3089:0.0:0.5577:0.1334	.	122	O60431	OR1I1_HUMAN	H	122	ENSP00000209540:R122H	ENSP00000209540:R122H	R	+	2	0	OR1I1	15059241	0.914000	0.31030	0.007000	0.13788	0.001000	0.01503	3.160000	0.50739	-0.192000	0.10432	-1.069000	0.02264	CGC		0.577	OR1I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465665.1			
OR51T1	401665	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	4903717	4903717	+	Silent	SNP	C	C	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr11:4903717C>T	ENST00000322049.1	+	1	588	c.588C>T	c.(586-588)atC>atT	p.I196I	OR51T1_ENST00000380378.1_Silent_p.I223I|MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron			Q8NGJ9	O51T1_HUMAN	olfactory receptor, family 51, subfamily T, member 1	196						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I223I(1)|p.I196I(1)		NS(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		AACCTTGGATCAGCAGTTTTT	0.443																																																	2	Substitution - coding silent(2)	kidney(2)											154.0	144.0	147.0					11																	4903717		2201	4298	6499	SO:0001819	synonymous_variant	401665			BK004283	CCDS31363.1	11p15.4	2012-08-09			ENSG00000176900	ENSG00000176900		"""GPCR / Class A : Olfactory receptors"""	15205	protein-coding gene	gene with protein product							Standard	NM_001004759		Approved		uc010qyp.2	Q8NGJ9	OTTHUMG00000066507	ENST00000322049.1:c.588C>T	11.37:g.4903717C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q6IFH9	Silent	SNP	ENST00000322049.1	37																																																																																					0.443	OR51T1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000142180.1		NM_001004759	
OR7A10	390892	hgsc.bcm.edu	37	19	14952560	14952560	+	Missense_Mutation	SNP	G	G	T	rs12985894	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr19:14952560G>T	ENST00000248058.1	-	1	129	c.130C>A	c.(130-132)Ctc>Atc	p.L44I		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	44						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|stomach(1)	19	Ovarian(108;0.203)					AGGATGATGAGCAGGTTCCCG	0.512													.|||	618	0.123403	0.143	0.1196	5008	,	,		18213	0.0903		0.1541	False		,,,				2504	0.1022																0								G	ILE/LEU	675,3731	285.7+/-278.4	58,559,1586	70.0	66.0	67.0		130	2.8	1.0	19	dbSNP_121	67	1455,7139	277.4+/-292.8	140,1175,2982	no	missense	OR7A10	NM_001005190.1	5	198,1734,4568	TT,TG,GG		16.9304,15.32,16.3846	possibly-damaging	44/310	14952560	2130,10870	2203	4297	6500	SO:0001583	missense	390892				CCDS32936.1	19p13.1	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8356	protein-coding gene	gene with protein product							Standard	NM_001005190		Approved		uc002mzx.1	O76100		ENST00000248058.1:c.130C>A	19.37:g.14952560G>T	ENSP00000248058:p.Leu44Ile	Somatic		WXS	Illumina HiSeq	Phase_I	Q6IFP0|Q96R97	Missense_Mutation	SNP	ENST00000248058.1	37	CCDS32936.1	260	0.11904761904761904	69	0.1402439024390244	48	0.13259668508287292	27	0.0472027972027972	116	0.15303430079155672	g	9.293	1.051138	0.19827	0.1532	0.169304	ENSG00000127515	ENST00000248058	T	0.02606	4.23	2.79	2.79	0.32731	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34133	U	0.004236	T	0.00039	0.0001	L	0.60904	1.88	0.48452	P	3.4199999999995345E-4	P	0.46327	0.876	P	0.54238	0.746	T	0.25293	-1.0136	9	0.72032	D	0.01	.	7.1625	0.25672	0.0:0.0:0.7333:0.2667	rs12985894	44	O76100	OR7AA_HUMAN	I	44	ENSP00000248058:L44I	ENSP00000248058:L44I	L	-	1	0	OR7A10	14813560	0.000000	0.05858	1.000000	0.80357	0.286000	0.27126	-0.617000	0.05584	1.572000	0.49736	0.430000	0.28490	CTC		0.512	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1		NM_001005190	
OSBPL3	26031	hgsc.bcm.edu;ucsc.edu	37	7	24839885	24839885	+	Frame_Shift_Del	DEL	C	C	-			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr7:24839885delC	ENST00000313367.2	-	23	3032	c.2581delG	c.(2581-2583)gacfs	p.D861fs	OSBPL3_ENST00000431825.2_Frame_Shift_Del_p.D794fs|OSBPL3_ENST00000487020.1_5'UTR|OSBPL3_ENST00000396429.1_Frame_Shift_Del_p.D825fs|OSBPL3_ENST00000353930.1_Frame_Shift_Del_p.D825fs|OSBPL3_ENST00000396431.1_Frame_Shift_Del_p.D830fs|OSBPL3_ENST00000409069.1_Frame_Shift_Del_p.D794fs|OSBPL3_ENST00000352860.1_Frame_Shift_Del_p.D830fs	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	861					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						ACCCAAGAGTCATCGTCGGAT	0.423																																																	0													79.0	75.0	76.0					7																	24839885		2203	4300	6503	SO:0001589	frameshift_variant	26031			AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.2581delG	7.37:g.24839885delC	ENSP00000315410:p.Asp861fs	Somatic		WXS	Illumina HiSeq	Phase_I	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Frame_Shift_Del	DEL	ENST00000313367.2	37	CCDS5390.1																																																																																				0.423	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2			
P2RY12	64805	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	151056476	151056476	+	Missense_Mutation	SNP	A	A	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr3:151056476A>G	ENST00000302632.3	-	3	457	c.158T>C	c.(157-159)aTc>aCc	p.I53T	MED12L_ENST00000491549.1_Intron|MED12L_ENST00000474524.1_Intron|MED12L_ENST00000273432.4_Intron	NM_022788.4|NM_176876.2	NP_073625.1|NP_795345.1	Q9H244	P2Y12_HUMAN	purinergic receptor P2Y, G-protein coupled, 12	53					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell projection organization (GO:0030030)|G-protein coupled purinergic nucleotide receptor signaling pathway (GO:0035589)|G-protein coupled receptor signaling pathway (GO:0007186)|hemostasis (GO:0007599)|negative regulation of cell differentiation (GO:0045596)|negative regulation of norepinephrine secretion (GO:0010700)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of GTPase activity (GO:0043547)|positive regulation of ion transport (GO:0043270)|potassium ion transmembrane transport (GO:0071805)|protein kinase B signaling (GO:0043491)|regulation of calcium ion transport (GO:0051924)	basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	ADP receptor activity (GO:0001621)|G-protein coupled adenosine receptor activity (GO:0001609)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.I53T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	17			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)		Clopidogrel(DB00758)|Epoprostenol(DB01240)|Prasugrel(DB06209)|Ticagrelor(DB08816)|Ticlopidine(DB00208)|Treprostinil(DB00374)	TTTACTCCGGATTTGAAAGAA	0.373																																																	1	Substitution - Missense(1)	kidney(1)											55.0	58.0	57.0					3																	151056476		2203	4300	6503	SO:0001583	missense	64805			AJ320495	CCDS3159.1	3q24-q25	2014-09-17			ENSG00000169313	ENSG00000169313		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	18124	protein-coding gene	gene with protein product		600515				11502873, 11104774	Standard	NM_022788		Approved	P2Y12, SP1999, HORK3	uc003eyw.1	Q9H244	OTTHUMG00000159863	ENST00000302632.3:c.158T>C	3.37:g.151056476A>G	ENSP00000307259:p.Ile53Thr	Somatic		WXS	Illumina HiSeq	Phase_I	D3DNJ5|Q546J7	Missense_Mutation	SNP	ENST00000302632.3	37	CCDS3159.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.941184	0.73557	.	.	ENSG00000169313	ENST00000302632;ENST00000455408	T	0.29655	1.56	5.17	5.17	0.71159	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.49389	0.1554	L	0.58354	1.805	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	T	0.37865	-0.9687	10	0.16896	T	0.51	-39.2572	15.3304	0.74203	1.0:0.0:0.0:0.0	.	53;53	A8K7T1;Q9H244	.;P2Y12_HUMAN	T	53	ENSP00000307259:I53T	ENSP00000307259:I53T	I	-	2	0	P2RY12	152539166	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.456000	0.90359	2.080000	0.62538	0.528000	0.53228	ATC		0.373	P2RY12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357796.1			
PHC2	1912	hgsc.bcm.edu	37	1	33820749	33820769	+	In_Frame_Del	DEL	GGCTGCTGCTGTTGTGGCTGT	GGCTGCTGCTGTTGTGGCTGT	-	rs138345405|rs142456432	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	GGCTGCTGCTGTTGTGGCTGT	GGCTGCTGCTGTTGTGGCTGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr1:33820749_33820769delGGCTGCTGCTGTTGTGGCTGT	ENST00000257118.5	-	7	1115_1135	c.1062_1082delACAGCCACAACAGCAGCAGCC	c.(1060-1083)ccacagccacaacagcagcagccg>ccg	p.354_361PQPQQQQP>P	PHC2_ENST00000431992.1_In_Frame_Del_p.325_332PQPQQQQP>P|RP11-415J8.5_ENST00000432703.1_RNA|PHC2_ENST00000419414.2_In_Frame_Del_p.354_361PQPQQQQP>P|PHC2_ENST00000373422.3_5'UTR|PHC2_ENST00000373416.1_5'UTR	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	354	Gln-rich.				multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				ctggggcggcggctgctgctgttgtggctgtggctgctgct	0.643																																																	0										14,4232		7,0,2116						-0.5	0.0		dbSNP_134	22	60,8166		25,10,4078	no	coding	PHC2	NM_198040.2		32,10,6194	A1A1,A1R,RR		0.7294,0.3297,0.5933				74,12398				SO:0001651	inframe_deletion	1912			AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"""Sterile alpha motif (SAM) domain containing"""	3183	protein-coding gene	gene with protein product		602979	"""early development regulator 2 (homolog of polyhomeotic 2)"", ""polyhomeotic-like 2 (Drosophila)"""	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.1062_1082delACAGCCACAACAGCAGCAGCC	1.37:g.33820749_33820769delGGCTGCTGCTGTTGTGGCTGT	ENSP00000257118:p.Pro354_Gln360del	Somatic		WXS	Illumina HiSeq	Phase_I	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	In_Frame_Del	DEL	ENST00000257118.5	37	CCDS378.1																																																																																				0.643	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1		NM_198040	
PI4KA	5297	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	21192985	21192985	+	Missense_Mutation	SNP	A	A	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr22:21192985A>C	ENST00000572273.1	-	2	247	c.17T>G	c.(16-18)tTc>tGc	p.F6C	PI4KA_ENST00000255882.6_Missense_Mutation_p.F64C			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	6					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.F6C(2)		breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			GATCCCATGGAAATCCACTGG	0.393																																					GBM(136;1332 1831 3115 23601 50806)												2	Substitution - Missense(2)	kidney(2)											103.0	103.0	103.0					22																	21192985		2203	4300	6503	SO:0001583	missense	5297			L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.17T>G	22.37:g.21192985A>C	ENSP00000458238:p.Phe6Cys	Somatic		WXS	Illumina HiSeq	Phase_I	Q7Z625|Q9UPG2	Missense_Mutation	SNP	ENST00000572273.1	37		.	.	.	.	.	.	.	.	.	.	A	13.17	2.155909	0.38021	.	.	ENSG00000241973	ENST00000255882;ENST00000449120	T	0.50277	0.75	5.4	5.4	0.78164	.	0.366843	0.31809	N	0.007037	T	0.45498	0.1345	L	0.29908	0.895	0.80722	D	1	B;P	0.36027	0.419;0.533	P;B	0.47102	0.537;0.235	T	0.41963	-0.9479	10	0.39692	T	0.17	-33.0893	10.4815	0.44695	0.8551:0.0:0.0:0.1449	.	64;6	D3DX33;P42356	.;PI4KA_HUMAN	C	6	ENSP00000402437:F6C	ENSP00000255882:F6C	F	-	2	0	PI4KA	19522985	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.457000	0.53007	2.270000	0.75569	0.459000	0.35465	TTC		0.393	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding			NM_058004	
PIF1	80119	hgsc.bcm.edu	37	15	65114484	65114484	+	Silent	SNP	G	G	A	rs8031690	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr15:65114484G>A	ENST00000268043.4	-	4	892	c.798C>T	c.(796-798)acC>acT	p.T266T	PIF1_ENST00000333425.6_Silent_p.T266T|PIF1_ENST00000559239.1_Silent_p.T266T					PIF1 5'-to-3' DNA helicase											kidney(1)|lung(1)	2						CATGGAGGGTGGTGCCCCCGA	0.602													G|||	661	0.131989	0.3563	0.0231	5008	,	,		15702	0.0		0.004	False		,,,				2504	0.1738																0								G		1287,3117	421.1+/-339.2	201,885,1116	55.0	60.0	58.0		798	3.1	1.0	15	dbSNP_116	58	35,8563	22.8+/-68.1	0,35,4264	yes	coding-synonymous	PIF1	NM_025049.2		201,920,5380	AA,AG,GG		0.4071,29.2234,10.1677		266/642	65114484	1322,11680	2202	4299	6501	SO:0001819	synonymous_variant	80119			AK026345	CCDS10195.2, CCDS66797.1	15q22.1	2013-05-13	2013-05-13	2006-11-24	ENSG00000140451	ENSG00000140451	3.6.4.12		26220	protein-coding gene	gene with protein product		610953	"""chromosome 15 open reading frame 20"", ""PIF1 5'-to-3' DNA helicase homolog (S. cerevisiae)"""	C15orf20		10926538, 16522649	Standard	NM_025049		Approved	FLJ22692	uc002ant.2	Q9H611	OTTHUMG00000132974	ENST00000268043.4:c.798C>T	15.37:g.65114484G>A		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000268043.4	37	CCDS10195.2																																																																																				0.602	PIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256533.1		NM_025049	
