#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
Unknown	0	broad.mit.edu	37	14	106974586	106974586	+	IGR	SNP	T	T	G			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr14:106974586T>G								IGHV1-46 (6798 upstream) : IGHV3-48 (19227 downstream)																							TGGCGTTGTCTCTGGAGATGG	0.507																																																	0																																										SO:0001628	intergenic_variant	8755																															14.37:g.106974586T>G		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.507									
BCO2	83875	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	112072899	112072899	+	Missense_Mutation	SNP	G	G	C			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr11:112072899G>C	ENST00000357685.5	+	8	1315	c.1180G>C	c.(1180-1182)Gaa>Caa	p.E394Q	BCO2_ENST00000393032.2_Missense_Mutation_p.E360Q|BCO2_ENST00000532593.1_Missense_Mutation_p.E289Q|BCO2_ENST00000531169.1_Missense_Mutation_p.E360Q|BCO2_ENST00000438022.1_Missense_Mutation_p.E360Q|BCO2_ENST00000361053.4_Missense_Mutation_p.E321Q|BCO2_ENST00000526088.1_Missense_Mutation_p.E360Q			Q9BYV7	BCDO2_HUMAN	beta-carotene oxygenase 2	394					carotene catabolic process (GO:0016121)|carotene metabolic process (GO:0016119)|carotenoid metabolic process (GO:0016116)|oxidation-reduction process (GO:0055114)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of reactive oxygen species metabolic process (GO:2000377)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	intracellular (GO:0005622)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)	p.E394Q(1)		NS(1)|breast(1)|kidney(3)|large_intestine(1)|lung(9)|skin(1)	16						GAAGGCTGGGGAAGGGCTTGA	0.398																																					GBM(177;1916 2099 21049 29541 39946)												1	Substitution - Missense(1)	kidney(1)											80.0	78.0	79.0					11																	112072899		2201	4297	6498	SO:0001583	missense	83875			AJ290393	CCDS8358.2, CCDS41716.1, CCDS58181.1, CCDS58182.1, CCDS58183.1	11q23.1	2014-05-12	2008-04-15	2008-04-15	ENSG00000197580	ENSG00000197580	1.13.11.71		18503	protein-coding gene	gene with protein product	"""beta-carotene 9',10' oxygenase"", ""carotenoid-9',10'-cleaving dioxygenase"""	611740	"""beta-carotene dioxygenase 2"""	BCDO2		11278918, 15983114, 15949678	Standard	NM_031938		Approved	FLJ34464, B-DIOX-II	uc001pnf.3	Q9BYV7	OTTHUMG00000167155	ENST00000357685.5:c.1180G>C	11.37:g.112072899G>C	ENSP00000350314:p.Glu394Gln	Somatic		WXS	Illumina HiSeq	Phase_I	B0YIX5|B4DNC3|E9PBI8|E9PJJ1|Q8IUS0|Q96JC8|Q96JY5	Missense_Mutation	SNP	ENST00000357685.5	37	CCDS8358.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.55|12.55	1.971159|1.971159	0.34754|0.34754	.|.	.|.	ENSG00000197580|ENSG00000197580	ENST00000357685;ENST00000393032;ENST00000361053;ENST00000438022;ENST00000526088;ENST00000532593;ENST00000531169|ENST00000530677	D;D;D;D;D;D;D|D	0.95137|0.95069	-3.62;-3.61;-3.61;-3.61;-3.61;-3.49;-3.61|-3.6	5.5|5.5	2.35|2.35	0.29111|0.29111	.|.	0.363862|.	0.33916|.	N|.	0.004440|.	D|D	0.91754|0.91754	0.7392|0.7392	L|L	0.41906|0.41906	1.305|1.305	0.36458|0.36458	D|D	0.866497|0.866497	B;B;B;B|.	0.28208|.	0.086;0.203;0.086;0.057|.	B;B;B;B|.	0.35353|.	0.142;0.123;0.201;0.042|.	D|D	0.89234|0.89234	0.3579|0.3579	10|7	0.37606|0.40728	T|T	0.19|0.16	-32.2856|-32.2856	6.9346|6.9346	0.24459|0.24459	0.1519:0.2572:0.5908:0.0|0.1519:0.2572:0.5908:0.0	.|.	371;321;394;221|.	C9JEZ9;E9PBI8;Q9BYV7;Q8NAZ7|.	.;.;BCDO2_HUMAN;.|.	Q|A	394;360;321;360;360;289;360|161	ENSP00000350314:E394Q;ENSP00000376752:E360Q;ENSP00000354338:E321Q;ENSP00000414843:E360Q;ENSP00000436615:E360Q;ENSP00000431802:E289Q;ENSP00000437053:E360Q|ENSP00000432045:G161A	ENSP00000350314:E394Q|ENSP00000432045:G161A	E|G	+|+	1|2	0|0	BCO2|BCO2	111578109|111578109	1.000000|1.000000	0.71417|0.71417	0.811000|0.811000	0.32455|0.32455	0.857000|0.857000	0.48899|0.48899	3.101000|3.101000	0.50283|0.50283	0.644000|0.644000	0.30656|0.30656	0.591000|0.591000	0.81541|0.81541	GAA|GGA		0.398	BCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256570.3		NM_001037290	
BHLHB9	80823	broad.mit.edu;hgsc.bcm.edu	37	X	102004560	102004560	+	Missense_Mutation	SNP	G	G	A			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chrX:102004560G>A	ENST00000372735.1	+	4	1222	c.637G>A	c.(637-639)Gac>Aac	p.D213N	BHLHB9_ENST00000448867.1_Missense_Mutation_p.D213N|BHLHB9_ENST00000361229.4_Missense_Mutation_p.D213N|BHLHB9_ENST00000447531.1_Missense_Mutation_p.D213N|BHLHB9_ENST00000457056.1_Missense_Mutation_p.D213N			Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class B, 9	213					learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neurogenesis (GO:0050769)|positive regulation of synapse assembly (GO:0051965)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)	p.D213N(1)		cervix(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						TAGGCCCAAGGACTGGTCTGA	0.463																																																	1	Substitution - Missense(1)	kidney(1)											117.0	121.0	120.0					X																	102004560		2203	4300	6503	SO:0001583	missense	80823			AB051488	CCDS14502.1	Xq23	2014-03-21			ENSG00000198908	ENSG00000198908		"""Basic helix-loop-helix proteins"", ""Armadillo repeat containing"""	29353	protein-coding gene	gene with protein product		300921				11214970, 15034937, 16221301	Standard	NM_030639		Approved	p60TRP, KIAA1701, GASP3	uc011mrv.2	Q6PI77	OTTHUMG00000022060	ENST00000372735.1:c.637G>A	X.37:g.102004560G>A	ENSP00000361820:p.Asp213Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q9C0G2	Missense_Mutation	SNP	ENST00000372735.1	37	CCDS14502.1	.	.	.	.	.	.	.	.	.	.	G	13.12	2.142946	0.37825	.	.	ENSG00000198908	ENST00000457056;ENST00000361229;ENST00000447531;ENST00000448867;ENST00000372735	T;T;T;T;T	0.12255	2.7;2.7;2.7;2.7;2.7	4.59	3.73	0.42828	.	0.315958	0.22869	N	0.054653	T	0.14570	0.0352	L	0.51422	1.61	0.26891	N	0.967312	D	0.54047	0.964	P	0.45310	0.476	T	0.08472	-1.0720	9	.	.	.	-17.8257	7.6784	0.28499	0.1138:0.0:0.8862:0.0	.	213	Q6PI77	BHLH9_HUMAN	N	213	ENSP00000403226:D213N;ENSP00000354675:D213N;ENSP00000405893:D213N;ENSP00000391722:D213N;ENSP00000361820:D213N	.	D	+	1	0	BHLHB9	101891216	1.000000	0.71417	0.936000	0.37596	0.959000	0.62525	2.247000	0.43151	1.283000	0.44513	0.597000	0.82753	GAC		0.463	BHLHB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057630.1		NM_030639	
SLX4IP	128710	broad.mit.edu;hgsc.bcm.edu	37	20	10603312	10603312	+	Missense_Mutation	SNP	A	A	C			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr20:10603312A>C	ENST00000334534.5	+	8	692	c.512A>C	c.(511-513)aAa>aCa	p.K171T		NM_001009608.1	NP_001009608.1	Q5VYV7	SLX4I_HUMAN	SLX4 interacting protein	171								p.K171T(1)									TTCAGTGTGAAAAGAACTGAA	0.418																																																	1	Substitution - Missense(1)	kidney(1)											47.0	45.0	46.0					20																	10603312		2203	4300	6503	SO:0001583	missense	0			AL035456	CCDS33439.1	20p12	2012-10-30	2012-10-30	2012-10-30	ENSG00000149346	ENSG00000149346			16225	protein-coding gene	gene with protein product		615958	"""chromosome 20 open reading frame 94"""	C20orf94		19596235	Standard	XM_005260664		Approved	dJ1099D15.3	uc010zre.2	Q5VYV7	OTTHUMG00000031873	ENST00000334534.5:c.512A>C	20.37:g.10603312A>C	ENSP00000335557:p.Lys171Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q05CG2|Q05CT9	Missense_Mutation	SNP	ENST00000334534.5	37	CCDS33439.1	.	.	.	.	.	.	.	.	.	.	A	10.86	1.468654	0.26335	.	.	ENSG00000149346	ENST00000334534	T	0.55760	0.5	5.75	2.17	0.27698	.	0.356586	0.28338	N	0.015716	T	0.47838	0.1467	L	0.43152	1.355	0.21841	N	0.999513	D	0.56746	0.977	P	0.51016	0.656	T	0.41466	-0.9507	10	0.72032	D	0.01	-1.5701	4.3636	0.11213	0.6463:0.0:0.219:0.1347	.	171	Q5VYV7	CT094_HUMAN	T	171	ENSP00000335557:K171T	ENSP00000335557:K171T	K	+	2	0	C20orf94	10551312	1.000000	0.71417	0.988000	0.46212	0.266000	0.26442	1.586000	0.36611	0.094000	0.17404	0.454000	0.30748	AAA		0.418	SLX4IP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078000.3		NM_001009608	