PLCD3	113026	hgsc.bcm.edu	37	17	43192549	43192550	+	Splice_Site	INS	-	-	C	rs35911033		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr17:43192549_43192550insC	ENST00000322765.5	-	10	1735_1736	c.1622_1623insG	c.(1621-1623)cga>cgGa	p.R541fs	PLCD3_ENST00000540511.1_5'UTR	NM_133373.3	NP_588614.1	Q8N3E9	PLCD3_HUMAN	phospholipase C, delta 3	541	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(2)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	17						GGGTGCAGGGTCGCAGGCGGGT	0.683													CC|C|CC|deletion	5007	0.9998	0.9992	1.0	5008	,	,		12665	1.0		1.0	False		,,,				2504	1.0																0										3966,10		1980,6,2						4.0	1.0		dbSNP_130	26	8012,10		4001,10,0	no	frameshift	PLCD3	NM_133373.3		5981,16,2	A1A1,A1R,RR		0.1247,0.2515,0.1667				11978,20				SO:0001630	splice_region_variant	113026			AC002117	CCDS74077.1	17q21	2012-04-20			ENSG00000161714	ENSG00000161714	3.1.4.11		9061	protein-coding gene	gene with protein product		608795				10702670, 9056492	Standard	NM_133373		Approved		uc002iib.3	Q8N3E9	OTTHUMG00000168029	ENST00000322765.5:c.1623+1->G	17.37:g.43192550_43192550dupC		Somatic		WXS	Illumina HiSeq	Phase_I	Q8TEC1|Q8TF37|Q96FL6	Frame_Shift_Ins	INS	ENST00000322765.5	37																																																																																					0.683	PLCD3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			NM_133373	Frame_Shift_Ins
PLD5	200150	broad.mit.edu;hgsc.bcm.edu	37	1	242253369	242253369	+	Silent	SNP	G	G	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr1:242253369G>A	ENST00000536534.2	-	10	1639	c.1398C>T	c.(1396-1398)ggC>ggT	p.G466G	PLD5_ENST00000442594.2_Silent_p.G374G|PLD5_ENST00000427495.1_Silent_p.G404G			Q8N7P1	PLD5_HUMAN	phospholipase D family, member 5	466						integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)	p.G466G(1)|p.G374G(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(22)|ovary(6)|skin(3)|urinary_tract(1)	55	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			CAAGGCCCGTGCCAGCATTCT	0.423																																																	2	Substitution - coding silent(2)	kidney(2)											137.0	130.0	132.0					1																	242253369		2203	4300	6503	SO:0001819	synonymous_variant	200150			AK098092	CCDS1621.1, CCDS1621.2, CCDS55692.1	1q43	2008-02-05			ENSG00000180287	ENSG00000180287			26879	protein-coding gene	gene with protein product							Standard	NM_001195811		Approved	FLJ40773	uc001hzn.2	Q8N7P1	OTTHUMG00000039867	ENST00000536534.2:c.1398C>T	1.37:g.242253369G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A1KXV0|B7Z324|Q494U9|Q8NB22	Silent	SNP	ENST00000536534.2	37	CCDS1621.2																																																																																				0.423	PLD5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397213.2		NM_152666	
PRB2	653247	hgsc.bcm.edu	37	12	11546808	11546808	+	Silent	SNP	A	A	G	rs1921331		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr12:11546808A>G	ENST00000389362.4	-	3	239	c.204T>C	c.(202-204)ccT>ccC	p.P68P	PRB2_ENST00000545829.1_5'Flank|PRB1_ENST00000546254.1_Intron	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	68	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].			P -> S (in Ref. 2; BX484538). {ECO:0000305}.		extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			GGGGACCTTGAGGCTGGTTGC	0.602																																																	0													126.0	142.0	136.0					12																	11546808		2163	4250	6413	SO:0001819	synonymous_variant	653247			K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335			9338	protein-coding gene	gene with protein product		168810				8554050	Standard	NM_006248		Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.204T>C	12.37:g.11546808A>G		Somatic		WXS	Illumina HiSeq	Phase_I	O00599|P02811|P04281	Silent	SNP	ENST00000389362.4	37	CCDS41757.2																																																																																				0.602	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2		NM_006248	
PRDM14	63978	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	70978469	70978469	+	Splice_Site	SNP	C	C	A	rs199708096		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr8:70978469C>A	ENST00000276594.2	-	5	1385		c.e5+1			NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14						cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)	p.?(1)		NS(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			TGTGCACTCACCTTCAGAGGG	0.552																																					NSCLC(129;99 1813 5906 40656 46114)												1	Unknown(1)	kidney(1)											58.0	62.0	61.0					8																	70978469		2203	4300	6503	SO:0001630	splice_region_variant	63978			AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"""Zinc fingers, C2H2-type"""	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.1183+1G>T	8.37:g.70978469C>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q86UX9	Splice_Site	SNP	ENST00000276594.2	37	CCDS6206.1	.	.	.	.	.	.	.	.	.	.	C	12.94	2.088788	0.36855	.	.	ENSG00000147596	ENST00000276594	.	.	.	5.16	4.22	0.49857	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4453	0.75225	0.0:0.8609:0.1391:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PRDM14	71141023	1.000000	0.71417	1.000000	0.80357	0.266000	0.26442	5.035000	0.64158	2.560000	0.86352	0.561000	0.74099	.		0.552	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1			Intron
PRKAR2B	5577	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	106799894	106799894	+	Splice_Site	SNP	C	C	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr7:106799894C>G	ENST00000265717.4	+	11	1383	c.1124C>G	c.(1123-1125)gCa>gGa	p.A375G		NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	375					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)	p.A375G(1)		breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						CTTTTCTCAGCAATGGATGTG	0.353																																																	1	Substitution - Missense(1)	kidney(1)											71.0	67.0	68.0					7																	106799894		2203	4300	6503	SO:0001630	splice_region_variant	5577				CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.1124-1C>G	7.37:g.106799894C>G		Somatic		WXS	Illumina HiSeq	Phase_I	A4D0R9	Missense_Mutation	SNP	ENST00000265717.4	37	CCDS5740.1	.	.	.	.	.	.	.	.	.	.	C	14.10	2.435852	0.43224	.	.	ENSG00000005249	ENST00000265717;ENST00000543645;ENST00000539794	D	0.93189	-3.18	5.86	5.86	0.93980	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.104471	0.64402	D	0.000005	D	0.85927	0.5811	N	0.25031	0.7	0.47009	D	0.999287	B	0.06786	0.001	B	0.10450	0.005	T	0.78497	-0.2181	9	.	.	.	.	7.6919	0.28573	0.0:0.8088:0.0:0.1912	.	375	P31323	KAP3_HUMAN	G	375;375;362	ENSP00000265717:A375G	.	A	+	2	0	PRKAR2B	106587130	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	4.051000	0.57412	2.781000	0.95711	0.650000	0.86243	GCA		0.353	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1			Missense_Mutation
PRPF3	9129	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	150312943	150312943	+	Silent	SNP	C	C	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr1:150312943C>T	ENST00000324862.6	+	9	1437	c.1272C>T	c.(1270-1272)ctC>ctT	p.L424L	PRPF3_ENST00000414970.2_Silent_p.L375L|PRPF3_ENST00000543398.1_3'UTR|PRPF3_ENST00000467329.1_3'UTR	NM_004698.2	NP_004689.1	O43395	PRPF3_HUMAN	pre-mRNA processing factor 3	424					mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 x U5 tri-snRNP complex (GO:0046540)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.L424L(1)		breast(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Lung NSC(24;5.57e-29)|Breast(34;0.000844)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)	Colorectal(1306;0.0149)		CAGCCCAGCTCAATCCTCCAG	0.373																																					Ovarian(168;1070 2670 5178 20729)												1	Substitution - coding silent(1)	kidney(1)											77.0	71.0	73.0					1																	150312943		2203	4300	6503	SO:0001819	synonymous_variant	9129			AF001947	CCDS951.1	1q21.1	2013-07-16	2013-06-10		ENSG00000117360	ENSG00000117360			17348	protein-coding gene	gene with protein product		607301	"""retinitis pigmentosa 18 (autosomal dominant)"", ""PRP3 pre-mRNA processing factor 3 homolog (yeast)"", ""PRP3 pre-mRNA processing factor 3 homolog (S. cerevisiae)"""	RP18			Standard	NM_004698		Approved	Prp3, hPrp3, SNRNP90	uc001eum.4	O43395	OTTHUMG00000012807	ENST00000324862.6:c.1272C>T	1.37:g.150312943C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B4DSY9|O43446|Q5VT54	Silent	SNP	ENST00000324862.6	37	CCDS951.1																																																																																				0.373	PRPF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035836.1		NM_004698	
PSMC4	5704	hgsc.bcm.edu	37	19	40480501	40480501	+	Silent	SNP	C	C	T	rs11542840	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr19:40480501C>T	ENST00000157812.2	+	5	738	c.540C>T	c.(538-540)gcC>gcT	p.A180A	PSMC4_ENST00000455878.2_Silent_p.A149A	NM_006503.3|NM_153001.2	NP_006494.1|NP_694546.1	P43686	PRS6B_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 4	180					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|blastocyst development (GO:0001824)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|inclusion body (GO:0016234)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					TGCGGGAGGCCGTGGAGCTCC	0.637													C|||	489	0.0976438	0.1316	0.0389	5008	,	,		18530	0.1587		0.0239	False		,,,				2504	0.1063				Colon(105;1478 1543 4034 6132 38638)												0								C	,	556,3850	247.2+/-255.5	43,470,1690	61.0	65.0	64.0		540,447	-10.6	0.1	19	dbSNP_120	64	247,8353	97.7+/-159.3	5,237,4058	no	coding-synonymous,coding-synonymous	PSMC4	NM_006503.2,NM_153001.1	,	48,707,5748	TT,TC,CC		2.8721,12.6192,6.1741	,	180/419,149/388	40480501	803,12203	2203	4300	6503	SO:0001819	synonymous_variant	5704			U27515	CCDS12547.1, CCDS46076.1	19q13.11-q13.13	2010-04-21			ENSG00000013275	ENSG00000013275		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9551	protein-coding gene	gene with protein product	"""protease 26S subunit 6"", ""Tat-binding protein 7"", ""MB67 interacting protein"""	602707		MIP224		9473509, 8603043	Standard	NM_006503		Approved	TBP7, S6, MGC8570, MGC13687, MGC23214, TBP-7	uc002omq.4	P43686		ENST00000157812.2:c.540C>T	19.37:g.40480501C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q96FV5|Q9UBM3|Q9UEX3	Silent	SNP	ENST00000157812.2	37	CCDS12547.1																																																																																				0.637	PSMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462485.1		NM_006503	
RAP1GDS1	5910	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	99355174	99355175	+	Missense_Mutation	DNP	GC	GC	AG			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr4:99355174_99355175GC>AG	ENST00000408927.3	+	13	1641_1642	c.1528_1529GC>AG	c.(1528-1530)GCt>AGt	p.A510S	RAP1GDS1_ENST00000339360.5_Missense_Mutation_p.A511S|RAP1GDS1_ENST00000453712.2_Missense_Mutation_p.A510S|RAP1GDS1_ENST00000408900.3_Missense_Mutation_p.A461S|RAP1GDS1_ENST00000264572.7_Missense_Mutation_p.A419S|RAP1GDS1_ENST00000380158.4_Missense_Mutation_p.A462S	NM_001100426.1|NM_001100427.1|NM_021159.4	NP_001093896.1|NP_001093897.1|NP_066982.3	P52306	GDS1_HUMAN	RAP1, GTP-GDP dissociation stimulator 1	510					myosin filament assembly (GO:0031034)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of Rho GTPase activity (GO:0032321)|vascular smooth muscle contraction (GO:0014829)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)	p.A510G(1)|p.A510T(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)	28				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)		GCAGAATGAAGCTCTTGTTGCT	0.351			T	NUP98	T-ALL																																			Dom	yes		4	4q21-q25	5910	"""RAP1, GTP-GDP dissociation stimulator 1"""		L	2	Substitution - Missense(2)	kidney(2)																																								SO:0001583	missense	5910				CCDS43253.1, CCDS43254.1, CCDS47105.1, CCDS47106.1, CCDS47107.1, CCDS47108.1	4q23-q25	2013-02-14			ENSG00000138698	ENSG00000138698		"""Armadillo repeat containing"""	9859	protein-coding gene	gene with protein product		179502				8262526, 17951244	Standard	NM_001100426		Approved	SmgGDS	uc003htw.4	P52306	OTTHUMG00000160987	Exception_encountered	4.37:g.99355174_99355175delinsAG	ENSP00000386153:p.Ala510Ser	Somatic		WXS	Illumina HiSeq	Phase_I	E9PH06|G5E9P9|Q499L7|Q4KMV2|Q4QQI8|Q9BUW9|Q9BUX6|Q9NYM2|Q9NZA8	Missense_Mutation	SNP	ENST00000408927.3	37	CCDS43253.1																																																																																				0.351	RAP1GDS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363273.2		NM_001100426	
RBMX	27316	hgsc.bcm.edu	37	X	135957716	135957716	+	Silent	SNP	A	A	G	rs142284545		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chrX:135957716A>G	ENST00000320676.7	-	6	724	c.570T>C	c.(568-570)taT>taC	p.Y190Y	RBMX_ENST00000570135.1_Silent_p.Y55Y|RBMX_ENST00000496459.2_5'Flank|RBMX_ENST00000565438.1_Silent_p.Y62Y|RBMX_ENST00000431446.3_Missense_Mutation_p.M82T|RBMX_ENST00000562646.1_Silent_p.Y190Y	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	190	Necessary for the association to nascent RNAPII transcripts and nuclear localization.				cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					GTGGACCTCCATAACTATCTC	0.393																																																	0													67.0	65.0	66.0					X																	135957716		2203	4300	6503	SO:0001819	synonymous_variant	27316				CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"""RNA binding motif (RRM) containing"""	9910	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G"""	300199	"""RNA binding motif protein, X chromosome"""			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.570T>C	X.37:g.135957716A>G		Somatic		WXS	Illumina HiSeq	Phase_I	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Missense_Mutation	SNP	ENST00000320676.7	37	CCDS14661.1	.	.	.	.	.	.	.	.	.	.	.	0.268	-0.994819	0.02145	.	.	ENSG00000147274	ENST00000431446	T	0.05649	3.41	5.6	-2.88	0.05682	.	.	.	.	.	T	0.04272	0.0118	.	.	.	0.80722	D	1	B	0.27997	0.197	B	0.04013	0.001	T	0.38693	-0.9649	7	.	.	.	.	14.6598	0.68861	0.5297:0.0:0.4703:0.0	.	82	B4E3U4	.	T	82	ENSP00000411989:M82T	.	M	-	2	0	RBMX	135785382	0.138000	0.22547	0.881000	0.34555	0.821000	0.46438	-0.253000	0.08794	-1.365000	0.02158	-2.240000	0.00288	ATG		0.393	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1		NM_002139	
REST	5978	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	57797456	57797456	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr4:57797456C>T	ENST00000309042.7	+	4	2746	c.2432C>T	c.(2431-2433)tCc>tTc	p.S811F		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	811	Pro-rich.				cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S811F(1)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					GAGCCAATTTCCAAAAAGCCT	0.517																																																	1	Substitution - Missense(1)	kidney(1)											96.0	107.0	103.0					4																	57797456		2203	4300	6503	SO:0001583	missense	5978			U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.2432C>T	4.37:g.57797456C>T	ENSP00000311816:p.Ser811Phe	Somatic		WXS	Illumina HiSeq	Phase_I	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Missense_Mutation	SNP	ENST00000309042.7	37	CCDS3509.1	.	.	.	.	.	.	.	.	.	.	C	11.05	1.523705	0.27299	.	.	ENSG00000084093	ENST00000309042;ENST00000358605	T	0.08458	3.09	4.52	3.68	0.42216	.	0.603484	0.13918	N	0.353760	T	0.07638	0.0192	N	0.08118	0	0.09310	N	1	P;P	0.49447	0.924;0.875	P;P	0.51135	0.66;0.459	T	0.25082	-1.0142	10	0.62326	D	0.03	-1.3409	8.4528	0.32882	0.0:0.8973:0.0:0.1027	.	788;811	F8WAN5;Q13127	.;REST_HUMAN	F	811;788	ENSP00000311816:S811F	ENSP00000311816:S811F	S	+	2	0	REST	57492213	0.027000	0.19231	0.006000	0.13384	0.002000	0.02628	3.919000	0.56439	1.504000	0.48704	0.655000	0.94253	TCC		0.517	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2		NM_005612	
RNU11	26824	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	28975159	28975159	+	lincRNA	SNP	T	T	C	rs528315170		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr1:28975159T>C	ENST00000427804.1	+	0	1376				RNU11_ENST00000387069.1_lincRNA																							ACTCGATTGCTCTGCGTGCGG	0.478													T|||	1	0.000199681	0.0	0.0	5008	,	,		17598	0.0		0.0	False		,,,				2504	0.001																0													158.0	150.0	152.0					1																	28975159		692	1591	2283			26824																															1.37:g.28975159T>C		Somatic		WXS	Illumina HiSeq	Phase_I		RNA	SNP	ENST00000427804.1	37																																																																																					0.478	RP11-442N24__B.1-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000010342.1			
SCN2A	6326	broad.mit.edu;hgsc.bcm.edu	37	2	166201197	166201197	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr2:166201197G>A	ENST00000375437.2	+	16	2985	c.2695G>A	c.(2695-2697)Ggc>Agc	p.G899S	SCN2A_ENST00000283256.6_Missense_Mutation_p.G899S|SCN2A_ENST00000357398.3_Missense_Mutation_p.G899S|SCN2A_ENST00000375427.2_Missense_Mutation_p.G899S	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	899					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.G899S(2)		NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGCTGTGGTCGGCATGCAGCT	0.438																																																	2	Substitution - Missense(2)	kidney(2)											168.0	160.0	163.0					2																	166201197		2203	4300	6503	SO:0001583	missense	6326			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10588	protein-coding gene	gene with protein product		182390	"""sodium channel, voltage-gated, type II, alpha 2 polypeptide"", ""sodium channel, voltage-gated, type II, alpha 1 polypeptide"""	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.2695G>A	2.37:g.166201197G>A	ENSP00000364586:p.Gly899Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	37	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	G	35	5.476049	0.96291	.	.	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D	0.97642	-4.47;-4.47;-4.47;-4.47	5.74	5.74	0.90152	Ion transport (1);	0.000000	0.64402	D	0.000002	D	0.99080	0.9684	H	0.95917	3.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.99160	1.0861	10	0.87932	D	0	.	19.9329	0.97127	0.0:0.0:1.0:0.0	.	899;899	Q99250-2;Q99250	.;SCN2A_HUMAN	S	899	ENSP00000364586:G899S;ENSP00000349973:G899S;ENSP00000283256:G899S;ENSP00000364576:G899S	ENSP00000283256:G899S	G	+	1	0	SCN2A	165909443	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.735000	0.98825	2.714000	0.92807	0.650000	0.86243	GGC		0.438	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2		NM_021007	
SETD2	29072	broad.mit.edu;ucsc.edu|broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	47165360	47165361	+	Nonsense_Mutation	DNP	GC	GC	AG			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G|C	G|C	G|C	A|G	G|C	G|C	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr3:47165360_47165361GC>AG	ENST00000409792.3	-	3	807_808	c.765_766GC>CT	c.(763-768)aaGCag>aaCTag	p.255_256KQ>N*		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	255					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.Q256*(1)|p.K255N(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		ATAGTGTCCTGCTTAGTATCTG	0.361			"""N, F, S, Mis"""		clear cell renal carcinoma																																			Rec	yes		3	3p21.31	29072	SET domain containing 2		E	2	Substitution - Nonsense(1)|Substitution - Missense(1)	kidney(2)																																								SO:0001587	stop_gained	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.765_766delinsAG	3.37:g.47165360_47165361delinsAG	ENSP00000386759:p.K255_Q256delinsN*	Somatic		WXS	Illumina GAIIx|Illumina HiSeq	Phase_I	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2																																																																																				0.361	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2		NM_014159	
SLC15A2	6565	broad.mit.edu;hgsc.bcm.edu	37	3	121613330	121613330	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr3:121613330C>G	ENST00000489711.1	+	1	395	c.7C>G	c.(7-9)Cct>Gct	p.P3A	SLC15A2_ENST00000295605.2_Missense_Mutation_p.P3A	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	3					drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)	p.P3A(1)		NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	AGCCATGAATCCTTTCCAGAA	0.493																																																	1	Substitution - Missense(1)	kidney(1)											130.0	141.0	138.0					3																	121613330		2203	4300	6503	SO:0001583	missense	6565			BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"""Solute carriers"""	10921	protein-coding gene	gene with protein product		602339	"""solute carrier family 15 (H+/peptide transporter), member 2"""			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.7C>G	3.37:g.121613330C>G	ENSP00000417085:p.Pro3Ala	Somatic		WXS	Illumina HiSeq	Phase_I	A8K1A5|B4E2A7	Missense_Mutation	SNP	ENST00000489711.1	37	CCDS3007.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.386224	0.25031	.	.	ENSG00000163406	ENST00000489711;ENST00000295605	T;T	0.02345	4.62;4.33	5.1	0.803	0.18691	Major facilitator superfamily domain, general substrate transporter (1);	0.330992	0.25890	N	0.027637	T	0.01421	0.0046	N	0.14661	0.345	0.26394	N	0.976536	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.46911	-0.9157	10	0.15952	T	0.53	-1.9071	2.5334	0.04709	0.36:0.3882:0.1572:0.0946	.	3;3	B4E2A7;Q16348	.;S15A2_HUMAN	A	3	ENSP00000417085:P3A;ENSP00000295605:P3A	ENSP00000295605:P3A	P	+	1	0	SLC15A2	123096020	0.007000	0.16637	0.968000	0.41197	0.984000	0.73092	-0.560000	0.05964	0.289000	0.22422	-0.270000	0.10280	CCT		0.493	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1		NM_021082	
SLC16A4	9122	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	110921782	110921782	+	Silent	SNP	A	A	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr1:110921782A>C	ENST00000369779.4	-	6	972	c.723T>G	c.(721-723)acT>acG	p.T241T	SLC16A4_ENST00000497687.1_5'UTR|SLC16A4_ENST00000369781.4_Intron|SLC16A4_ENST00000541986.1_Silent_p.T179T|SLC16A4_ENST00000437429.2_Silent_p.T131T|SLC16A4_ENST00000472422.2_Silent_p.T193T	NM_001201547.1|NM_004696.2	NP_001188476.1|NP_004687.1	O15374	MOT5_HUMAN	solute carrier family 16, member 4	241					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)	p.T241T(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(3)|prostate(1)|stomach(2)	16		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	CCTTCTGCGTAGTACTGTCCT	0.423																																																	1	Substitution - coding silent(1)	kidney(1)											227.0	213.0	217.0					1																	110921782		2203	4300	6503	SO:0001819	synonymous_variant	9122			U59185	CCDS823.1, CCDS55621.1, CCDS55622.1, CCDS55623.1, CCDS55624.1	1p13.3	2013-07-18	2013-07-18		ENSG00000168679	ENSG00000168679		"""Solute carriers"""	10925	protein-coding gene	gene with protein product		603878	"""solute carrier family 16 (monocarboxylic acid transporters), member 4"", ""solute carrier family 16, member 4 (monocarboxylic acid transporter 5)"""			9425115	Standard	NM_004696		Approved	MCT4, MCT5	uc001dzo.2	O15374	OTTHUMG00000011285	ENST00000369779.4:c.723T>G	1.37:g.110921782A>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8K3V5|B2R9C9|B4DJ67|B4DPX7|E7EPY8|G3V175|Q5T612|Q8WU09	Silent	SNP	ENST00000369779.4	37	CCDS823.1																																																																																				0.423	SLC16A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031115.3		NM_004696	
SLC17A6	57084	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	22364813	22364813	+	Missense_Mutation	SNP	C	C	A	rs373587525		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr11:22364813C>A	ENST00000263160.3	+	3	797	c.360C>A	c.(358-360)gaC>gaA	p.D120E		NM_020346.2	NP_065079.1	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 6	120					ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)	p.D120E(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)	50						TCAACTGGGACCCGGAAACCG	0.517																																																	1	Substitution - Missense(1)	kidney(1)											95.0	104.0	101.0					11																	22364813		2203	4300	6503	SO:0001583	missense	57084			AB032435	CCDS7856.1	11p14.3	2013-07-18	2013-07-18		ENSG00000091664	ENSG00000091664		"""Solute carriers"""	16703	protein-coding gene	gene with protein product	"""vesicular glutamate transporter 2"", ""differentiation-associated Na-dependent inorganic phosphate cotransporter"""	607563	"""solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6"""			11306821	Standard	NM_020346		Approved	DNPI, VGLUT2	uc001mqk.3	Q9P2U8	OTTHUMG00000166063	ENST00000263160.3:c.360C>A	11.37:g.22364813C>A	ENSP00000263160:p.Asp120Glu	Somatic		WXS	Illumina HiSeq	Phase_I	A6NKS2	Missense_Mutation	SNP	ENST00000263160.3	37	CCDS7856.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.978623	0.74360	.	.	ENSG00000091664	ENST00000263160;ENST00000546171	T	0.60040	0.22	5.4	3.51	0.40186	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.67429	0.2892	M	0.81179	2.53	0.50813	D	0.999899	P	0.51653	0.947	P	0.55222	0.771	T	0.70174	-0.4944	10	0.59425	D	0.04	.	8.1357	0.31054	0.0:0.7373:0.0:0.2627	.	120	Q9P2U8	VGLU2_HUMAN	E	120;8	ENSP00000263160:D120E	ENSP00000263160:D120E	D	+	3	2	SLC17A6	22321389	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.671000	0.25172	2.517000	0.84864	0.655000	0.94253	GAC		0.517	SLC17A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387671.1		NM_020346	