C2orf78	388960	hgsc.bcm.edu	37	2	74043341	74043342	+	Frame_Shift_Ins	INS	-	-	C	rs74479148|rs148619800		TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr2:74043341_74043342insC	ENST00000409561.1	+	3	2112_2113	c.1991_1992insC	c.(1990-1995)aaccgcfs	p.R665fs		NM_001080474.1	NP_001073943.1	A6NCI8	CB078_HUMAN	chromosome 2 open reading frame 78	665										cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|soft_tissue(1)|urinary_tract(1)	34						AACACCCAAAACCGCCAGCCAT	0.495																																																	0																																										SO:0001589	frameshift_variant	388960			AC092653, AC136006, AK125975	CCDS46338.1	2p13.2	2008-07-18			ENSG00000187833	ENSG00000187833			34349	protein-coding gene	gene with protein product							Standard	NM_001080474		Approved	FLJ43987, hCG1989538, COG5373	uc002sjr.1	A6NCI8	OTTHUMG00000152819	ENST00000409561.1:c.1993dupC	2.37:g.74043343_74043343dupC	ENSP00000387124:p.Arg665fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Ins	INS	ENST00000409561.1	37	CCDS46338.1																																																																																				0.495	C2orf78-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328083.1		NM_001080474	
NDNF	79625	broad.mit.edu;ucsc.edu	37	4	121958431	121958431	+	Missense_Mutation	SNP	C	C	A			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr4:121958431C>A	ENST00000379692.4	-	4	1221	c.695G>T	c.(694-696)aGt>aTt	p.S232I	NDNF_ENST00000506900.1_5'UTR	NM_024574.3	NP_078850.3	Q8TB73	NDNF_HUMAN	neuron-derived neurotrophic factor	232					cell growth (GO:0016049)|extracellular matrix organization (GO:0030198)|negative regulation of neuron apoptotic process (GO:0043524)|neuron migration (GO:0001764)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron projection development (GO:0010976)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)	p.S232I(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(3)|skin(1)|urinary_tract(1)	29						ATCATCTGCACTCAGTTTTGC	0.448																																																	1	Substitution - Missense(1)	kidney(1)											143.0	145.0	145.0					4																	121958431		2203	4300	6503	SO:0001583	missense	0			BC019351	CCDS3717.2	4q27	2011-07-05	2011-07-05	2011-07-05	ENSG00000173376	ENSG00000173376			26256	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 31"""	C4orf31		12975309, 20969804	Standard	NM_024574		Approved	FLJ23191	uc003idq.1	Q8TB73	OTTHUMG00000132973	ENST00000379692.4:c.695G>T	4.37:g.121958431C>A	ENSP00000369014:p.Ser232Ile	Somatic		WXS	Illumina GAIIx	Phase_I	A8K0Q0|Q6UWE5|Q9H5P7	Missense_Mutation	SNP	ENST00000379692.4	37	CCDS3717.2	.	.	.	.	.	.	.	.	.	.	C	11.25	1.583158	0.28268	.	.	ENSG00000173376	ENST00000379692	.	.	.	5.7	2.76	0.32466	.	0.153854	0.64402	N	0.000001	T	0.45216	0.1331	L	0.47716	1.5	0.43512	D	0.995773	B	0.06786	0.001	B	0.08055	0.003	T	0.37244	-0.9714	9	0.49607	T	0.09	-6.2617	5.6922	0.17835	0.1112:0.6315:0.1215:0.1358	.	232	Q8TB73	NDNF_HUMAN	I	232	.	ENSP00000369014:S232I	S	-	2	0	NDNF	122177881	0.701000	0.27806	0.846000	0.33378	0.990000	0.78478	1.002000	0.29796	0.696000	0.31696	0.655000	0.94253	AGT		0.448	NDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256532.2		NM_024574	
C5orf42	65250	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	37168941	37168941	+	Silent	SNP	T	T	C			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr5:37168941T>C	ENST00000508244.1	-	33	7278	c.7185A>G	c.(7183-7185)aaA>aaG	p.K2395K	C5orf42_ENST00000425232.2_Silent_p.K2395K|C5orf42_ENST00000274258.7_Silent_p.K1275K			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2395						integral component of membrane (GO:0016021)		p.K2395K(1)|p.K1275K(1)		breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			ATCTTGGGTATTTTCTTTCTT	0.363																																																	2	Substitution - coding silent(2)	kidney(2)											179.0	180.0	179.0					5																	37168941		2203	4300	6503	SO:0001819	synonymous_variant	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.7185A>G	5.37:g.37168941T>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	37	CCDS34146.2																																																																																				0.363	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1		NM_023073	
CD180	4064	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	66479407	66479407	+	Silent	SNP	G	G	A			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr5:66479407G>A	ENST00000256447.4	-	3	1421	c.1264C>T	c.(1264-1266)Cta>Tta	p.L422L	CTD-2306M10.1_ENST00000602471.1_lincRNA	NM_005582.2	NP_005573.2	Q99467	CD180_HUMAN	CD180 molecule	422					B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L422L(1)		cervix(1)|endometrium(2)|kidney(7)|large_intestine(12)|liver(1)|lung(8)|ovary(1)|stomach(2)	34		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)		AGGAGTTCTAGCTGAGGACAT	0.458																																																	1	Substitution - coding silent(1)	kidney(1)											168.0	172.0	171.0					5																	66479407		2203	4300	6503	SO:0001819	synonymous_variant	4064			D83597	CCDS3992.1	5q12	2008-02-05	2006-03-28	2005-06-07	ENSG00000134061	ENSG00000134061		"""CD molecules"""	6726	protein-coding gene	gene with protein product		602226	"""lymphocyte antigen 64 (mouse) homolog, radioprotective, 105kD"", ""CD180 antigen"""	LY64		9763566, 8975706	Standard	NM_005582		Approved	RP105, Ly78	uc003juy.2	Q99467	OTTHUMG00000131229	ENST00000256447.4:c.1264C>T	5.37:g.66479407G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B2R7Z7|Q32MM5	Silent	SNP	ENST00000256447.4	37	CCDS3992.1																																																																																				0.458	CD180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253973.2		NM_005582	
CDHR1	92211	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	85960393	85960393	+	Missense_Mutation	SNP	G	G	T			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr10:85960393G>T	ENST00000372117.3	+	6	578	c.475G>T	c.(475-477)Gca>Tca	p.A159S	CDHR1_ENST00000440770.2_5'Flank|CDHR1_ENST00000332904.3_Missense_Mutation_p.A159S	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	159	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)	p.A159S(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						TAAGGTCCATGCAGTGGACAG	0.602																																																	1	Substitution - Missense(1)	kidney(1)											109.0	78.0	88.0					10																	85960393		2203	4300	6503	SO:0001583	missense	92211			AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.475G>T	10.37:g.85960393G>T	ENSP00000361189:p.Ala159Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q69YZ8|Q8IXY5	Missense_Mutation	SNP	ENST00000372117.3	37	CCDS7372.1	.	.	.	.	.	.	.	.	.	.	G	15.84	2.951168	0.53186	.	.	ENSG00000148600	ENST00000332904;ENST00000372117	T;T	0.61510	0.1;0.1	5.31	5.31	0.75309	Cadherin (5);Cadherin-like (1);	0.110612	0.64402	D	0.000010	T	0.81221	0.4777	M	0.93016	3.37	0.80722	D	1	D;D	0.76494	0.999;0.994	D;D	0.65874	0.939;0.917	D	0.86155	0.1590	10	0.87932	D	0	-10.4224	17.7406	0.88406	0.0:0.0:1.0:0.0	.	159;159	Q96JP9-2;Q96JP9	.;CDHR1_HUMAN	S	159	ENSP00000331063:A159S;ENSP00000361189:A159S	ENSP00000331063:A159S	A	+	1	0	CDHR1	85950373	1.000000	0.71417	0.090000	0.20809	0.161000	0.22273	8.998000	0.93550	2.466000	0.83321	0.563000	0.77884	GCA		0.602	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1		NM_033100	