SLC6A12	6539	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	319083	319083	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr12:319083T>C	ENST00000428720.1	-	3	813	c.70A>G	c.(70-72)Aag>Gag	p.K24E	SLC6A12_ENST00000359674.4_Missense_Mutation_p.K24E|SLC6A12_ENST00000536824.1_Missense_Mutation_p.K24E|SLC6A12_ENST00000424061.2_Missense_Mutation_p.K24E|SLC6A12_ENST00000397296.2_Missense_Mutation_p.K24E	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	24					amino acid transport (GO:0006865)|cellular hyperosmotic response (GO:0071474)|cellular water homeostasis (GO:0009992)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|response to organic substance (GO:0010033)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)	p.K24E(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			TGGTCCAACTTCTCTCCCTCC	0.622																																																	1	Substitution - Missense(1)	kidney(1)											145.0	122.0	130.0					12																	319083		2203	4300	6503	SO:0001583	missense	6539			L42300	CCDS8501.1	12p13	2013-07-19	2013-07-19		ENSG00000111181	ENSG00000111181		"""Solute carriers"""	11045	protein-coding gene	gene with protein product	"""betaine/GABA transporter-1"""	603080	"""solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12"""			7589472	Standard	NM_003044		Approved	BGT-1	uc009zdh.2	P48065	OTTHUMG00000090309	ENST00000428720.1:c.70A>G	12.37:g.319083T>C	ENSP00000388184:p.Lys24Glu	Somatic		WXS	Illumina HiSeq	Phase_I	A0AV52|B2R992|D3DUN8	Missense_Mutation	SNP	ENST00000428720.1	37	CCDS8501.1	.	.	.	.	.	.	.	.	.	.	T	4.862	0.160226	0.09287	.	.	ENSG00000111181	ENST00000359674;ENST00000397296;ENST00000428720;ENST00000424061;ENST00000536824;ENST00000537793;ENST00000535347	T;T;T;T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66;-0.66;-0.37;0.68	5.33	4.18	0.49190	.	0.797910	0.11225	N	0.586291	T	0.45498	0.1345	N	0.14661	0.345	0.21473	N	0.999671	B	0.02656	0.0	B	0.04013	0.001	T	0.44982	-0.9292	10	0.02654	T	1	.	5.1352	0.14932	0.0:0.1464:0.1627:0.6908	.	24	P48065	S6A12_HUMAN	E	24	ENSP00000352702:K24E;ENSP00000380464:K24E;ENSP00000388184:K24E;ENSP00000399136:K24E;ENSP00000444268:K24E;ENSP00000439351:K24E;ENSP00000446082:K24E	ENSP00000352702:K24E	K	-	1	0	SLC6A12	189344	0.003000	0.15002	0.503000	0.27626	0.192000	0.23643	1.173000	0.31920	2.135000	0.66039	0.460000	0.39030	AAG		0.622	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2		NM_003044	
SLC17A8	246213	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	100813894	100813894	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr12:100813894C>T	ENST00000323346.5	+	12	2040	c.1727C>T	c.(1726-1728)aCa>aTa	p.T576I	SLC17A8_ENST00000392989.3_Missense_Mutation_p.T526I	NM_001145288.1|NM_139319.2	NP_001138760.1|NP_647480.1	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 8	576					ion transport (GO:0006811)|neurotransmitter transport (GO:0006836)|sensory perception of sound (GO:0007605)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)	p.T576I(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	44						GAAGAGCTGACATCCTACCAG	0.428																																																	1	Substitution - Missense(1)	kidney(1)											78.0	69.0	72.0					12																	100813894		2203	4300	6503	SO:0001583	missense	246213			AJ459241	CCDS9077.1, CCDS44957.1	12q23.1	2013-07-18	2013-07-18		ENSG00000179520	ENSG00000179520		"""Solute carriers"""	20151	protein-coding gene	gene with protein product	"""vesicular glutamate transporter 3"""	607557	"""deafness, autosomal dominant 25"", ""solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8"""	DFNA25		12151341	Standard	NM_139319		Approved	VGLUT3	uc010svi.2	Q8NDX2	OTTHUMG00000170358	ENST00000323346.5:c.1727C>T	12.37:g.100813894C>T	ENSP00000316909:p.Thr576Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B3KXZ6|B7ZKV4|Q17RQ8	Missense_Mutation	SNP	ENST00000323346.5	37	CCDS9077.1	.	.	.	.	.	.	.	.	.	.	C	4.291	0.053131	0.08291	.	.	ENSG00000179520	ENST00000323346;ENST00000392989	T;T	0.68903	0.07;-0.36	4.8	2.95	0.34219	.	0.546235	0.20488	N	0.091353	T	0.40839	0.1133	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.20042	-1.0287	10	0.34782	T	0.22	.	5.6785	0.17761	0.1561:0.6785:0.0:0.1654	.	576;526	Q8NDX2;Q8NDX2-2	VGLU3_HUMAN;.	I	576;526	ENSP00000316909:T576I;ENSP00000376715:T526I	ENSP00000316909:T576I	T	+	2	0	SLC17A8	99338025	0.000000	0.05858	0.061000	0.19648	0.711000	0.40976	0.062000	0.14389	0.549000	0.28973	0.591000	0.81541	ACA		0.428	SLC17A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408673.2		NM_139319	
SMC2	10592	broad.mit.edu;ucsc.edu	37	9	106864804	106864804	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr9:106864804C>A	ENST00000286398.7	+	9	1258	c.970C>A	c.(970-972)Ctg>Atg	p.L324M	SMC2_ENST00000374793.3_Missense_Mutation_p.L324M|SMC2_ENST00000303219.8_Missense_Mutation_p.L324M|SMC2_ENST00000374787.3_Missense_Mutation_p.L324M	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	324					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)	p.L324M(2)		breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						GAAGAAAAATCTGGCATGTGA	0.403																																																	2	Substitution - Missense(2)	kidney(2)											89.0	89.0	89.0					9																	106864804		2203	4300	6503	SO:0001583	missense	10592			AF092563	CCDS35086.1	9q31.1	2008-05-14	2006-07-06	2006-07-06	ENSG00000136824	ENSG00000136824		"""Structural maintenance of chromosomes proteins"""	14011	protein-coding gene	gene with protein product		605576	"""SMC2 (structural maintenance of chromosomes 2, yeast)-like 1"", ""SMC2 structural maintenance of chromosomes 2-like 1 (yeast)"""	SMC2L1		9789013	Standard	NM_006444		Approved	hCAP-E, CAP-E	uc011lvl.2	O95347	OTTHUMG00000020401	ENST00000286398.7:c.970C>A	9.37:g.106864804C>A	ENSP00000286398:p.Leu324Met	Somatic		WXS	Illumina GAIIx	Phase_I	Q6IEE0|Q9P1P2	Missense_Mutation	SNP	ENST00000286398.7	37	CCDS35086.1	.	.	.	.	.	.	.	.	.	.	C	11.69	1.715070	0.30413	.	.	ENSG00000136824	ENST00000286398;ENST00000374793;ENST00000303219;ENST00000536893;ENST00000374787	D;D;D;D	0.82711	-1.5;-1.5;-1.64;-1.5	5.79	2.83	0.33086	RecF/RecN/SMC (1);	0.487586	0.20799	N	0.085477	T	0.75413	0.3846	L	0.35288	1.05	0.33209	D	0.553145	B;B;B	0.30361	0.277;0.251;0.056	B;B;B	0.41666	0.363;0.213;0.16	T	0.75221	-0.3394	10	0.40728	T	0.16	-6.5011	3.6685	0.08265	0.3143:0.469:0.0:0.2167	.	324;324;324	A8K984;O95347;Q2KQ72	.;SMC2_HUMAN;.	M	324	ENSP00000286398:L324M;ENSP00000363925:L324M;ENSP00000306152:L324M;ENSP00000363919:L324M	ENSP00000286398:L324M	L	+	1	2	SMC2	105904625	0.996000	0.38824	0.987000	0.45799	0.669000	0.39330	1.472000	0.35376	1.457000	0.47850	0.585000	0.79938	CTG		0.403	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1			
SPRY4	81848	hgsc.bcm.edu	37	5	141694415	141694415	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr5:141694415G>A	ENST00000434127.2	-	2	502	c.259C>T	c.(259-261)Cac>Tac	p.H87Y	SPRY4_ENST00000503582.1_5'Flank|SPRY4_ENST00000344120.4_Missense_Mutation_p.H110Y	NM_001127496.1	NP_001120968.1	Q9C004	SPY4_HUMAN	sprouty homolog 4 (Drosophila)	87					multicellular organismal development (GO:0007275)|negative regulation of MAP kinase activity (GO:0043407)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(1)	18		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATCCAATGGTGGGTGACATCC	0.677									Testicular Cancer, Familial Clustering of																																								0													44.0	52.0	49.0					5																	141694415		2201	4300	6501	SO:0001583	missense	81848	Familial Cancer Database		AF227516	CCDS4274.1, CCDS47296.1	5q31.3	2010-08-05			ENSG00000187678	ENSG00000187678			15533	protein-coding gene	gene with protein product		607984				16465403	Standard	NM_030964		Approved		uc010jgi.1	Q9C004	OTTHUMG00000129663	ENST00000434127.2:c.259C>T	5.37:g.141694415G>A	ENSP00000399468:p.His87Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	A4FVB2|A4FVB3|Q6QIX2|Q9C003	Missense_Mutation	SNP	ENST00000434127.2	37	CCDS47296.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.972530	0.74246	.	.	ENSG00000187678	ENST00000344120;ENST00000434127;ENST00000359661	T;T	0.65549	-0.16;-0.15	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.75317	0.3833	L	0.47716	1.5	0.80722	D	1	D;D	0.71674	0.998;0.993	D;D	0.80764	0.994;0.979	T	0.72899	-0.4152	10	0.44086	T	0.13	-24.1631	19.982	0.97329	0.0:0.0:1.0:0.0	.	87;87	Q9C004-2;Q9C004	.;SPY4_HUMAN	Y	110;87;87	ENSP00000344967:H110Y;ENSP00000399468:H87Y	ENSP00000344967:H110Y	H	-	1	0	SPRY4	141674599	1.000000	0.71417	0.990000	0.47175	0.433000	0.31745	9.434000	0.97515	2.737000	0.93849	0.561000	0.74099	CAC		0.677	SPRY4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370652.1			
STARD13	90627	broad.mit.edu;hgsc.bcm.edu	37	13	33684212	33684212	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr13:33684212G>T	ENST00000336934.5	-	12	2961	c.2845C>A	c.(2845-2847)Ccg>Acg	p.P949T	STARD13_ENST00000399365.3_Missense_Mutation_p.P831T|STARD13_ENST00000255486.4_Missense_Mutation_p.P941T	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	949	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)	p.P949T(1)		breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		AGCTTCAGCGGGTTCCCGTCG	0.547											OREG0022359	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - Missense(1)	kidney(1)											44.0	42.0	43.0					13																	33684212		2203	4300	6503	SO:0001583	missense	90627			AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	19164	protein-coding gene	gene with protein product		609866	"""START domain containing 13"", ""long intergenic non-protein coding RNA 464"""	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.2845C>A	13.37:g.33684212G>T	ENSP00000338785:p.Pro949Thr	Somatic	841	WXS	Illumina HiSeq	Phase_I	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Missense_Mutation	SNP	ENST00000336934.5	37	CCDS9348.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.461316	0.84317	.	.	ENSG00000133121	ENST00000399365;ENST00000255486;ENST00000336934	T;T;T	0.32023	1.47;1.47;1.47	5.34	5.34	0.76211	Lipid-binding START (3);START-like domain (1);	0.053197	0.85682	D	0.000000	T	0.60728	0.2291	M	0.89785	3.06	0.80722	D	1	D;D;P	0.56968	0.973;0.978;0.878	D;D;P	0.69654	0.942;0.965;0.904	T	0.67841	-0.5566	10	0.87932	D	0	.	12.7228	0.57152	0.0755:0.0:0.9245:0.0	.	914;949;941	Q9Y3M8-4;Q9Y3M8;Q9Y3M8-2	.;STA13_HUMAN;.	T	831;941;949	ENSP00000382300:P831T;ENSP00000255486:P941T;ENSP00000338785:P949T	ENSP00000255486:P941T	P	-	1	0	STARD13	32582212	1.000000	0.71417	0.858000	0.33744	0.940000	0.58332	7.900000	0.87376	2.657000	0.90304	0.655000	0.94253	CCG		0.547	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2		NM_001243466	
SUGT1	10910	broad.mit.edu;hgsc.bcm.edu	37	13	53231666	53231666	+	Splice_Site	SNP	G	G	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr13:53231666G>C	ENST00000343788.6	+	3	178		c.e3-1		SUGT1_ENST00000310528.8_Splice_Site|SUGT1_ENST00000483074.1_Splice_Site|SUGT1_ENST00000535397.1_Splice_Site	NM_001130912.1	NP_001124384.1	Q9Y2Z0	SUGT1_HUMAN	SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae)						innate immune response (GO:0045087)|mitotic nuclear division (GO:0007067)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)		p.?(2)		kidney(3)|large_intestine(3)|lung(2)	8		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.25e-08)		TGTTTTTGTAGGAGCTGACTA	0.338																																																	2	Unknown(2)	kidney(2)											73.0	65.0	68.0					13																	53231666		2203	4300	6503	SO:0001630	splice_region_variant	10910			AF068289	CCDS9436.1, CCDS45050.1	13q14.3	2014-03-20			ENSG00000165416	ENSG00000165416			16987	protein-coding gene	gene with protein product		604098				10445024	Standard	NM_006704		Approved	SGT1	uc001vhc.2	Q9Y2Z0	OTTHUMG00000016977	ENST00000343788.6:c.97-1G>C	13.37:g.53231666G>C		Somatic		WXS	Illumina HiSeq	Phase_I	A2A303|Q5JAK5|Q5TAM6|Q6VXY6	Splice_Site	SNP	ENST00000343788.6	37	CCDS45050.1	.	.	.	.	.	.	.	.	.	.	G	16.61	3.171794	0.57584	.	.	ENSG00000165416	ENST00000343788;ENST00000310528	.	.	.	4.21	4.21	0.49690	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6949	0.77488	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SUGT1	52129667	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	6.982000	0.76173	2.047000	0.60756	0.467000	0.42956	.		0.338	SUGT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045104.2			Intron
TADA1	117143	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	166833059	166833059	+	Splice_Site	SNP	A	A	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr1:166833059A>T	ENST00000367874.4	-	4	424		c.e4+1		TADA1_ENST00000467021.1_5'Flank	NM_053053.3	NP_444281.1	Q96BN2	TADA1_HUMAN	transcriptional adaptor 1						chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)	p.?(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	11						AGAACAACCTACATCAAATTT	0.398																																																	1	Unknown(1)	kidney(1)											72.0	75.0	74.0					1																	166833059		2203	4300	6503	SO:0001630	splice_region_variant	117143			BC015401	CCDS1255.1	1q24.1	2009-10-02	2009-10-02	2009-10-02	ENSG00000152382	ENSG00000152382			30631	protein-coding gene	gene with protein product		612763	"""transcriptional adaptor 1 (HFI1 homolog, yeast)-like"", ""transcriptional adaptor 1 (HFI1 homolog, yeast)"""	TADA1L		11564863	Standard	NM_053053		Approved	STAF42, ADA1, hADA1, HFI1	uc001gdw.3	Q96BN2	OTTHUMG00000034321	ENST00000367874.4:c.330+1T>A	1.37:g.166833059A>T		Somatic		WXS	Illumina HiSeq	Phase_I	A8K4J9	Splice_Site	SNP	ENST00000367874.4	37	CCDS1255.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.211420	0.79240	.	.	ENSG00000152382	ENST00000367874	.	.	.	6.17	6.17	0.99709	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7743	0.69713	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TADA1	165099683	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	8.038000	0.88943	2.371000	0.80710	0.533000	0.62120	.		0.398	TADA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082881.1		NM_053053	Intron