CHD7	55636	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	61763106	61763106	+	Missense_Mutation	SNP	G	G	A	rs372644599		TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr8:61763106G>A	ENST00000423902.2	+	26	5938	c.5459G>A	c.(5458-5460)cGa>cAa	p.R1820Q	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1820					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R1820Q(2)		NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			TTTCTGGAACGAGTCGGTATG	0.507																																																	2	Substitution - Missense(2)	kidney(2)						G	GLN/ARG	1,4281		0,1,2140	50.0	59.0	56.0		5459	5.5	1.0	8		56	1,8491		0,1,4245	no	missense	CHD7	NM_017780.3	43	0,2,6385	AA,AG,GG		0.0118,0.0234,0.0157	probably-damaging	1820/2998	61763106	2,12772	2141	4246	6387	SO:0001583	missense	55636			AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.5459G>A	8.37:g.61763106G>A	ENSP00000392028:p.Arg1820Gln	Somatic		WXS	Illumina HiSeq	Phase_I	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	37	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	G	37	6.037820	0.97226	2.34E-4	1.18E-4	ENSG00000171316	ENST00000307121;ENST00000423902	D	0.92397	-3.03	5.49	5.49	0.81192	.	0.000000	0.64402	D	0.000002	D	0.93926	0.8056	M	0.75615	2.305	0.80722	D	1	D	0.56746	0.977	P	0.49561	0.615	D	0.94461	0.7676	10	0.72032	D	0.01	-8.3022	19.3689	0.94477	0.0:0.0:1.0:0.0	.	1820	Q9P2D1	CHD7_HUMAN	Q	1820	ENSP00000392028:R1820Q	ENSP00000307304:R1820Q	R	+	2	0	CHD7	61925660	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.579000	0.87056	0.650000	0.86243	CGA		0.507	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2		XM_098762	
CNTNAP2	26047	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	147336210	147336210	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr7:147336210G>A	ENST00000361727.3	+	13	2426	c.1910G>A	c.(1909-1911)tGg>tAg	p.W637*		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	637	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)	p.W637*(1)		NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			GACAAAGTGTGGACCATAGTG	0.463										HNSCC(39;0.1)																																							1	Substitution - Nonsense(1)	kidney(1)											119.0	117.0	118.0					7																	147336210		2203	4300	6503	SO:0001587	stop_gained	26047			AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.1910G>A	7.37:g.147336210G>A	ENSP00000354778:p.Trp637*	Somatic		WXS	Illumina HiSeq	Phase_I	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Nonsense_Mutation	SNP	ENST00000361727.3	37	CCDS5889.1	.	.	.	.	.	.	.	.	.	.	G	38	6.906195	0.97924	.	.	ENSG00000174469	ENST00000361727;ENST00000455301	.	.	.	5.74	4.85	0.62838	.	0.078743	0.56097	D	0.000029	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.3879	0.74718	0.0:0.0:0.8599:0.14	.	.	.	.	X	637;28	.	ENSP00000354778:W637X	W	+	2	0	CNTNAP2	146967143	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.912000	0.75753	1.542000	0.49330	0.561000	0.74099	TGG		0.463	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1			
CYTH2	9266	broad.mit.edu	37	19	48977567	48977567	+	Silent	SNP	C	C	T			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr19:48977567C>T	ENST00000452733.2	+	7	1152	c.676C>T	c.(676-678)Ctg>Ttg	p.L226L	CYTH2_ENST00000427476.1_Silent_p.L226L			Q99418	CYH2_HUMAN	cytohesin 2	226					actin cytoskeleton organization (GO:0030036)|endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|inositol 1,4,5 trisphosphate binding (GO:0070679)|lipid binding (GO:0008289)	p.L226L(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15						GGGCGGGGACCTGCCTGAGGA	0.652																																																	1	Substitution - coding silent(1)	kidney(1)											69.0	63.0	65.0					19																	48977567		2203	4300	6503	SO:0001819	synonymous_variant	9266			X99753	CCDS12722.1	19q13.32	2014-05-02	2008-08-14	2008-08-14	ENSG00000105443	ENSG00000105443		"""Pleckstrin homology (PH) domain containing"""	9502	protein-coding gene	gene with protein product		602488	"""pleckstrin homology, Sec7 and coiled/coil domains 2 (cytohesin-2)"", ""pleckstrin homology, Sec7 and coiled-coil domains 2"""	PSCD2L, PSCD2		8706128, 8945478, 20525696	Standard	NM_004228		Approved	CTS18.1, Sec7p-L, ARNO, Sec7p-like, cytohesin-2	uc002pjj.4	Q99418	OTTHUMG00000150245	ENST00000452733.2:c.676C>T	19.37:g.48977567C>T		Somatic		WXS	Illumina GAIIx	Phase_I	A8K8P0|Q8IXY9|Q92958	Silent	SNP	ENST00000452733.2	37	CCDS12722.1																																																																																				0.652	CYTH2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317060.1		NM_004228	
DHX15	1665	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	24572443	24572444	+	Nonsense_Mutation	DNP	GC	GC	AT			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr4:24572443_24572444GC>AT	ENST00000336812.4	-	3	690_691	c.534_535GC>AT	c.(532-537)atGCga>atATga	p.178_179MR>I*		NM_001358.2	NP_001349.2	O43143	DHX15_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 15	178	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|U12-type spliceosomal complex (GO:0005689)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)	p.R179*(1)|p.M178I(1)		breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	30		Breast(46;0.0503)				GGTAATGATCGCATGTACTCCA	0.416																																																	2	Substitution - Nonsense(1)|Substitution - Missense(1)	kidney(2)																																								SO:0001587	stop_gained	1665			AB001636	CCDS33966.1	4p15.3	2013-05-13	2013-05-13	2003-06-20	ENSG00000109606	ENSG00000109606		"""DEAH-boxes"""	2738	protein-coding gene	gene with protein product		603403	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 15"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 15"""	DDX15		9388478	Standard	NM_001358		Approved	HRH2, DBP1, PRP43, PrPp43p, PRPF43	uc003gqx.3	O43143	OTTHUMG00000160304	ENST00000336812.4:c.534_535delinsAT	4.37:g.24572443_24572444delinsAT	ENSP00000336741:p.M178_R179delinsI*	Somatic		WXS	Illumina HiSeq	Phase_I	Q9NQT7	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000336812.4	37	CCDS33966.1																																																																																				0.416	DHX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360143.1		NM_001358	
DRGX	644168	broad.mit.edu;ucsc.edu	37	10	50574424	50574424	+	Missense_Mutation	SNP	C	C	A			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr10:50574424C>A	ENST00000374139.2	-	6	539	c.529G>T	c.(529-531)Ggc>Tgc	p.G177C	DRGX_ENST00000434016.1_Missense_Mutation_p.G182C			A6NNA5	DRGX_HUMAN	dorsal root ganglia homeobox	177					axon guidance (GO:0007411)|detection of chemical stimulus (GO:0009593)|detection of temperature stimulus (GO:0016048)|dorsal spinal cord development (GO:0021516)|neuron migration (GO:0001764)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of mechanical stimulus (GO:0050954)|transcription, DNA-templated (GO:0006351)|trigeminal nerve development (GO:0021559)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.G182C(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)	11						CACAGTGGGCCCCCTGGAAAA	0.577																																																	1	Substitution - Missense(1)	kidney(1)											42.0	46.0	45.0					10																	50574424		1998	4179	6177	SO:0001583	missense	644168				CCDS44388.1, CCDS44388.2	10q11.23	2011-06-20	2007-07-26	2007-07-26	ENSG00000165606	ENSG00000165606		"""Homeoboxes / PRD class"""	21536	protein-coding gene	gene with protein product	"""paired-like homeodomain trancription factor DRG11"""	606701	"""paired related homeobox-like 1"""	PRRXL1		7496632	Standard	NM_001276451		Approved	DRG11	uc021pqd.2	A6NNA5	OTTHUMG00000018192	ENST00000374139.2:c.529G>T	10.37:g.50574424C>A	ENSP00000363254:p.Gly177Cys	Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000374139.2	37		.	.	.	.	.	.	.	.	.	.	C	19.39	3.818071	0.71028	.	.	ENSG00000165606	ENST00000374139;ENST00000434016	D;D	0.91894	-2.93;-2.89	5.54	4.64	0.57946	.	0.324843	0.36444	N	0.002589	D	0.83644	0.5299	N	0.08118	0	0.34905	D	0.746879	P	0.49696	0.927	P	0.45946	0.498	D	0.86775	0.1975	10	0.66056	D	0.02	.	6.7254	0.23353	0.0:0.7001:0.0:0.2999	.	182	C9JW76	.	C	177;182	ENSP00000363254:G177C;ENSP00000401653:G182C	ENSP00000363254:G177C	G	-	1	0	DRGX	50244430	0.994000	0.37717	1.000000	0.80357	0.997000	0.91878	1.166000	0.31834	1.337000	0.45525	0.655000	0.94253	GGC		0.577	DRGX-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047987.2		XM_060970	
EBF1	1879	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	158250251	158250251	+	Silent	SNP	A	A	G			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr5:158250251A>G	ENST00000313708.6	-	8	993	c.711T>C	c.(709-711)aaT>aaC	p.N237N	EBF1_ENST00000518836.1_5'UTR|EBF1_ENST00000380654.4_Silent_p.N214N|EBF1_ENST00000517373.1_Silent_p.N237N	NM_024007.3	NP_076870.1	Q9UH73	COE1_HUMAN	early B-cell factor 1	237	Interaction with DNA. {ECO:0000250}.				multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|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.N237N(1)	HMGA2/EBF1(2)	breast(3)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CATGCTTGGAATTATTATGGA	0.488			T	HMGA2	lipoma																																			Dom	yes		5	5q34	1879	early B-cell factor 1		M	1	Substitution - coding silent(1)	kidney(1)											86.0	71.0	76.0					5																	158250251		2203	4300	6503	SO:0001819	synonymous_variant	1879			AF208502	CCDS4343.1	5q34	2008-02-05	2006-09-26	2006-09-26	ENSG00000164330	ENSG00000164330			3126	protein-coding gene	gene with protein product		164343	"""early B-cell factor"""	EBF		8012110	Standard	NM_024007		Approved	OLF1	uc010jip.3	Q9UH73	OTTHUMG00000130304	ENST00000313708.6:c.711T>C	5.37:g.158250251A>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q8IW11	Silent	SNP	ENST00000313708.6	37	CCDS4343.1																																																																																				0.488	EBF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252649.1		NM_024007	
EGF	1950	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	110909739	110909739	+	Splice_Site	SNP	G	G	T			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr4:110909739G>T	ENST00000265171.5	+	18	3053		c.e18-1		EGF_ENST00000509793.1_Splice_Site|EGF_ENST00000503392.1_Splice_Site	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor						activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)	p.?(1)		breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	TTTGCCCACAGATATAGATGA	0.428																																																	1	Unknown(1)	kidney(1)											154.0	159.0	158.0					4																	110909739		2203	4300	6503	SO:0001630	splice_region_variant	1950			X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"""epidermal growth factor (beta-urogastrone)"""				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.2609-1G>T	4.37:g.110909739G>T		Somatic		WXS	Illumina HiSeq	Phase_I	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Splice_Site	SNP	ENST00000265171.5	37	CCDS3689.1	.	.	.	.	.	.	.	.	.	.	G	19.55	3.848082	0.71603	.	.	ENSG00000138798	ENST00000509793;ENST00000265171;ENST00000503392	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3079	0.94171	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	EGF	111129188	1.000000	0.71417	0.998000	0.56505	0.872000	0.50106	7.080000	0.76837	2.550000	0.86006	0.655000	0.94253	.		0.428	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1			Intron
EGFL6	25975	broad.mit.edu;hgsc.bcm.edu	37	X	13636139	13636139	+	Missense_Mutation	SNP	A	A	T			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chrX:13636139A>T	ENST00000361306.1	+	8	1326	c.1069A>T	c.(1069-1071)Ata>Tta	p.I357L	EGFL6_ENST00000380602.3_Missense_Mutation_p.I357L	NM_001167890.1|NM_015507.3	NP_001161362.1|NP_056322.2	Q8IUX8	EGFL6_HUMAN	EGF-like-domain, multiple 6	357					cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)	p.I357L(2)		breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)|skin(3)	23						GAAGAATGACATAGAGGAGCG	0.393																																																	2	Substitution - Missense(2)	kidney(2)											49.0	52.0	51.0					X																	13636139		2203	4298	6501	SO:0001583	missense	25975			AF186084	CCDS14155.1, CCDS55370.1	Xp22	2008-02-05	2002-10-09		ENSG00000198759	ENSG00000198759			3235	protein-coding gene	gene with protein product		300239	"""MAM and EGF domain containing"""	MAEG		10610727	Standard	NM_015507		Approved		uc004cvj.3	Q8IUX8	OTTHUMG00000021155	ENST00000361306.1:c.1069A>T	X.37:g.13636139A>T	ENSP00000355126:p.Ile357Leu	Somatic		WXS	Illumina HiSeq	Phase_I	B2RCB1|Q6UXJ1|Q8NBV0|Q8WYG3|Q9NY67|Q9NZL7|Q9UFK6	Missense_Mutation	SNP	ENST00000361306.1	37	CCDS14155.1	.	.	.	.	.	.	.	.	.	.	A	4.588	0.109305	0.08780	.	.	ENSG00000198759	ENST00000361306;ENST00000380602	T;T	0.71461	-0.57;-0.44	5.49	1.94	0.25998	.	0.965368	0.08608	N	0.920387	T	0.59293	0.2183	L	0.38175	1.15	0.09310	N	1	B;B	0.22983	0.013;0.078	B;B	0.19391	0.012;0.025	T	0.44190	-0.9344	10	0.27785	T	0.31	.	9.1895	0.37191	0.5093:0.0:0.4907:0.0	.	357;357	Q8IUX8-2;Q8IUX8	.;EGFL6_HUMAN	L	357	ENSP00000355126:I357L;ENSP00000369976:I357L	ENSP00000355126:I357L	I	+	1	0	EGFL6	13546060	0.060000	0.20803	0.001000	0.08648	0.218000	0.24690	0.406000	0.21032	0.417000	0.25871	-0.456000	0.05471	ATA		0.393	EGFL6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055800.1		NM_015507	
EXOC6	54536	hgsc.bcm.edu;ucsc.edu	37	10	94669364	94669364	+	Missense_Mutation	SNP	A	A	C			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr10:94669364A>C	ENST00000260762.6	+	6	653	c.639A>C	c.(637-639)aaA>aaC	p.K213N	EXOC6_ENST00000371552.4_Missense_Mutation_p.K208N|EXOC6_ENST00000497262.1_3'UTR|EXOC6_ENST00000443748.2_Missense_Mutation_p.K213N|EXOC6_ENST00000371547.4_Missense_Mutation_p.K229N	NM_019053.4	NP_061926.3	Q8TAG9	EXOC6_HUMAN	exocyst complex component 6	213					cellular protein metabolic process (GO:0044267)|erythrocyte differentiation (GO:0030218)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	26		Colorectal(252;0.123)				ATTCTGACAAAATAGGTGAAA	0.299																																																	0													48.0	48.0	48.0					10																	94669364		2203	4300	6503	SO:0001583	missense	54536			BC028395	CCDS7424.2, CCDS31247.1	10q23.33	2013-01-22	2006-11-07	2006-11-07	ENSG00000138190	ENSG00000138190			23196	protein-coding gene	gene with protein product		609672	"""SEC15-like 1 (S. cerevisiae)"""	SEC15L1		8889548	Standard	NM_001013848		Approved	SEC15L, FLJ1125, DKFZp761I2124, MGC33397, Sec15p, EXOC6A	uc001kig.3	Q8TAG9	OTTHUMG00000018767	ENST00000260762.6:c.639A>C	10.37:g.94669364A>C	ENSP00000260762:p.Lys213Asn	Somatic		WXS	Illumina HiSeq	Phase_I	E9PHI3|Q5VXH8|Q9NZ24	Missense_Mutation	SNP	ENST00000260762.6	37	CCDS7424.2	.	.	.	.	.	.	.	.	.	.	A	22.8	4.342471	0.81911	.	.	ENSG00000138190	ENST00000371547;ENST00000371552;ENST00000443748;ENST00000260762	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	5.69	5.69	0.88448	.	0.042983	0.85682	D	0.000000	T	0.45538	0.1347	M	0.62266	1.93	0.29680	N	0.841814	P;P;P;P;P	0.50066	0.924;0.931;0.76;0.76;0.76	P;P;B;B;P	0.52267	0.694;0.522;0.365;0.365;0.467	T	0.50841	-0.8780	10	0.66056	D	0.02	-20.5851	15.9417	0.79758	1.0:0.0:0.0:0.0	.	229;213;205;213;208	F2Z2Q3;E7EW84;B4DEZ1;Q8TAG9;E9PHI3	.;.;.;EXOC6_HUMAN;.	N	229;208;213;213	ENSP00000360602:K229N;ENSP00000360607:K208N;ENSP00000396206:K213N;ENSP00000260762:K213N	ENSP00000260762:K213N	K	+	3	2	EXOC6	94659344	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.571000	0.60879	2.174000	0.68829	0.528000	0.53228	AAA		0.299	EXOC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049410.2		NM_019053	
FBN1	2200	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	48764807	48764807	+	Missense_Mutation	SNP	C	C	A	rs531751210		TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr15:48764807C>A	ENST00000316623.5	-	35	4732	c.4277G>T	c.(4276-4278)gGa>gTa	p.G1426V		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1426	EGF-like 24; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.G1426V(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		ACAGCGGTATCCTCCTGGTGC	0.542																																																	1	Substitution - Missense(1)	kidney(1)											143.0	132.0	136.0					15																	48764807		2198	4296	6494	SO:0001583	missense	2200			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"""Marfan syndrome"""	134797	"""fibrillin 1 (Marfan syndrome)"""	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.4277G>T	15.37:g.48764807C>A	ENSP00000325527:p.Gly1426Val	Somatic		WXS	Illumina HiSeq	Phase_I	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.722549	0.89298	.	.	ENSG00000166147	ENST00000316623;ENST00000544030	D	0.93426	-3.22	5.81	5.81	0.92471	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.96981	0.9014	M	0.83774	2.66	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	D	0.96939	0.9686	10	0.66056	D	0.02	.	19.6746	0.95926	0.0:1.0:0.0:0.0	.	1426	P35555	FBN1_HUMAN	V	1426;316	ENSP00000325527:G1426V	ENSP00000325527:G1426V	G	-	2	0	FBN1	46552099	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	6.089000	0.71384	2.747000	0.94245	0.650000	0.86243	GGA		0.542	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			