TAF2	6873	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	120814248	120814248	+	Missense_Mutation	SNP	A	A	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr8:120814248A>G	ENST00000378164.2	-	6	876	c.578T>C	c.(577-579)gTt>gCt	p.V193A		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	193					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.V193A(2)		NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			GTATGAATCAACACAAGGGAA	0.343																																																	2	Substitution - Missense(2)	kidney(2)											60.0	55.0	57.0					8																	120814248		2203	4300	6503	SO:0001583	missense	6873			AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"""	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.578T>C	8.37:g.120814248A>G	ENSP00000367406:p.Val193Ala	Somatic		WXS	Illumina HiSeq	Phase_I	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Missense_Mutation	SNP	ENST00000378164.2	37	CCDS34937.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.647970	0.87958	.	.	ENSG00000064313	ENST00000378164	T	0.59906	0.23	5.89	5.89	0.94794	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77485	0.4137	M	0.85542	2.76	0.80722	D	1	D	0.60160	0.987	D	0.63192	0.912	T	0.81573	-0.0871	10	0.87932	D	0	-21.1168	16.3127	0.82898	1.0:0.0:0.0:0.0	.	193	Q6P1X5	TAF2_HUMAN	A	193	ENSP00000367406:V193A	ENSP00000367406:V193A	V	-	2	0	TAF2	120883429	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.288000	0.96055	2.246000	0.74042	0.533000	0.62120	GTT		0.343	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1		NM_003184	
TECPR2	9895	broad.mit.edu;hgsc.bcm.edu	37	14	102916037	102916037	+	Silent	SNP	G	G	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr14:102916037G>A	ENST00000359520.7	+	14	3373	c.3147G>A	c.(3145-3147)tcG>tcA	p.S1049S	TECPR2_ENST00000558678.1_Silent_p.S1049S	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	1049					autophagy (GO:0006914)|cell death (GO:0008219)			p.S1049S(2)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						CCACTCACTCGGTGGCCACAG	0.562																																																	2	Substitution - coding silent(2)	lung(1)|kidney(1)											116.0	107.0	110.0					14																	102916037		2203	4300	6503	SO:0001819	synonymous_variant	9895			AB019441	CCDS32162.1, CCDS58337.1	14q32.33	2009-02-27	2009-02-27	2009-02-27		ENSG00000196663			19957	protein-coding gene	gene with protein product		615000	"""KIAA0329"""	KIAA0329		9205841	Standard	NM_014844		Approved		uc001ylw.2	O15040		ENST00000359520.7:c.3147G>A	14.37:g.102916037G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Silent	SNP	ENST00000359520.7	37	CCDS32162.1																																																																																				0.562	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2		NM_014844	
AC005013.5	0	hgsc.bcm.edu	37	7	28997498	28997498	+	lincRNA	DEL	C	C	-	rs67010340		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr7:28997498delC	ENST00000436594.1	+	0	192				TRIL_ENST00000322982.3_RNA																							GGGGGCTCGGCCAGCGAGCTG	0.667													C|CC|C|insertion	5008	1.0	1.0	1.0	5008	,	,		16023	1.0		1.0	False		,,,				2504	1.0																0													3.0	2.0	3.0					7																	28997498		1595	3489	5084			9865																															7.37:g.28997498delC		Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Del	DEL	ENST00000436594.1	37																																																																																					0.667	AC005013.5-001	KNOWN	basic|exp_conf	lincRNA	lincRNA	OTTHUMT00000327953.3			
TNPO3	23534	broad.mit.edu;ucsc.edu	37	7	128607436	128607436	+	Missense_Mutation	SNP	C	C	A	rs188168905		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr7:128607436C>A	ENST00000265388.5	-	21	2752	c.2609G>T	c.(2608-2610)cGa>cTa	p.R870L	TNPO3_ENST00000482320.1_Missense_Mutation_p.R804L|TNPO3_ENST00000471234.1_Missense_Mutation_p.R806L|TNPO3_ENST00000393245.1_Missense_Mutation_p.R904L|TNPO3_ENST00000471166.1_Missense_Mutation_p.R904L			Q9Y5L0	TNPO3_HUMAN	transportin 3	870					splicing factor protein import into nucleus (GO:0035048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	receptor activity (GO:0004872)	p.R904L(1)|p.R870L(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(3)	22						TTCTAACCATCGACAAAAAGT	0.408																																					Pancreas(147;583 2585 39696 52331)												2	Substitution - Missense(2)	kidney(2)											95.0	87.0	90.0					7																	128607436		2203	4300	6503	SO:0001583	missense	23534			AF145029	CCDS5809.1, CCDS55162.1	7q32.2	2014-02-03			ENSG00000064419	ENSG00000064419		"""Importins"""	17103	protein-coding gene	gene with protein product	"""importin 12"""	610032	"""limb girdle muscular dystrophy 1F (autosomal dominant)"""	LGMD1F		10366588, 10713112, 23543484, 23667635	Standard	NM_012470		Approved	TRN-SR, MTR10A, TRN-SR2, IPO12	uc003vol.2	Q9Y5L0	OTTHUMG00000158409	ENST00000265388.5:c.2609G>T	7.37:g.128607436C>A	ENSP00000265388:p.Arg870Leu	Somatic		WXS	Illumina GAIIx	Phase_I	A4D1K9|C9IZM0|Q6NUM1|Q96G71|Q96GU9|Q9Y3R2	Missense_Mutation	SNP	ENST00000265388.5	37	CCDS5809.1	.	.	.	.	.	.	.	.	.	.	C	17.68	3.449664	0.63178	.	.	ENSG00000064419	ENST00000393245;ENST00000265388;ENST00000482320;ENST00000471234;ENST00000471166	.	.	.	5.81	5.81	0.92471	Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	T	0.43875	0.1267	N	0.22421	0.69	0.80722	D	1	B;B;B;B	0.31209	0.064;0.313;0.205;0.13	B;B;B;B	0.24541	0.018;0.024;0.054;0.024	T	0.30446	-0.9978	9	0.28530	T	0.3	.	17.5723	0.87937	0.0:1.0:0.0:0.0	.	806;904;870;870	C9IZM0;C9J7E5;Q9Y5L0-3;Q9Y5L0	.;.;.;TNPO3_HUMAN	L	904;870;804;806;904	.	ENSP00000265388:R870L	R	-	2	0	TNPO3	128394672	1.000000	0.71417	0.996000	0.52242	0.942000	0.58702	7.531000	0.81973	2.736000	0.93811	0.655000	0.94253	CGA		0.408	TNPO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350929.1		NM_012470	
TSC2	7249	hgsc.bcm.edu;ucsc.edu	37	16	2112006	2112006	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr16:2112006G>T	ENST00000219476.3	+	12	1884	c.1254G>T	c.(1252-1254)agG>agT	p.R418S	TSC2_ENST00000568454.1_Missense_Mutation_p.R429S|TSC2_ENST00000353929.4_Missense_Mutation_p.R418S|TSC2_ENST00000350773.4_Missense_Mutation_p.R418S|TSC2_ENST00000382538.6_Missense_Mutation_p.R369S|TSC2_ENST00000401874.2_Missense_Mutation_p.R418S|TSC2_ENST00000439673.2_Missense_Mutation_p.R381S	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	418					acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				CGGACCAGAGGCCTGTGAGAC	0.607			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis																														yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"""E, O"""	0													67.0	63.0	64.0					16																	2112006		2198	4300	6498	SO:0001583	missense	7249	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 160"""	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.1254G>T	16.37:g.2112006G>T	ENSP00000219476:p.Arg418Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Missense_Mutation	SNP	ENST00000219476.3	37	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	.	14.41	2.527320	0.44969	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	T;T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14;-0.14	4.95	-1.96	0.07525	Armadillo-like helical (1);Armadillo-type fold (1);Tuberin, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.74824	0.3767	M	0.83384	2.64	0.58432	D	0.999999	D;D;D;D;D;D	0.89917	1.0;0.999;0.999;0.995;0.999;0.995	D;D;D;D;D;D	0.91635	0.999;0.999;0.997;0.996;0.998;0.989	T	0.73363	-0.4006	10	0.41790	T	0.15	-25.2882	10.3747	0.44075	0.7045:0.0:0.2955:0.0	.	369;381;418;418;418;418	B4DIL8;P49815-6;P49815-4;P49815-3;P49815-5;P49815	.;.;.;.;.;TSC2_HUMAN	S	418;418;418;381;369;418	ENSP00000219476:R418S;ENSP00000384468:R418S;ENSP00000248099:R418S;ENSP00000399232:R381S;ENSP00000371978:R369S;ENSP00000344383:R418S	ENSP00000219476:R418S	R	+	3	2	TSC2	2052007	1.000000	0.71417	0.995000	0.50966	0.196000	0.23810	1.017000	0.29989	-0.154000	0.11118	-0.258000	0.10820	AGG		0.607	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2		NM_000548	
TTLL3	26140	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	9868880	9868880	+	Silent	SNP	T	T	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr3:9868880T>C	ENST00000547186.1	+	9	1290	c.1074T>C	c.(1072-1074)taT>taC	p.Y358Y	TTLL3_ENST00000397241.1_Silent_p.Y146Y|TTLL3_ENST00000455274.1_Silent_p.Y146Y|TTLL3_ENST00000466245.1_Intron|TTLL3_ENST00000430793.1_Silent_p.Y146Y|TTLL3_ENST00000426895.4_Silent_p.Y501Y|TTLL3_ENST00000383827.1_Silent_p.Y146Y|ARPC4-TTLL3_ENST00000397256.1_Silent_p.Y419Y|TTLL3_ENST00000427853.3_Silent_p.Y146Y	NM_001025930.3	NP_001021100.3	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	358	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				axoneme assembly (GO:0035082)|cilium assembly (GO:0042384)|protein polyglycylation (GO:0018094)	axoneme (GO:0005930)|cilium (GO:0005929)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	protein-glycine ligase activity (GO:0070735)|protein-glycine ligase activity, initiating (GO:0070736)	p.Y358Y(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	Medulloblastoma(99;0.227)					GCGACAGCTATATCCGCTTTT	0.582																																																	1	Substitution - coding silent(1)	kidney(1)											122.0	109.0	113.0					3																	9868880		2203	4300	6503	SO:0001819	synonymous_variant	26140				CCDS43048.1, CCDS43048.2	3p25.3	2013-02-14			ENSG00000214021	ENSG00000214021		"""Tubulin tyrosine ligase-like family"""	24483	protein-coding gene	gene with protein product						11054573	Standard	NR_037162		Approved	DKFZP434B103, HOTTL	uc003btg.4	Q9Y4R7	OTTHUMG00000128439	ENST00000547186.1:c.1074T>C	3.37:g.9868880T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q4KMS8|Q6AWA3|Q6ZU95|Q8NDN8|Q96GG8|Q9H876|Q9UI99	Silent	SNP	ENST00000547186.1	37		.	.	.	.	.	.	.	.	.	.	T	7.869	0.727681	0.15439	.	.	ENSG00000214021	ENST00000310252	T	0.06142	3.34	5.09	0.124	0.14714	.	0.174244	0.39146	U	0.001455	T	0.14399	0.0348	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.01480	-1.1344	7	0.87932	D	0	.	11.0341	0.47791	0.0:0.6551:0.0:0.3449	.	.	.	.	H	314	ENSP00000312148:Y314H	ENSP00000312148:Y314H	Y	+	1	0	TTLL3	9843880	0.998000	0.40836	0.998000	0.56505	0.789000	0.44602	1.150000	0.31639	0.079000	0.16929	-0.479000	0.04858	TAT		0.582	TTLL3-203	KNOWN	basic	protein_coding	protein_coding			NM_001025930.2	
TTN	7273	broad.mit.edu;ucsc.edu	37	2	179575503	179575503	+	Missense_Mutation	SNP	C	C	T	rs397517529		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr2:179575503C>T	ENST00000591111.1	-	96	27594	c.27370G>A	c.(27370-27372)Gga>Aga	p.G9124R	TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.G9441R|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.G8197R			Q8WZ42	TITIN_HUMAN	titin	13255	Ig-like 74.				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.G8197R(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)			TGGTACTTTCCGCCACTTCGT	0.488																																																	1	Substitution - Missense(1)	kidney(1)											151.0	145.0	147.0					2																	179575503		1983	4171	6154	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.27370G>A	2.37:g.179575503C>T	ENSP00000465570:p.Gly9124Arg	Somatic		WXS	Illumina GAIIx	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		.	.	.	.	.	.	.	.	.	.	C	14.49	2.551573	0.45487	.	.	ENSG00000155657	ENST00000342992	T	0.44881	0.91	6.17	6.17	0.99709	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.53126	0.1777	L	0.58510	1.815	0.80722	D	1	D	0.60575	0.988	P	0.52514	0.701	T	0.53613	-0.8414	9	0.87932	D	0	.	15.8933	0.79318	0.0:0.9342:0.0:0.0658	.	9124	Q8WZ42	TITIN_HUMAN	R	8197	ENSP00000343764:G8197R	ENSP00000343764:G8197R	G	-	1	0	TTN	179283748	0.988000	0.35896	0.823000	0.32752	0.822000	0.46500	2.609000	0.46317	2.941000	0.99782	0.655000	0.94253	GGA		0.488	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1		NM_133378	
UHRF1BP1L	23074	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	100478292	100478292	+	Missense_Mutation	SNP	T	T	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr12:100478292T>A	ENST00000279907.7	-	10	1462	c.1250A>T	c.(1249-1251)aAa>aTa	p.K417I	UHRF1BP1L_ENST00000545232.2_Missense_Mutation_p.K67I|UHRF1BP1L_ENST00000356828.3_Missense_Mutation_p.K417I	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	417								p.K417I(2)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(21)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	50						TGTTGGGGATTTAGGAGGTGA	0.408																																																	2	Substitution - Missense(2)	kidney(2)											279.0	233.0	249.0					12																	100478292		2203	4300	6503	SO:0001583	missense	23074				CCDS31882.1, CCDS31883.1	12q23.1	2011-04-15	2008-08-15		ENSG00000111647	ENSG00000111647			29102	protein-coding gene	gene with protein product							Standard	XM_005268737		Approved	KIAA0701	uc001tgq.3	A0JNW5	OTTHUMG00000170195	ENST00000279907.7:c.1250A>T	12.37:g.100478292T>A	ENSP00000279907:p.Lys417Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Missense_Mutation	SNP	ENST00000279907.7	37	CCDS31882.1	.	.	.	.	.	.	.	.	.	.	T	14.55	2.569634	0.45798	.	.	ENSG00000111647	ENST00000279907;ENST00000545232;ENST00000356828;ENST00000551973	T;T;T;T	0.35048	2.75;2.72;1.39;1.33	5.48	3.04	0.35103	.	0.351569	0.28612	N	0.014734	T	0.31702	0.0805	L	0.40543	1.245	0.38662	D	0.952095	B;B	0.28324	0.207;0.059	B;B	0.30646	0.118;0.031	T	0.16276	-1.0408	10	0.51188	T	0.08	-11.333	13.4774	0.61316	0.0:0.0:0.3672:0.6328	.	417;417	A0JNW5-2;A0JNW5	.;UH1BL_HUMAN	I	417;67;417;67	ENSP00000279907:K417I;ENSP00000444824:K67I;ENSP00000349285:K417I;ENSP00000448226:K67I	ENSP00000279907:K417I	K	-	2	0	UHRF1BP1L	99002423	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.108000	0.31123	0.428000	0.26173	-0.323000	0.08544	AAA		0.408	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1		NM_001006947	
UTP15	84135	broad.mit.edu;ucsc.edu	37	5	72864335	72864335	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr5:72864335G>A	ENST00000296792.4	+	4	529	c.274G>A	c.(274-276)Ggt>Agt	p.G92S	UTP15_ENST00000508491.1_Missense_Mutation_p.G73S|UTP15_ENST00000543251.1_5'UTR|ANKRA2_ENST00000296785.3_5'Flank	NM_001284431.1|NM_032175.2	NP_001271360.1|NP_115551.2	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein, homolog (S. cerevisiae)	92					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.G92S(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	15		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)		TCGACAAGATGGTAGATTGCT	0.423																																																	1	Substitution - Missense(1)	kidney(1)											116.0	119.0	118.0					5																	72864335		2203	4300	6503	SO:0001583	missense	84135			AL831972	CCDS34186.1, CCDS68893.1, CCDS68894.1	5q13.2	2013-01-10	2006-04-20		ENSG00000164338	ENSG00000164338		"""WD repeat domain containing"""	25758	protein-coding gene	gene with protein product			"""UTP15, U3 small nucleolar ribonucleoprotein, homolog (yeast)"""			12477932	Standard	NM_032175		Approved	FLJ12787, NET21, FLJ23637	uc003kcw.1	Q8TED0	OTTHUMG00000162453	ENST00000296792.4:c.274G>A	5.37:g.72864335G>A	ENSP00000296792:p.Gly92Ser	Somatic		WXS	Illumina GAIIx	Phase_I	B4DU75|B4DXK8|Q6IA60|Q96E08|Q9H9F8	Missense_Mutation	SNP	ENST00000296792.4	37	CCDS34186.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.560954|5.560954	0.96527|0.96527	.|.	.|.	ENSG00000164338|ENSG00000164338	ENST00000296792;ENST00000508491|ENST00000509005	T;T|.	0.21543|.	2.0;2.0|.	5.55|5.55	5.55|5.55	0.83447|0.83447	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.83912|0.83912	0.5357|0.5357	M|M	0.86953|0.86953	2.85|2.85	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	D|D	0.85555|0.85555	0.1224|0.1224	9|5	.|.	.|.	.|.	.|.	19.5283|19.5283	0.95215|0.95215	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	73;92|.	B4DXK8;Q8TED0|.	.;UTP15_HUMAN|.	S|I	92;73|118	ENSP00000296792:G92S;ENSP00000424609:G73S|.	.|.	G|M	+|+	1|3	0|0	UTP15|UTP15	72900091|72900091	1.000000|1.000000	0.71417|0.71417	0.960000|0.960000	0.40013|0.40013	0.993000|0.993000	0.82548|0.82548	9.162000|9.162000	0.94745|0.94745	2.596000|2.596000	0.87737|0.87737	0.655000|0.655000	0.94253|0.94253	GGT|ATG		0.423	UTP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368965.1		NM_032175	
VHL	7428	broad.mit.edu;ucsc.edu	37	3	10191570	10191570	+	Missense_Mutation	SNP	T	T	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr3:10191570T>G	ENST00000256474.2	+	3	1403	c.563T>G	c.(562-564)cTg>cGg	p.L188R	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Missense_Mutation_p.L147R	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	188			L -> P (in VHLD; type I-II). {ECO:0000269|PubMed:9829912}.|L -> Q (in VHLD; type I). {ECO:0000269|PubMed:8956040}.|L -> V (in ECYT2, pheochromocytoma and VHLD; type IIA; dbSNP:rs5030824). {ECO:0000269|PubMed:12000816, ECO:0000269|PubMed:12844285}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.L188P(4)|p.L188fs*14(2)|p.L188Q(2)|p.D187_L188del(2)|p.L188R(2)|p.D187_N193del(1)|p.E189fs*27(1)|p.Y185fs*11(1)|p.D187fs*14(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TACGAAGATCTGGAAGACCAC	0.502		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	16	Substitution - Missense(8)|Deletion - Frameshift(4)|Deletion - In frame(3)|Insertion - Frameshift(1)	kidney(16)	GRCh37	CD962181|CM951299|CM982013	VHL	D|M							76.0	69.0	72.0					3																	10191570		2203	4300	6503	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.563T>G	3.37:g.10191570T>G	ENSP00000256474:p.Leu188Arg	Somatic		WXS	Illumina GAIIx	Phase_I	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.434167	0.83776	.	.	ENSG00000134086	ENST00000256474;ENST00000345392;ENST00000450183	D;D	0.99878	-7.42;-7.42	4.97	4.97	0.65823	von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);von Hippel-Lindau disease tumor suppressor, alpha domain (1);	0.000000	0.64402	D	0.000002	D	0.99799	0.9914	M	0.73962	2.25	0.48975	D	0.999731	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.96566	0.9419	10	0.87932	D	0	-7.586	12.9354	0.58311	0.0:0.0:0.0:1.0	.	147;188	P40337-2;P40337	.;VHL_HUMAN	R	188;147;106	ENSP00000256474:L188R;ENSP00000344757:L147R	ENSP00000256474:L188R	L	+	2	0	VHL	10166570	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.790000	0.69038	2.209000	0.71365	0.533000	0.62120	CTG		0.502	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
CFAP44	55779	broad.mit.edu;ucsc.edu	37	3	113022837	113022837	+	Missense_Mutation	SNP	T	T	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr3:113022837T>G	ENST00000393845.2	-	32	5069	c.5003A>C	c.(5002-5004)aAa>aCa	p.K1668T	WDR52_ENST00000308346.6_Missense_Mutation_p.K271T	NM_001164496.1	NP_001157968.1												p.K816T(1)		breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						TTTGTTAAGTTTTTGCTGCTT	0.448																																																	1	Substitution - Missense(1)	kidney(1)											284.0	215.0	236.0					3																	113022837		692	1591	2283	SO:0001583	missense	55779																														ENST00000393845.2:c.5003A>C	3.37:g.113022837T>G	ENSP00000377428:p.Lys1668Thr	Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000393845.2	37	CCDS54624.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.29|14.29	2.489995|2.489995	0.44249|0.44249	.|.	.|.	ENSG00000206530|ENSG00000206530	ENST00000465636|ENST00000393845;ENST00000308346	.|T;T	.|0.39592	.|1.07;1.07	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	0.986238|0.986238	0.08305|0.08305	N|N	0.966345|0.966345	T|T	0.48926|0.48926	0.1527|0.1527	L|L	0.29908|0.29908	0.895|0.895	0.30290|0.30290	N|N	0.790507|0.790507	.|D	.|0.62365	.|0.991	.|P	.|0.56751	.|0.805	T|T	0.37103|0.37103	-0.9720|-0.9720	6|10	.|0.20519	.|T	.|0.43	-28.0071|-28.0071	14.8967|14.8967	0.70649|0.70649	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1668	.|Q96MT7-2	.|.	N|T	804|1668;271	.|ENSP00000377428:K1668T;ENSP00000311497:K271T	.|ENSP00000311497:K271T	K|K	-|-	3|2	2|0	WDR52|WDR52	114505527|114505527	0.999000|0.999000	0.42202|0.42202	0.973000|0.973000	0.42090|0.42090	0.006000|0.006000	0.05464|0.05464	5.551000|5.551000	0.67274|0.67274	2.154000|2.154000	0.67381|0.67381	0.533000|0.533000	0.62120|0.62120	AAA|AAA		0.448	WDR52-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				
ZAN	7455	hgsc.bcm.edu	37	7	100371476	100371477	+	RNA	INS	-	-	G	rs148800656|rs200325383|rs372381708	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr7:100371476_100371477insG	ENST00000348028.3	+	0	5932_5933				ZAN_ENST00000427578.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000421100.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.?(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			GCTGCTCCGTTTCGGGCCTCAG	0.624													G|-|G|deletion	2230	0.445288	0.2133	0.5418	5008	,	,		17915	0.7867		0.3419	False		,,,				2504	0.4448																1	Unknown(1)	upper_aerodigestive_tract(1)							,	906,2950		139,628,1161					,	4.6	0.9		dbSNP_134	33	2934,5018		557,1820,1599	no	frameshift,frameshift	ZAN	NM_173059.1,NM_003386.1	,	696,2448,2760	A1A1,A1R,RR		36.8964,23.4959,32.5203	,	,		3840,7968						7455			U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"""zonadhesin"""			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100371476_100371477insG		Somatic		WXS	Illumina HiSeq	Phase_I	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Frame_Shift_Ins	INS	ENST00000348028.3	37																																																																																					0.624	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1		NM_003386	
ZNF208	7757	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	22170044	22170044	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr19:22170044C>G	ENST00000397126.4	-	3	348	c.200G>C	c.(199-201)aGa>aCa	p.R67T	ZNF208_ENST00000601773.1_Missense_Mutation_p.R67T|ZNF208_ENST00000597040.1_Missense_Mutation_p.R35T|ZNF208_ENST00000599916.1_Missense_Mutation_p.R67T	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	67	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R67T(3)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				CATCTCATGTCTCTTCATATT	0.418																																																	3	Substitution - Missense(3)	kidney(3)											72.0	75.0	74.0					19																	22170044		2198	4299	6497	SO:0001583	missense	7757			BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"""Zinc fingers, C2H2-type"", ""-"""	12999	protein-coding gene	gene with protein product	"""zinc finger protein 95"""	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.200G>C	19.37:g.22170044C>G	ENSP00000380315:p.Arg67Thr	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	C	4.344	0.063354	0.08388	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.07444	3.19	0.207	0.207	0.15214	Krueppel-associated box (1);	.	.	.	.	T	0.11110	0.0271	.	.	.	0.09310	N	1	D;P	0.58268	0.982;0.868	P;P	0.52554	0.702;0.572	T	0.29941	-0.9995	7	0.28530	T	0.3	.	.	.	.	.	67;67	O43345;F8WEA0	ZN208_HUMAN;.	T	67	ENSP00000380315:R67T	ENSP00000380315:R67T	R	-	2	0	ZNF208	21961884	0.175000	0.23083	0.047000	0.18901	0.047000	0.14425	0.646000	0.24797	0.284000	0.22305	0.289000	0.19496	AGA		0.418	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1		NM_007153	
ZNF544	27300	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	58772269	58772269	+	Silent	SNP	T	T	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr19:58772269T>C	ENST00000596652.1	+	6	531	c.297T>C	c.(295-297)gcT>gcC	p.A99A	ZNF544_ENST00000600220.1_Silent_p.A71A|ZNF544_ENST00000594384.1_3'UTR|ZNF544_ENST00000269829.4_Silent_p.A99A|ZNF544_ENST00000599227.1_3'UTR|CTD-3138B18.4_ENST00000600029.1_Intron|ZNF544_ENST00000599953.1_5'UTR|ZNF544_ENST00000600044.1_Silent_p.A71A|ZNF544_ENST00000415203.2_Silent_p.A71A|CTD-3138B18.5_ENST00000597230.1_RNA|ZNF544_ENST00000596825.1_3'UTR|ZNF544_ENST00000596929.1_Intron|ZNF544_ENST00000595981.1_Intron			Q6NX49	ZN544_HUMAN	zinc finger protein 544	99					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A99A(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|skin(1)|urinary_tract(1)	18		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)		AAGATCGAGCTAGGGAAGAAC	0.463																																																	1	Substitution - coding silent(1)	kidney(1)											62.0	60.0	61.0					19																	58772269		2203	4300	6503	SO:0001819	synonymous_variant	27300			AF020591	CCDS12973.1	19q13.43	2013-01-08				ENSG00000198131		"""Zinc fingers, C2H2-type"", ""-"""	16759	protein-coding gene	gene with protein product	"""zinc finger protein AF020591"""						Standard	NM_014480		Approved	AF020591	uc010euo.3	Q6NX49		ENST00000596652.1:c.297T>C	19.37:g.58772269T>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8K6J1|Q9UEX4	Silent	SNP	ENST00000596652.1	37	CCDS12973.1																																																																																				0.463	ZNF544-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466754.1		NM_014480	
ZNF436	80818	broad.mit.edu	37	1	23696047	23696047	+	5'Flank	SNP	A	A	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr1:23696047A>G	ENST00000314011.4	-	0	0				Y_RNA_ENST00000364535.1_RNA|C1orf213_ENST00000335648.3_Missense_Mutation_p.Y86C|C1orf213_ENST00000518821.1_Intron|ZNF436_ENST00000374608.3_5'Flank|C1orf213_ENST00000437367.2_Intron|C1orf213_ENST00000454117.1_Intron|C1orf213_ENST00000458053.1_Intron	NM_001077195.1	NP_001070663.1	Q9C0F3	ZN436_HUMAN	zinc finger protein 436						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Y86C(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;5.97e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000977)|KIRC - Kidney renal clear cell carcinoma(1967;0.00336)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		AAGCCCAGATATCGTAGGCTG	0.567																																																	1	Substitution - Missense(1)	kidney(1)											66.0	66.0	66.0					1																	23696047		2203	4300	6503	SO:0001631	upstream_gene_variant	148898			AB051497	CCDS233.1	1p36	2013-01-08			ENSG00000125945	ENSG00000125945		"""Zinc fingers, C2H2-type"", ""-"""	20814	protein-coding gene	gene with protein product		611703				11214970	Standard	NM_001077195		Approved	KIAA1710, Zfp46	uc001bgt.3	Q9C0F3	OTTHUMG00000003232		1.37:g.23696047A>G	Exception_encountered	Somatic		WXS	Illumina GAIIx	Phase_I	Q658I9	Missense_Mutation	SNP	ENST00000314011.4	37	CCDS233.1	.	.	.	.	.	.	.	.	.	.	A	3.785	-0.044933	0.07452	.	.	ENSG00000249087	ENST00000335648	.	.	.	3.29	-0.673	0.11373	.	.	.	.	.	T	0.30634	0.0771	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25916	-1.0118	7	0.87932	D	0	.	7.919	0.29835	0.6888:0.0:0.3112:0.0	.	86	Q8NC38	CA213_HUMAN	C	86	.	ENSP00000441287:Y86C	Y	+	2	0	C1orf213	23568634	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.061000	0.14366	-0.472000	0.06881	-1.162000	0.01777	TAT		0.567	ZNF436-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008908.1		NM_030634	