FREM2	341640	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	39452971	39452971	+	Missense_Mutation	SNP	A	A	G			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr13:39452971A>G	ENST00000280481.7	+	23	9079	c.8863A>G	c.(8863-8865)Aaa>Gaa	p.K2955E		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2955					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.K2955E(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CTTAAAGGACAAAGCTCAGCC	0.428																																																	1	Substitution - Missense(1)	kidney(1)											129.0	119.0	123.0					13																	39452971		2203	4300	6503	SO:0001583	missense	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.8863A>G	13.37:g.39452971A>G	ENSP00000280481:p.Lys2955Glu	Somatic		WXS	Illumina HiSeq	Phase_I	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	A	32	5.130212	0.94473	.	.	ENSG00000150893	ENST00000280481	T	0.63096	-0.02	5.84	5.84	0.93424	.	0.048532	0.85682	D	0.000000	T	0.71056	0.3295	M	0.85630	2.765	0.80722	D	1	P	0.43973	0.823	B	0.43413	0.419	T	0.77270	-0.2650	10	0.72032	D	0.01	.	16.2167	0.82231	1.0:0.0:0.0:0.0	.	2955	Q5SZK8	FREM2_HUMAN	E	2955	ENSP00000280481:K2955E	ENSP00000280481:K2955E	K	+	1	0	FREM2	38350971	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.307000	0.96226	2.231000	0.72958	0.533000	0.62120	AAA		0.428	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2		NM_207361	
GAB4	128954	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	17472966	17472966	+	Missense_Mutation	SNP	C	C	G			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr22:17472966C>G	ENST00000400588.1	-	2	382	c.275G>C	c.(274-276)cGc>cCc	p.R92P	GAB4_ENST00000523144.1_5'UTR	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	92	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.							p.R92P(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(24)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44		all_epithelial(15;0.112)|Lung NSC(13;0.248)				GTTGATGGTGCGCAGGGGCTT	0.502																																																	1	Substitution - Missense(1)	kidney(1)											211.0	222.0	218.0					22																	17472966		2195	4300	6495	SO:0001583	missense	128954			AK057252	CCDS42976.1	22q11.2	2013-01-10			ENSG00000215568	ENSG00000215568		"""Pleckstrin homology (PH) domain containing"""	18325	protein-coding gene	gene with protein product							Standard	NM_001037814		Approved		uc002zlw.3	Q2WGN9	OTTHUMG00000149992	ENST00000400588.1:c.275G>C	22.37:g.17472966C>G	ENSP00000383431:p.Arg92Pro	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000400588.1	37	CCDS42976.1	.	.	.	.	.	.	.	.	.	.	C	12.25	1.881448	0.33255	.	.	ENSG00000215568	ENST00000400588	T	0.12569	2.67	1.81	1.81	0.25067	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.64402	U	0.000001	T	0.34221	0.0890	M	0.80746	2.51	0.54753	D	0.999982	D	0.89917	1.0	D	0.87578	0.998	T	0.15292	-1.0442	10	0.54805	T	0.06	.	9.5993	0.39593	0.0:1.0:0.0:0.0	.	92	Q2WGN9	GAB4_HUMAN	P	92	ENSP00000383431:R92P	ENSP00000383431:R92P	R	-	2	0	GAB4	15852966	1.000000	0.71417	0.953000	0.39169	0.042000	0.13812	6.911000	0.75746	1.301000	0.44836	0.591000	0.81541	CGC		0.502	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1		XM_372882	
GGNBP2	79893	hgsc.bcm.edu;ucsc.edu	37	17	34913158	34913158	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr17:34913158delC	ENST00000304718.4	+	4	726	c.410delC	c.(409-411)acafs	p.T137fs		NM_024835.3	NP_079111.1	Q9H3C7	GGNB2_HUMAN	gametogenetin binding protein 2	137					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)	38		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		AAGCTTTATACATTATTTTAT	0.393																																																	0													78.0	76.0	77.0					17																	34913158		2203	4300	6503	SO:0001589	frameshift_variant	79893			AF126964	CCDS11314.1	17q21.1	2014-05-06	2007-08-20	2007-08-20	ENSG00000005955	ENSG00000278311			19357	protein-coding gene	gene with protein product		612275	"""zinc finger protein 403"""	ZNF403		11728448	Standard	NM_024835		Approved	ZFP403, LZK1, FLJ22561, FLJ21230, DIF-3, DIF3	uc002hnb.3	Q9H3C7	OTTHUMG00000188440	ENST00000304718.4:c.410delC	17.37:g.34913158delC	ENSP00000307617:p.Thr137fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2RPK7|Q96T90|Q9GZR8|Q9H767	Frame_Shift_Del	DEL	ENST00000304718.4	37	CCDS11314.1																																																																																				0.393	GGNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256684.2		NM_024835	
GNAS	2778	broad.mit.edu	37	20	57429460	57429460	+	Missense_Mutation	SNP	C	C	A			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr20:57429460C>A	ENST00000306120.3	+	1	950	c.950C>A	c.(949-951)cCc>cAc	p.P317H	GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371102.4_Silent_p.S380S|GNAS_ENST00000371075.3_Intron|GNAS_ENST00000313949.7_Intron|GNAS_ENST00000371098.2_Intron|GNAS_ENST00000371100.4_Silent_p.S380S|GNAS_ENST00000371099.2_Silent_p.S380S			P63092	GNAS2_HUMAN	GNAS complex locus	0					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.S380S(1)		adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			GGTACGGATCCCCTGCCGCCG	0.677			Mis		pituitary adenoma		"""McCune-Albright syndrome; pseudohypoparathyroidism, type IA"""			TSP Lung(22;0.16)																											Colon(117;935 1597 6045 8307 46442)			Dom	yes		20	20q13.2	2778	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	yes	E	1	Substitution - coding silent(1)	kidney(1)											9.0	15.0	13.0					20																	57429460		1894	4066	5960	SO:0001583	missense	2778			M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"""secretogranin VI"""	139320	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000306120.3:c.950C>A	20.37:g.57429460C>A	ENSP00000302237:p.Pro317His	Somatic		WXS	Illumina GAIIx	Phase_I	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Silent	SNP	ENST00000306120.3	37		.	.	.	.	.	.	.	.	.	.	C	11.29	1.595588	0.28445	.	.	ENSG00000087460	ENST00000306120	.	.	.	4.23	2.08	0.27032	.	.	.	.	.	T	0.60869	0.2302	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59484	-0.7446	5	0.72032	D	0.01	.	6.6222	0.22810	0.0:0.7388:0.0:0.2612	.	.	.	.	H	317	.	ENSP00000302237:P317H	P	+	2	0	GNAS	56862855	0.001000	0.12720	0.200000	0.23457	0.257000	0.26127	0.048000	0.14078	0.406000	0.25560	0.462000	0.41574	CCC		0.677	GNAS-050	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000267987.1		NM_000516	