SLC35F6	54978	broad.mit.edu	37	2	27001276	27001276	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr2:27001276G>A	ENST00000344420.5	+	6	1075	c.1013G>A	c.(1012-1014)cGt>cAt	p.R338H	CENPA_ENST00000475662.1_Intron|SLC35F6_ENST00000416475.2_Missense_Mutation_p.R255H	NM_017877.3	NP_060347.2	Q8N357	S35F6_HUMAN	solute carrier family 35, member F6	338					negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|positive regulation of cell proliferation (GO:0008284)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)		p.R338H(1)									GGGCTACACCGTCCGCTGCTG	0.642																																																	1	Substitution - Missense(1)	kidney(1)											64.0	63.0	64.0					2																	27001276		2203	4300	6503	SO:0001583	missense	0			AK075164	CCDS1728.1	2p24.1	2012-12-13	2012-12-07	2012-12-07	ENSG00000213699	ENSG00000213699			26055	protein-coding gene	gene with protein product	"""ANT2-binding protein"", ""transport and golgi organization 9 homolog (Drosophila)"""		"""chromosome 2 open reading frame 18"""	C2orf18		15911612, 19154410	Standard	NM_017877		Approved	FLJ20555, ANT2BP, TANGO9	uc002rhp.1	Q8N357	OTTHUMG00000128407	ENST00000344420.5:c.1013G>A	2.37:g.27001276G>A	ENSP00000345528:p.Arg338His	Somatic		WXS	Illumina GAIIx	Phase_I	D6W543|Q53GK2|Q8NBX6|Q9NWX0	Missense_Mutation	SNP	ENST00000344420.5	37	CCDS1728.1	.	.	.	.	.	.	.	.	.	.	G	13.63	2.295371	0.40594	.	.	ENSG00000213699	ENST00000344420;ENST00000416475	.	.	.	5.72	1.26	0.21427	.	0.231174	0.41097	N	0.000956	T	0.54727	0.1876	M	0.61703	1.905	0.80722	D	1	B;B;B	0.14438	0.002;0.01;0.002	B;B;B	0.04013	0.001;0.001;0.001	T	0.51301	-0.8723	9	0.44086	T	0.13	-8.3975	9.825	0.40905	0.4037:0.0:0.5963:0.0	.	191;255;338	E7ET27;B4DLH2;Q8N357	.;.;CB018_HUMAN	H	338;255	.	ENSP00000345528:R338H	R	+	2	0	C2orf18	26854780	0.990000	0.36364	0.641000	0.29422	0.729000	0.41735	1.476000	0.35420	0.323000	0.23307	0.561000	0.74099	CGT		0.642	SLC35F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250187.2		NM_017877	
Unknown	0	broad.mit.edu	37	Y	21154403	21154403	+	IGR	SNP	T	T	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chrY:21154403T>G								TTTY14 (114289 upstream) : RNU6-255P (26465 downstream)																							AGACTGGCTGTTGACTGCAGG	0.507																																																	0																																										SO:0001628	intergenic_variant	100133941																															Y.37:g.21154403T>G		Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP		37																																																																																				0	0.507									
DENND2C	163259	broad.mit.edu	37	1	115151368	115151368	+	Missense_Mutation	SNP	A	A	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr1:115151368A>G	ENST00000393274.1	-	10	2121	c.1496T>C	c.(1495-1497)cTa>cCa	p.L499P	DENND2C_ENST00000393276.3_Missense_Mutation_p.L442P|DENND2C_ENST00000393277.1_Missense_Mutation_p.L499P|DENND2C_ENST00000481894.1_5'UTR	NM_001256404.1	NP_001243333.1	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	499					positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.L442P(1)		NS(2)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|skin(3)	37	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTTCTTCTGTAGAGACACCAC	0.473																																																	1	Substitution - Missense(1)	kidney(1)											155.0	146.0	149.0					1																	115151368		2203	4300	6503	SO:0001583	missense	163259				CCDS875.1, CCDS58018.1	1p13.2-p13.1	2012-10-03			ENSG00000175984	ENSG00000175984		"""DENN/MADD domain containing"""	24748	protein-coding gene	gene with protein product							Standard	NM_198459		Approved	FLJ37099, DKFZp686G0351, DKFZp779P1149, dJ1156J9.1, RP5-1156J9.1	uc001efd.1	Q68D51	OTTHUMG00000011893	ENST00000393274.1:c.1496T>C	1.37:g.115151368A>G	ENSP00000376955:p.Leu499Pro	Somatic		WXS	Illumina GAIIx	Phase_I	B1AL26|Q5TCX6|Q6P3R3	Missense_Mutation	SNP	ENST00000393274.1	37	CCDS58018.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.674077	0.88445	.	.	ENSG00000175984	ENST00000393276;ENST00000393274;ENST00000369540;ENST00000393277	T;T;T	0.16743	3.4;3.08;2.32	5.39	5.39	0.77823	uDENN (2);	0.000000	0.64402	D	0.000001	T	0.30603	0.0770	M	0.69248	2.105	0.80722	D	1	D;P	0.89917	1.0;0.951	D;P	0.68943	0.961;0.858	T	0.07751	-1.0756	10	0.87932	D	0	.	15.428	0.75069	1.0:0.0:0.0:0.0	.	499;442	Q68D51;Q68D51-3	DEN2C_HUMAN;.	P	442;499;499;499	ENSP00000376957:L442P;ENSP00000376955:L499P;ENSP00000376958:L499P	ENSP00000358553:L499P	L	-	2	0	DENND2C	114952891	1.000000	0.71417	0.963000	0.40424	0.995000	0.86356	8.861000	0.92277	2.051000	0.60960	0.533000	0.62120	CTA		0.473	DENND2C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000314822.1		NM_198459	
DHX57	90957	broad.mit.edu	37	2	39088979	39088979	+	Splice_Site	SNP	C	C	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr2:39088979C>A	ENST00000295373.6	-	5	699	c.573G>T	c.(571-573)agG>agT	p.R191S	AC018693.6_ENST00000442829.1_RNA|DHX57_ENST00000479345.2_5'UTR	NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	191	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.						ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R191S(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				TGAAACCATACCTGTCAAGGG	0.393																																					Melanoma(191;1090 2095 4375 23729 47341)												1	Substitution - Missense(1)	kidney(1)											42.0	39.0	40.0					2																	39088979		2203	4298	6501	SO:0001630	splice_region_variant	90957			AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"""DEAH-boxes"""	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.573-1G>T	2.37:g.39088979C>A		Somatic		WXS	Illumina GAIIx	Phase_I	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Missense_Mutation	SNP	ENST00000295373.6	37	CCDS1800.1	.	.	.	.	.	.	.	.	.	.	C	18.53	3.643374	0.67244	.	.	ENSG00000163214	ENST00000295373;ENST00000355320;ENST00000417233	T	0.51817	0.69	5.41	-0.819	0.10829	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (1);UBA-like (1);	0.000000	0.56097	D	0.000024	T	0.42585	0.1209	N	0.25201	0.72	0.58432	D	0.999994	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.995	T	0.42965	-0.9420	10	0.09590	T	0.72	.	7.0248	0.24934	0.0:0.5609:0.1104:0.3287	.	191;191	Q6P158-2;Q6P158	.;DHX57_HUMAN	S	191;89;89	ENSP00000295373:R191S	ENSP00000295373:R191S	R	-	3	2	DHX57	38942483	0.999000	0.42202	0.994000	0.49952	0.964000	0.63967	0.692000	0.25482	0.092000	0.17331	0.655000	0.94253	AGG		0.393	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2		NM_145646	Missense_Mutation
DNMT1	1786	broad.mit.edu	37	19	10257171	10257171	+	Missense_Mutation	SNP	T	T	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr19:10257171T>G	ENST00000340748.4	-	27	2937	c.2702A>C	c.(2701-2703)gAg>gCg	p.E901A	DNMT1_ENST00000359526.4_Missense_Mutation_p.E917A|DNMT1_ENST00000589538.1_5'Flank|DNMT1_ENST00000540357.1_Missense_Mutation_p.E901A			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	901					cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.E901A(1)		breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	TTGCCTCATCTCAGCCAGACG	0.577																																																	1	Substitution - Missense(1)	kidney(1)											59.0	59.0	59.0					19																	10257171		2203	4300	6503	SO:0001583	missense	1786			X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.2702A>C	19.37:g.10257171T>G	ENSP00000345739:p.Glu901Ala	Somatic		WXS	Illumina GAIIx	Phase_I	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Missense_Mutation	SNP	ENST00000340748.4	37	CCDS12228.1	.	.	.	.	.	.	.	.	.	.	T	17.81	3.479789	0.63849	.	.	ENSG00000130816	ENST00000359526;ENST00000540357;ENST00000340748;ENST00000541266	T;T;T	0.24723	1.84;1.84;1.84	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.29976	0.0750	L	0.56769	1.78	0.80722	D	1	B;B;B	0.23891	0.069;0.069;0.093	B;B;B	0.29862	0.108;0.108;0.05	T	0.04495	-1.0947	10	0.29301	T	0.29	.	14.9998	0.71462	0.0:0.0:0.0:1.0	.	901;917;901	F5GX68;P26358-2;P26358	.;.;DNMT1_HUMAN	A	917;901;901;769	ENSP00000352516:E917A;ENSP00000440457:E901A;ENSP00000345739:E901A	ENSP00000345739:E901A	E	-	2	0	DNMT1	10118171	1.000000	0.71417	0.933000	0.37362	0.990000	0.78478	6.034000	0.70933	2.181000	0.69327	0.533000	0.62120	GAG		0.577	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1		NM_001379	
FKBP15	23307	broad.mit.edu	37	9	115932150	115932151	+	In_Frame_Ins	INS	-	-	TTC	rs370557763|rs113480096|rs62620695	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr9:115932150_115932151insTTC	ENST00000238256.3	-	26	2955_2956	c.2838_2839insGAA	c.(2836-2841)gaaaaa>gaaGAAaaa	p.946_947insE		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	946					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						tcttctgctttttcttcttctt	0.525																																																	0																																										SO:0001652	inframe_insertion	23307			AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.2836_2838dupGAA	9.37:g.115932157_115932159dupTTC	ENSP00000238256:p.Glu946_Glu946dup	Somatic		WXS	Illumina GAIIx	Phase_I	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	In_Frame_Ins	INS	ENST00000238256.3	37	CCDS48007.1																																																																																				0.525	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			NM_015258	
HTRA3	94031	broad.mit.edu	37	4	8288470	8288470	+	Missense_Mutation	SNP	A	A	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr4:8288470A>G	ENST00000307358.2	+	3	872	c.668A>G	c.(667-669)gAc>gGc	p.D223G	HTRA3_ENST00000382512.3_Missense_Mutation_p.D223G	NM_053044.3	NP_444272.1	P83110	HTRA3_HUMAN	HtrA serine peptidase 3	223	Serine protease.				negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.D223G(1)		central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|prostate(1)|urinary_tract(1)	18						AAAGACATCGACAAGAAGTCG	0.622																																																	1	Substitution - Missense(1)	kidney(1)											78.0	65.0	70.0					4																	8288470		2203	4300	6503	SO:0001583	missense	94031			AY040094	CCDS3400.1, CCDS75105.1	4p16.1	2008-02-05			ENSG00000170801	ENSG00000170801			30406	protein-coding gene	gene with protein product	"""pregnancy-related serine protease"""	608785				12513693, 14500695	Standard	XM_005248040		Approved	Tasp, Prsp	uc003gla.3	P83110	OTTHUMG00000090561	ENST00000307358.2:c.668A>G	4.37:g.8288470A>G	ENSP00000303766:p.Asp223Gly	Somatic		WXS	Illumina GAIIx	Phase_I	Q7Z7A2	Missense_Mutation	SNP	ENST00000307358.2	37	CCDS3400.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.135120	0.77662	.	.	ENSG00000170801	ENST00000307358;ENST00000382512	D;D	0.90732	-2.72;-2.72	4.08	4.08	0.47627	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	0.000000	0.85682	D	0.000000	D	0.94545	0.8243	M	0.88775	2.98	0.80722	D	1	P;B	0.48162	0.906;0.228	P;B	0.55667	0.781;0.069	D	0.95267	0.8374	10	0.87932	D	0	-12.714	13.0418	0.58904	1.0:0.0:0.0:0.0	.	223;223	P83110;P83110-2	HTRA3_HUMAN;.	G	223	ENSP00000303766:D223G;ENSP00000371952:D223G	ENSP00000303766:D223G	D	+	2	0	HTRA3	8339370	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	8.562000	0.90719	1.488000	0.48433	0.379000	0.24179	GAC		0.622	HTRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092669.1		NM_053044	
Unknown	0	broad.mit.edu	37	1	16974549	16974549	+	IGR	SNP	C	C	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr1:16974549C>G								CROCCP2 (13495 upstream) : RNU1-3 (18730 downstream)																							GGGCTGAGTGCAGCGCCTGCT	0.692																																																	0																																										SO:0001628	intergenic_variant	11209																															1.37:g.16974549C>G		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.692									
MUC4	4585	broad.mit.edu	37	3	195507324	195507324	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr3:195507324G>C	ENST00000463781.3	-	2	11586	c.11127C>G	c.(11125-11127)caC>caG	p.H3709Q	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H3709Q|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.H3709Q(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGTGTGACCTGAGG	0.572																																																	1	Substitution - Missense(1)	kidney(1)											66.0	57.0	59.0					3																	195507324		660	1591	2251	SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11127C>G	3.37:g.195507324G>C	ENSP00000417498:p.His3709Gln	Somatic		WXS	Illumina GAIIx	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	4.440	0.081383	0.08533	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32753	1.52;1.44	0.885	-1.56	0.08532	.	.	.	.	.	T	0.22244	0.0536	N	0.19112	0.55	0.09310	N	1	P	0.44006	0.824	P	0.48770	0.589	T	0.18116	-1.0347	8	.	.	.	.	5.328	0.15917	0.2604:0.0:0.7396:0.0	.	3581	E7ESK3	.	Q	3709	ENSP00000417498:H3709Q;ENSP00000420243:H3709Q	.	H	-	3	2	MUC4	196992103	0.869000	0.29996	0.010000	0.14722	0.046000	0.14306	1.281000	0.33214	-0.535000	0.06307	0.064000	0.15345	CAC		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC4	4585	broad.mit.edu	37	3	195509127	195509127	+	Silent	SNP	A	A	G	rs71637183|rs200879287		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr3:195509127A>G	ENST00000463781.3	-	2	9783	c.9324T>C	c.(9322-9324)acT>acC	p.T3108T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.T3108T|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T3108T(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGGGCTAGTGACAGGAA	0.587																																																	1	Substitution - coding silent(1)	kidney(1)											19.0	11.0	13.0					3																	195509127		669	1553	2222	SO:0001819	synonymous_variant	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9324T>C	3.37:g.195509127A>G		Somatic		WXS	Illumina GAIIx	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																				0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC6	4588	broad.mit.edu	37	11	1021245	1021245	+	Missense_Mutation	SNP	C	C	T	rs202188897	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr11:1021245C>T	ENST00000421673.2	-	27	3609	c.3559G>A	c.(3559-3561)Gac>Aac	p.D1187N		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1187					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)	p.D1187N(2)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TCCTCGTGGTCGAAGTACTCA	0.642													c|||	5	0.000998403	0.0	0.0	5008	,	,		15857	0.001		0.001	False		,,,				2504	0.0031																2	Substitution - Missense(2)	kidney(2)							ASN/ASP	0,4236		0,0,2118	61.0	67.0	65.0		3559	1.8	0.9	11		65	2,8418		0,2,4208	yes	missense	MUC6	NM_005961.2	23	0,2,6326	TT,TC,CC		0.0238,0.0,0.0158	possibly-damaging	1187/2440	1021245	2,12654	2118	4210	6328	SO:0001583	missense	4588			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.3559G>A	11.37:g.1021245C>T	ENSP00000406861:p.Asp1187Asn	Somatic		WXS	Illumina GAIIx	Phase_I	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	c	13.23	2.174891	0.38413	0.0	2.38E-4	ENSG00000184956	ENST00000421673	T	0.22945	1.93	2.75	1.8	0.24995	.	.	.	.	.	T	0.14830	0.0358	L	0.41573	1.285	0.24816	N	0.992619	P	0.46784	0.884	B	0.31245	0.126	T	0.12344	-1.0551	9	0.36615	T	0.2	.	7.0795	0.25223	0.0:0.862:0.0:0.138	.	1187	Q6W4X9	MUC6_HUMAN	N	1187	ENSP00000406861:D1187N	ENSP00000406861:D1187N	D	-	1	0	MUC6	1011245	0.999000	0.42202	0.860000	0.33809	0.884000	0.51177	2.316000	0.43761	0.273000	0.22049	0.290000	0.19541	GAC		0.642	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2		XM_290540	
NBPF10	100132406	broad.mit.edu	37	1	145311931	145311931	+	Missense_Mutation	SNP	C	C	T	rs200450624	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr1:145311931C>T	ENST00000369338.1	+	10	1370	c.1180C>T	c.(1180-1182)Cgt>Tgt	p.R394C	NBPF10_ENST00000342960.5_Intron|NBPF10_ENST00000369339.3_Intron|RP11-458D21.5_ENST00000468030.1_Intron			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	667						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.R394C(1)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GGAGCAACAGCGTGTTGGCTT	0.453																																																	1	Substitution - Missense(1)	kidney(1)											11.0	14.0	13.0					1																	145311931		689	1581	2270	SO:0001583	missense	100132406			BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369338.1:c.1180C>T	1.37:g.145311931C>T	ENSP00000358344:p.Arg394Cys	Somatic		WXS	Illumina GAIIx	Phase_I	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369338.1	37		.	.	.	.	.	.	.	.	.	.	.	1.619	-0.521902	0.04171	.	.	ENSG00000163386	ENST00000369338;ENST00000369364	T	0.07021	3.23	0.532	-1.06	0.10002	.	.	.	.	.	T	0.03053	0.0090	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.41448	-0.9508	5	0.66056	D	0.02	.	.	.	.	.	.	.	.	C	394;71	ENSP00000358344:R394C	ENSP00000358344:R394C	R	+	1	0	NBPF10	144023288	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.125000	0.10579	-0.446000	0.07149	0.064000	0.15345	CGT		0.453	NBPF10-003	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038552.1		NM_001039703	
OR4N2	390429	broad.mit.edu	37	14	20296229	20296229	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr14:20296229C>A	ENST00000315947.1	+	1	622	c.622C>A	c.(622-624)Ctc>Atc	p.L208I	OR4N2_ENST00000568211.1_3'UTR	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	208						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L208I(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CCTGATGACACTCCTGTGCTT	0.517																																																	1	Substitution - Missense(1)	kidney(1)											135.0	134.0	135.0					14																	20296229		2203	4300	6503	SO:0001583	missense	390429				CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"""GPCR / Class A : Olfactory receptors"""	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.622C>A	14.37:g.20296229C>A	ENSP00000319601:p.Leu208Ile	Somatic		WXS	Illumina GAIIx	Phase_I	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	37	CCDS32022.1	.	.	.	.	.	.	.	.	.	.	.	10.98	1.504857	0.26949	.	.	ENSG00000176294	ENST00000315947	T	0.39406	1.08	4.52	3.62	0.41486	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43919	D	0.000512	T	0.42314	0.1197	L	0.48362	1.52	0.09310	N	1	P	0.39903	0.694	P	0.49683	0.619	T	0.19418	-1.0306	10	0.38643	T	0.18	-12.3251	6.1749	0.20439	0.0:0.7981:0.0:0.2019	.	208	Q8NGD1	OR4N2_HUMAN	I	208	ENSP00000319601:L208I	ENSP00000319601:L208I	L	+	1	0	OR4N2	19366069	0.000000	0.05858	0.022000	0.16811	0.377000	0.30045	-0.872000	0.04219	2.483000	0.83821	0.585000	0.79938	CTC		0.517	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2			
SMG1P7	100506060	broad.mit.edu	37	16	70268080	70268081	+	RNA	DNP	TG	TG	CA			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr16:70268080_70268081TG>CA	ENST00000459379.1	-	0	0																											GTCTTACTGTTGGCTAAAAGGC	0.376																																																	0																																												0																														Exception_encountered	16.37:g.70268080_70268081delinsCA		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000459379.1	37																																																																																					0.376	snoU13.216-201	NOVEL	basic	snoRNA	snoRNA				
WARS	7453	broad.mit.edu	37	14	100809696	100809696	+	Silent	SNP	A	A	G			TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr14:100809696A>G	ENST00000355338.2	-	8	1473	c.855T>C	c.(853-855)gcT>gcC	p.A285A	RP11-638I2.9_ENST00000556212.1_RNA|RP11-638I2.8_ENST00000557226.1_RNA|WARS_ENST00000344102.5_Silent_p.A244A|WARS_ENST00000392882.2_Silent_p.A285A|WARS_ENST00000556645.1_Silent_p.A244A|WARS_ENST00000557135.1_Silent_p.A285A|WARS_ENST00000358655.4_Silent_p.A244A	NM_173701.1	NP_776049.1	P23381	SYWC_HUMAN	tryptophanyl-tRNA synthetase	285					angiogenesis (GO:0001525)|gene expression (GO:0010467)|negative regulation of cell proliferation (GO:0008285)|regulation of angiogenesis (GO:0045765)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)|tryptophanyl-tRNA aminoacylation (GO:0006436)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tryptophan-tRNA ligase activity (GO:0004830)	p.A285A(1)		breast(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	20		all_cancers(154;0.00223)|all_lung(585;2.48e-06)|all_epithelial(191;0.000564)|Melanoma(154;0.152)			L-Tryptophan(DB00150)	AGGAGGGAGCAGCCTGGATGG	0.453																																																	1	Substitution - coding silent(1)	kidney(1)											104.0	89.0	94.0					14																	100809696		2203	4300	6503	SO:0001819	synonymous_variant	7453			M61715	CCDS9960.1, CCDS9961.1	14q32.2	2014-03-19			ENSG00000140105	ENSG00000140105	6.1.1.2	"""Aminoacyl tRNA synthetases / Class I"""	12729	protein-coding gene	gene with protein product	"""tryptophan tRNA ligase 1, cytoplasmic"""	191050		IFI53		1537332, 1763065	Standard	NM_004184		Approved	IFP53	uc001yhl.1	P23381	OTTHUMG00000171572	ENST00000355338.2:c.855T>C	14.37:g.100809696A>G		Somatic		WXS	Illumina GAIIx	Phase_I	A6NGN1|A6NID3|P78535|Q502Y0|Q53XB6|Q9UDI5|Q9UDL3	Silent	SNP	ENST00000355338.2	37	CCDS9960.1	.	.	.	.	.	.	.	.	.	.	A	11.48	1.650191	0.29336	.	.	ENSG00000140105	ENST00000554601	.	.	.	6.07	-6.54	0.01860	.	.	.	.	.	T	0.48114	0.1482	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51965	-0.8638	4	.	.	.	-3.2056	7.8711	0.29567	0.6946:0.096:0.1131:0.0963	.	.	.	.	P	38	.	.	L	-	2	0	WARS	99879449	0.000000	0.05858	0.751000	0.31187	0.987000	0.75469	-1.836000	0.01690	-0.971000	0.03564	-1.007000	0.02485	CTG		0.453	WARS-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414236.1		NM_004184	
DDX11L1	100287102	broad.mit.edu	37	1	14976	14976	+	RNA	SNP	G	G	A	rs71252251	byFrequency	TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr1:14976G>A	ENST00000456328.2	+	0	1657					NR_046018.2|NR_051986.1				DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1																		CTACCCTTGCGCCTCATGACC	0.582																																																	0																																												653635			AM992871		1p36.33	2012-02-23	2012-02-23		ENSG00000223972	ENSG00000223972			37102	pseudogene	pseudogene			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 like 1"""			19476624	Standard	NR_046018		Approved		uc010nxq.1		OTTHUMG00000000961		1.37:g.14976G>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000456328.2	37																																																																																					0.582	DDX11L1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000362751.1			
CFAP44	55779	broad.mit.edu	37	3	113049451	113049451	+	Missense_Mutation	SNP	A	A	C	rs79365690|rs370566069		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr3:113049451A>C	ENST00000393845.2	-	26	3746	c.3680T>G	c.(3679-3681)gTt>gGt	p.V1227G	WDR52_ENST00000308346.6_5'Flank	NM_001164496.1	NP_001157968.1												p.V375G(5)		breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						TTCCTCAACAACAGCCACTTT	0.408																																																	5	Substitution - Missense(5)	kidney(5)																																								SO:0001583	missense	55779																														ENST00000393845.2:c.3680T>G	3.37:g.113049451A>C	ENSP00000377428:p.Val1227Gly	Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000393845.2	37	CCDS54624.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.22|14.22	2.469473|2.469473	0.43839|0.43839	.|.	.|.	ENSG00000206530|ENSG00000206530	ENST00000465636|ENST00000393845	.|T	.|0.11821	.|2.74	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	.|0.643254	.|0.11770	.|U	.|0.531195	T|T	0.27349|0.27349	0.0671|0.0671	L|L	0.56769|0.56769	1.78|1.78	0.80722|0.80722	D|D	1|1	.|D	.|0.57899	.|0.981	.|P	.|0.56563	.|0.801	T|T	0.01169|0.01169	-1.1430|-1.1430	5|10	.|0.87932	.|D	.|0	-19.8203|-19.8203	8.8767|8.8767	0.35350|0.35350	0.854:0.0:0.146:0.0|0.854:0.0:0.146:0.0	.|.	.|1227	.|Q96MT7-2	.|.	W|G	363|1227	.|ENSP00000377428:V1227G	.|ENSP00000377428:V1227G	C|V	-|-	3|2	2|0	WDR52|WDR52	114532141|114532141	0.947000|0.947000	0.32204|0.32204	0.873000|0.873000	0.34254|0.34254	0.340000|0.340000	0.28889|0.28889	3.859000|3.859000	0.55987|0.55987	2.081000|2.081000	0.62600|0.62600	0.459000|0.459000	0.35465|0.35465	TGT|GTT		0.408	WDR52-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				
ZNF98	148198	broad.mit.edu	37	19	22574468	22574468	+	Silent	SNP	G	G	A	rs553087662		TCGA-B0-4712-01A-01D-1501-10	TCGA-B0-4712-11A-02D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	032b33f8-ff79-47de-8cb2-d744eab8bd1a	b7ef4bb0-2d50-47f1-80df-3aae8da90df4	g.chr19:22574468G>A	ENST00000357774.5	-	4	1690	c.1569C>T	c.(1567-1569)tgC>tgT	p.C523C		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	523					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C523C(2)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				AGGCTTTGCCGCATTCTTCAC	0.383													a|||	1	0.000199681	0.0	0.0	5008	,	,		20081	0.0		0.001	False		,,,				2504	0.0																2	Substitution - coding silent(2)	kidney(2)											75.0	63.0	67.0					19																	22574468		2178	4275	6453	SO:0001819	synonymous_variant	148198				CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"""Zinc fingers, C2H2-type"", ""-"""	13174	protein-coding gene	gene with protein product	"""zinc finger protein 739"""	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.1569C>T	19.37:g.22574468G>A		Somatic		WXS	Illumina GAIIx	Phase_I		Silent	SNP	ENST00000357774.5	37	CCDS46031.1																																																																																				0.383	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1		NM_001098626	