HAP1	9001	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	39889026	39889026	+	Missense_Mutation	SNP	G	G	A			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr17:39889026G>A	ENST00000310778.5	-	2	503	c.494C>T	c.(493-495)cCa>cTa	p.P165L	HAP1_ENST00000347901.4_Missense_Mutation_p.P165L|JUP_ENST00000540235.1_Intron|RN7SL399P_ENST00000471648.2_RNA|HAP1_ENST00000393939.2_Missense_Mutation_p.P165L|HAP1_ENST00000341193.5_Missense_Mutation_p.P165L			P54257	HAP1_HUMAN	huntingtin-associated protein 1	165	HAP1 N-terminal.				anterograde axon cargo transport (GO:0008089)|autophagy (GO:0006914)|brain development (GO:0007420)|cell projection organization (GO:0030030)|exocytosis (GO:0006887)|negative regulation of beta-amyloid formation (GO:1902430)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|positive regulation of neurotrophin production (GO:0032901)|positive regulation of nonmotile primary cilium assembly (GO:1902857)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|protein localization (GO:0008104)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of organelle transport along microtubule (GO:1902513)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)|vesicle transport along microtubule (GO:0047496)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|inclusion body (GO:0016234)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synapse (GO:0045202)	brain-derived neurotrophic factor binding (GO:0048403)|ion channel binding (GO:0044325)	p.P165L(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(4)|skin(1)	21		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			CTTTTTGACTGGCGGAGGTAG	0.517																																																	1	Substitution - Missense(1)	kidney(1)											129.0	112.0	118.0					17																	39889026		2203	4300	6503	SO:0001583	missense	9001			AF040723	CCDS11406.1, CCDS42338.1, CCDS42339.1	17q21.2-q21.3	2008-04-23	2008-04-23		ENSG00000173805	ENSG00000173805			4812	protein-coding gene	gene with protein product	"""neuroan 1"""	600947		HAP2		7477378, 9668110	Standard	NM_177977		Approved	HLP, hHLP1, HIP5	uc002hxn.1	P54257	OTTHUMG00000133498	ENST00000310778.5:c.494C>T	17.37:g.39889026G>A	ENSP00000309392:p.Pro165Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A8MQB5|O75358|Q59GK4|Q9H4G3|Q9HA98|Q9NY90	Missense_Mutation	SNP	ENST00000310778.5	37		.	.	.	.	.	.	.	.	.	.	G	14.72	2.619943	0.46736	.	.	ENSG00000173805	ENST00000393939;ENST00000310778;ENST00000347901;ENST00000341193	T;T;T;T	0.18657	2.2;2.2;2.2;2.2	3.0	3.0	0.34707	.	0.000000	0.37761	N	0.001941	T	0.37517	0.1006	L	0.57536	1.79	0.09310	N	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.998;0.999	T	0.02774	-1.1112	10	0.45353	T	0.12	-6.6984	9.7308	0.40359	0.0:0.0:1.0:0.0	.	165;165;165;165	P54257-3;P54257-4;P54257-2;P54257	.;.;.;HAP1_HUMAN	L	165	ENSP00000377513:P165L;ENSP00000309392:P165L;ENSP00000334002:P165L;ENSP00000343170:P165L	ENSP00000309392:P165L	P	-	2	0	HAP1	37142552	0.047000	0.20315	0.009000	0.14445	0.007000	0.05969	1.368000	0.34216	1.985000	0.57927	0.455000	0.32223	CCA		0.517	HAP1-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000389619.1		NM_003949	
HCFC1	3054	hgsc.bcm.edu	37	X	153222971	153222972	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chrX:153222971_153222972insG	ENST00000310441.7	-	13	3112_3113	c.2146_2147insC	c.(2146-2148)ctgfs	p.L716fs	HCFC1_ENST00000461098.1_5'Flank|HCFC1_ENST00000369984.4_Frame_Shift_Ins_p.L716fs|HCFC1_ENST00000354233.3_Frame_Shift_Ins_p.L647fs	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	716	Interaction with SIN3A.				cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TCCCGCTGGCAGGGGCCCTTTG	0.644																																																	0																																										SO:0001589	frameshift_variant	3054				CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"""VP16-accessory protein"", ""protein phosphatase 1, regulatory subunit 89"""	300019	"""mental retardation, X-linked 3"", ""host cell factor C1 (VP16-accessory protein)"""	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.2147dupC	X.37:g.153222975_153222975dupG	ENSP00000309555:p.Leu716fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q6P4G5	Frame_Shift_Ins	INS	ENST00000310441.7	37	CCDS44020.1																																																																																				0.644	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4		NM_005334	
HDAC10	83933	broad.mit.edu	37	22	50689480	50689480	+	De_novo_Start_OutOfFrame	SNP	C	C	A			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr22:50689480C>A	ENST00000216271.5	-	0	334				MAPK12_ENST00000497036.1_5'UTR|HDAC10_ENST00000448072.1_De_novo_Start_OutOfFrame|HDAC10_ENST00000498366.1_Intron|HDAC10_ENST00000349505.4_5'Flank	NM_001159286.1|NM_032019.5	NP_001152758.1|NP_114408.3	Q969S8	HDA10_HUMAN	histone deacetylase 10						chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|oligodendrocyte development (GO:0014003)|protein deacetylation (GO:0006476)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)			endometrium(2)|kidney(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	8		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CGTGGTCACCCTGGGTTCCCA	0.701																																																	0													35.0	33.0	34.0					22																	50689480		2184	4296	6480			83933			AF393962	CCDS14088.1, CCDS54545.1	22q13.31	2008-06-10			ENSG00000100429	ENSG00000100429			18128	protein-coding gene	gene with protein product		608544				11677242, 11726666	Standard	NM_032019		Approved	DKFZP761B039	uc003bkg.3	Q969S8	OTTHUMG00000044647	ENST00000216271.5:c.-19G>T	22.37:g.50689480C>A		Somatic		WXS	Illumina GAIIx	Phase_I	Q08AP4|Q6STF9|Q96P77|Q96P78|Q9H028|Q9UGX1|Q9UGX2	Translation_Start_Site	SNP	ENST00000216271.5	37	CCDS14088.1																																																																																				0.701	HDAC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104141.4		NM_032019	
HYOU1	10525	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	118916498	118916498	+	Missense_Mutation	SNP	C	C	A			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr11:118916498C>A	ENST00000404233.3	-	25	3057	c.2933G>T	c.(2932-2934)gGa>gTa	p.G978V	HYOU1_ENST00000525859.1_Missense_Mutation_p.G916V|HYOU1_ENST00000529972.1_Missense_Mutation_p.G916V|RP11-110I1.6_ENST00000531886.1_RNA	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	978					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)	p.G978V(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		CTCACCTGCTCCAGGACCTCC	0.567																																																	1	Substitution - Missense(1)	kidney(1)											74.0	66.0	69.0					11																	118916498		2200	4295	6495	SO:0001583	missense	10525			U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"""Heat shock proteins / HSP70"""	16931	protein-coding gene	gene with protein product	"""glucose-regulated protein 170"""	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.2933G>T	11.37:g.118916498C>A	ENSP00000384144:p.Gly978Val	Somatic		WXS	Illumina HiSeq	Phase_I	A8C1Z0|B7Z909|Q2I204|Q53H25	Missense_Mutation	SNP	ENST00000404233.3	37	CCDS8408.1	.	.	.	.	.	.	.	.	.	.	C	13.24	2.176820	0.38413	.	.	ENSG00000149428	ENST00000404233;ENST00000353883;ENST00000529972;ENST00000535579;ENST00000525859;ENST00000544701	T;T;T	0.01464	4.9;4.86;4.86	5.41	2.56	0.30785	.	0.687166	0.14557	N	0.312325	T	0.01940	0.0061	L	0.47716	1.5	0.58432	D	0.999993	B;P;B;B	0.36048	0.1;0.534;0.191;0.191	B;B;B;B	0.35470	0.033;0.203;0.076;0.076	T	0.60999	-0.7151	10	0.30854	T	0.27	-5.4377	4.9577	0.14050	0.0:0.5886:0.1651:0.2463	.	970;960;978;978	B3KXH0;B7Z2N4;Q9Y4L1;A8C1Z0	.;.;HYOU1_HUMAN;.	V	978;970;916;827;916;959	ENSP00000384144:G978V;ENSP00000437313:G916V;ENSP00000433397:G916V	ENSP00000278752:G970V	G	-	2	0	HYOU1	118421708	0.912000	0.30974	0.661000	0.29709	0.860000	0.49131	-0.070000	0.11523	0.420000	0.25954	-0.119000	0.15052	GGA		0.567	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1		NM_006389	
IGLL1	3543	broad.mit.edu;ucsc.edu	37	22	23915501	23915501	+	Silent	SNP	G	G	A	rs1064418	byFrequency	TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr22:23915501G>A	ENST00000330377.2	-	3	711	c.594C>T	c.(592-594)caC>caT	p.H198H	IGLL1_ENST00000249053.3_3'UTR|AP000345.2_ENST00000454863.1_RNA|AP000345.2_ENST00000458318.1_RNA	NM_020070.3	NP_064455.1	P15814	IGLL1_HUMAN	immunoglobulin lambda-like polypeptide 1	198	C region (By similarity to lambda light- chain).|Ig-like C1-type.				immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)		p.H198H(1)		kidney(1)|large_intestine(1)|lung(5)|skin(4)|stomach(1)	12						TGCTCCCTTCGTGCATGACCT	0.632													g|||	2	0.000399361	0.0008	0.0	5008	,	,		17185	0.001		0.0	False		,,,				2504	0.0																1	Substitution - coding silent(1)	kidney(1)											73.0	69.0	71.0					22																	23915501		2203	4300	6503	SO:0001819	synonymous_variant	3543			X52204	CCDS13809.1, CCDS13810.1	22q11.23	2014-09-17			ENSG00000128322	ENSG00000128322		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	5870	protein-coding gene	gene with protein product		146770		IGLL		3139558, 2511029	Standard	NM_020070		Approved	IGVPB, IGL5, 14.1, CD179B	uc002zxd.3	P15814	OTTHUMG00000150673	ENST00000330377.2:c.594C>T	22.37:g.23915501G>A		Somatic		WXS	Illumina GAIIx	Phase_I	Q0P681	Silent	SNP	ENST00000330377.2	37	CCDS13809.1																																																																																				0.632	IGLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319569.1		NM_020070	
IL6	3569	hgsc.bcm.edu;ucsc.edu	37	7	22771126	22771126	+	Silent	SNP	T	T	G			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr7:22771126T>G	ENST00000404625.1	+	6	1032	c.573T>G	c.(571-573)acT>acG	p.T191T	IL6_ENST00000401630.3_Silent_p.T168T|IL6_ENST00000258743.5_Silent_p.T191T|IL6_ENST00000407492.1_Silent_p.T115T			P05231	IL6_HUMAN	interleukin 6	191					acute-phase response (GO:0006953)|aging (GO:0007568)|bone remodeling (GO:0046849)|branching involved in salivary gland morphogenesis (GO:0060445)|cell growth (GO:0016049)|cell redox homeostasis (GO:0045454)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endocrine pancreas development (GO:0031018)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|glucagon secretion (GO:0070091)|hepatic immune response (GO:0002384)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of hormone secretion (GO:0046888)|negative regulation of lipid storage (GO:0010888)|negative regulation of muscle organ development (GO:0048635)|negative regulation of neuron death (GO:1901215)|negative regulation of protein kinase activity (GO:0006469)|neuron projection development (GO:0031175)|neutrophil apoptotic process (GO:0001781)|neutrophil mediated immunity (GO:0002446)|platelet activation (GO:0030168)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell activation (GO:0050871)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of angiogenesis (GO:0045765)|regulation of cell shape (GO:0008360)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of vascular endothelial growth factor production (GO:0010574)|response to amino acid (GO:0043200)|response to antibiotic (GO:0046677)|response to caffeine (GO:0031000)|response to calcium ion (GO:0051592)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to glucocorticoid (GO:0051384)|response to heat (GO:0009408)|response to insulin (GO:0032868)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to peptidoglycan (GO:0032494)|T-helper 17 cell lineage commitment (GO:0072540)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|interleukin-6 receptor binding (GO:0005138)			breast(1)|endometrium(2)|large_intestine(4)|lung(1)	8					Ginseng(DB01404)	ACATGACAACTCATCTCATTC	0.517																																					Esophageal Squamous(47;342 1214 13936 33513)												0													79.0	69.0	72.0					7																	22771126		2203	4300	6503	SO:0001819	synonymous_variant	3569			M18403	CCDS5375.1	7p21-p15	2014-04-04	2014-04-04		ENSG00000136244	ENSG00000136244		"""Interleukins and interleukin receptors"", ""Interferons"""	6018	protein-coding gene	gene with protein product	"""interferon, beta 2"""	147620	"""interleukin 6 (interferon, beta 2)"""	IFNB2		3294161	Standard	NM_000600		Approved	IL-6, BSF2, HGF, HSF	uc003svj.4	P05231	OTTHUMG00000023178	ENST00000404625.1:c.573T>G	7.37:g.22771126T>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q9UCU2|Q9UCU3|Q9UCU4	Silent	SNP	ENST00000404625.1	37	CCDS5375.1																																																																																				0.517	IL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250225.2		NM_000600	
ITSN2	50618	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	24469086	24469086	+	Silent	SNP	A	A	G			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr2:24469086A>G	ENST00000355123.4	-	29	3932	c.3489T>C	c.(3487-3489)gaT>gaC	p.D1163D	ITSN2_ENST00000361999.3_Silent_p.D1136D|ITSN2_ENST00000406921.3_Silent_p.D1163D	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1163	SH3 5. {ECO:0000255|PROSITE- ProRule:PRU00192}.				endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)	p.D1162D(1)|p.D1163D(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTGCCACCAATCAGGATCAT	0.413																																																	2	Substitution - coding silent(2)	kidney(2)											174.0	153.0	160.0					2																	24469086		2203	4300	6503	SO:0001819	synonymous_variant	50618			AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"""Rho guanine nucleotide exchange factors"", ""EF-hand domain containing"""	6184	protein-coding gene	gene with protein product	"""SH3 domain protein 1B"", ""SH3P18-like WASP associated protein"""	604464	"""SH3 domain protein 1B"""	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.3489T>C	2.37:g.24469086A>G		Somatic		WXS	Illumina HiSeq	Phase_I	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Silent	SNP	ENST00000355123.4	37	CCDS1710.2	.	.	.	.	.	.	.	.	.	.	A	9.416	1.081828	0.20309	.	.	ENSG00000198399	ENST00000416160	.	.	.	5.59	2.76	0.32466	.	.	.	.	.	T	0.56366	0.1980	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50734	-0.8793	4	.	.	.	.	8.0511	0.30579	0.3832:0.0:0.6168:0.0	.	.	.	.	T	91	.	.	I	-	2	0	ITSN2	24322590	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	0.927000	0.28818	0.817000	0.34445	-0.456000	0.05471	ATT		0.413	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2		NM_006277	
ITGB6	3694	broad.mit.edu;ucsc.edu	37	2	160983104	160983104	+	Missense_Mutation	SNP	C	C	A	rs143914557		TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr2:160983104C>A	ENST00000283249.2	-	11	1906	c.1669G>T	c.(1669-1671)Gac>Tac	p.D557Y	ITGB6_ENST00000428609.2_Missense_Mutation_p.D515Y|ITGB6_ENST00000409872.1_Missense_Mutation_p.D557Y|ITGB6_ENST00000409967.2_Intron	NM_001282353.1|NM_001282354.1|NM_001282388.1	NP_001269282.1|NP_001269283.1|NP_001269317.1	P18564	ITB6_HUMAN	integrin, beta 6	557	Cysteine-rich tandem repeats.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|multicellular organismal development (GO:0007275)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	virus receptor activity (GO:0001618)	p.D557Y(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23						CAGTCACAGTCGCCGTTACCT	0.522																																																	1	Substitution - Missense(1)	kidney(1)						C	TYR/ASP	0,4406		0,0,2203	77.0	75.0	75.0		1669	4.2	1.0	2	dbSNP_134	75	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ITGB6	NM_000888.3	160	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	benign	557/789	160983104	1,13005	2203	4300	6503	SO:0001583	missense	3694				CCDS2212.1, CCDS63040.1, CCDS74596.1, CCDS74597.1	2q24.2	2010-03-23			ENSG00000115221	ENSG00000115221		"""Integrins"""	6161	protein-coding gene	gene with protein product		147558				1729173, 8120056	Standard	NM_001282353		Approved		uc002ubh.2	P18564	OTTHUMG00000132026	ENST00000283249.2:c.1669G>T	2.37:g.160983104C>A	ENSP00000283249:p.Asp557Tyr	Somatic		WXS	Illumina GAIIx	Phase_I	B2R9W5|C9JA97|Q0VA95|Q16500|Q53RG5|Q53RR6	Missense_Mutation	SNP	ENST00000283249.2	37	CCDS2212.1	.	.	.	.	.	.	.	.	.	.	C	13.27	2.186758	0.38609	0.0	1.16E-4	ENSG00000115221	ENST00000283249;ENST00000428609;ENST00000409872	D;D;D	0.93076	-3.16;-3.16;-3.16	5.1	4.17	0.49024	EGF, extracellular (1);	0.300984	0.36034	N	0.002825	D	0.90000	0.6878	L	0.41824	1.3	0.46981	D	0.999274	B;B	0.02656	0.0;0.0	B;B	0.12837	0.008;0.008	D	0.87537	0.2456	10	0.62326	D	0.03	.	15.4831	0.75542	0.1386:0.8614:0.0:0.0	.	515;557	E9PEE8;P18564	.;ITB6_HUMAN	Y	557;515;557	ENSP00000283249:D557Y;ENSP00000408024:D515Y;ENSP00000386367:D557Y	ENSP00000283249:D557Y	D	-	1	0	ITGB6	160691350	0.938000	0.31826	1.000000	0.80357	0.648000	0.38561	2.095000	0.41729	2.543000	0.85770	0.655000	0.94253	GAC		0.522	ITGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255036.1		NM_000888	
JMY	133746	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	78573870	78573870	+	Missense_Mutation	SNP	G	G	A			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr5:78573870G>A	ENST00000396137.4	+	2	1632	c.1170G>A	c.(1168-1170)atG>atA	p.M390I		NM_152405.4	NP_689618.4	Q8N9B5	JMY_HUMAN	junction mediating and regulatory protein, p53 cofactor	390					'de novo' actin filament nucleation (GO:0070060)|actin polymerization-dependent cell motility (GO:0070358)|Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of apoptotic process (GO:0043065)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.M36I(1)|p.M390I(1)		endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|urinary_tract(1)	16		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)		TCCGAGACATGAGAGAACTTG	0.438																																																	2	Substitution - Missense(2)	kidney(2)											135.0	128.0	130.0					5																	78573870		1907	4124	6031	SO:0001583	missense	133746			AK095189	CCDS4047.3	5q14.1	2010-03-23			ENSG00000152409	ENSG00000152409			28916	protein-coding gene	gene with protein product		604279				10518217	Standard	NM_152405		Approved	FLJ37870	uc003kfx.4	Q8N9B5	OTTHUMG00000131301	ENST00000396137.4:c.1170G>A	5.37:g.78573870G>A	ENSP00000379441:p.Met390Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A1L4P5|B5MDS2|B5MDT0	Missense_Mutation	SNP	ENST00000396137.4	37	CCDS4047.3	.	.	.	.	.	.	.	.	.	.	G	20.3	3.968994	0.74131	.	.	ENSG00000152409	ENST00000282259;ENST00000396137	T	0.07444	3.19	5.37	5.37	0.77165	.	0.043024	0.85682	D	0.000000	T	0.20047	0.0482	M	0.79693	2.465	0.58432	D	0.999998	P	0.39737	0.685	B	0.42343	0.384	T	0.01464	-1.1348	10	0.87932	D	0	.	19.0949	0.93246	0.0:0.0:1.0:0.0	.	390	Q8N9B5	JMY_HUMAN	I	390	ENSP00000379441:M390I	ENSP00000282259:M390I	M	+	3	0	JMY	78609626	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.980000	0.76160	2.525000	0.85131	0.650000	0.86243	ATG		0.438	JMY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254070.4		NM_152405	
KDM5C	8242	hgsc.bcm.edu	37	X	53223905	53223905	+	Missense_Mutation	SNP	C	C	T			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chrX:53223905C>T	ENST00000375401.3	-	23	3986	c.3454G>A	c.(3454-3456)Gag>Aag	p.E1152K	KDM5C_ENST00000375383.3_Missense_Mutation_p.E1111K|KDM5C_ENST00000452825.3_Missense_Mutation_p.E1085K|KDM5C_ENST00000375379.3_Missense_Mutation_p.E1152K|KDM5C_ENST00000404049.3_Missense_Mutation_p.E1151K	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	1152					histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						TGTTCCCCCTCCTTGAAGGCC	0.607			"""N, F, S"""		clear cell renal carcinoma																																			Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	0													169.0	119.0	136.0					X																	53223905		2203	4300	6503	SO:0001583	missense	8242			Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	11114	protein-coding gene	gene with protein product		314690	"""Jumonji, AT rich interactive domain 1C (RBP2-like)"", ""Smcy homolog, X-linked (mouse)"", ""jumonji, AT rich interactive domain 1C"", ""mental retardation, X-linked 13"""	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.3454G>A	X.37:g.53223905C>T	ENSP00000364550:p.Glu1152Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Missense_Mutation	SNP	ENST00000375401.3	37	CCDS14351.1	.	.	.	.	.	.	.	.	.	.	c	21.7	4.184278	0.78677	.	.	ENSG00000126012	ENST00000452825;ENST00000375401;ENST00000404049;ENST00000375379;ENST00000375383	D;D;D;D;D	0.86694	-2.16;-1.87;-1.87;-1.87;-2.01	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	D	0.92763	0.7699	M	0.80616	2.505	0.47737	D	0.999505	D;D;D	0.67145	0.996;0.985;0.985	D;P;P	0.67900	0.954;0.901;0.901	D	0.93636	0.6960	10	0.66056	D	0.02	-19.4892	14.082	0.64929	0.0:1.0:0.0:0.0	.	1085;1151;1152	F5H3T1;B0QZ44;P41229	.;.;KDM5C_HUMAN	K	1085;1152;1151;1152;1111	ENSP00000445176:E1085K;ENSP00000364550:E1152K;ENSP00000385394:E1151K;ENSP00000364528:E1152K;ENSP00000364532:E1111K	ENSP00000364528:E1152K	E	-	1	0	KDM5C	53240630	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.600000	0.67599	1.893000	0.54813	0.525000	0.51046	GAG		0.607	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2		NM_004187	
CFAP74	85452	broad.mit.edu;ucsc.edu	37	1	1919956	1919956	+	Missense_Mutation	SNP	C	C	A			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr1:1919956C>A	ENST00000434971.2	-	4	323	c.291G>T	c.(289-291)aaG>aaT	p.K97N				Q69YW0	CA222_HUMAN		0								p.K97N(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|stomach(1)	11	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.82e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.75e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CTCACCTCATCTTCTCAGTGA	0.587																																																	2	Substitution - Missense(2)	kidney(2)											87.0	91.0	90.0					1																	1919956		2084	4225	6309	SO:0001583	missense	85452																														ENST00000434971.2:c.291G>T	1.37:g.1919956C>A	ENSP00000408078:p.Lys97Asn	Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000434971.2	37		.	.	.	.	.	.	.	.	.	.	C	10.31	1.315088	0.23908	.	.	ENSG00000142609	ENST00000270720;ENST00000378590;ENST00000434971	T;T	0.62498	0.02;0.05	3.89	-2.12	0.07165	.	0.082857	0.45867	D	0.000325	T	0.68705	0.3030	M	0.67953	2.075	0.20764	N	0.999859	D;D	0.89917	0.999;1.0	D;D	0.87578	0.996;0.998	T	0.59958	-0.7356	10	0.66056	D	0.02	-17.8513	4.7183	0.12906	0.0:0.4279:0.1807:0.3914	.	97;97	Q9C0B2-2;Q9C0B2	.;K1751_HUMAN	N	97;88;97	ENSP00000367853:K88N;ENSP00000408078:K97N	ENSP00000270720:K97N	K	-	3	2	C1orf222	1909816	0.019000	0.18553	0.048000	0.18961	0.124000	0.20399	-0.510000	0.06328	-0.514000	0.06488	-0.391000	0.06502	AAG		0.587	C1orf222-201	KNOWN	basic	protein_coding	protein_coding				
KIF22	3835	broad.mit.edu;hgsc.bcm.edu	37	16	29810383	29810383	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr16:29810383delA	ENST00000160827.4	+	5	677	c.637delA	c.(637-639)aagfs	p.K213fs	KIF22_ENST00000569382.2_Frame_Shift_Del_p.K145fs|KIF22_ENST00000561482.1_Frame_Shift_Del_p.K145fs|KIF22_ENST00000400751.5_Frame_Shift_Del_p.K145fs|KIF22_ENST00000400750.2_5'UTR	NM_001256269.1|NM_007317.2	NP_001243198.1|NP_015556.1	Q14807	KIF22_HUMAN	kinesin family member 22	213	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|DNA repair (GO:0006281)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)			endometrium(1)|large_intestine(1)|lung(11)|skin(1)	14						TCTCTCCCAGAAGCCCATCAG	0.577																																																	0													72.0	77.0	76.0					16																	29810383		2197	4296	6493	SO:0001589	frameshift_variant	3835			D38751	CCDS10653.1, CCDS58444.1	16p11.2	2008-03-03	2003-01-09	2003-01-10	ENSG00000079616	ENSG00000079616		"""Kinesins"""	6391	protein-coding gene	gene with protein product		603213	"""kinesin-like 4"""	KNSL4		8599929, 11416179	Standard	NM_007317		Approved	Kid, OBP-1, OBP-2	uc002dts.4	Q14807	OTTHUMG00000097771	ENST00000160827.4:c.637delA	16.37:g.29810383delA	ENSP00000160827:p.Lys213fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2R5M0|B7Z265|O60845|O94814|Q53F58|Q9BT46	Frame_Shift_Del	DEL	ENST00000160827.4	37	CCDS10653.1																																																																																				0.577	KIF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215012.2			
KIR3DL3	115653	broad.mit.edu	37	19	55239272	55239272	+	Missense_Mutation	SNP	C	C	T			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr19:55239272C>T	ENST00000291860.1	+	4	569	c.551C>T	c.(550-552)cCc>cTc	p.P184L	KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000538269.1_Intron|KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000402254.2_Intron|CTB-61M7.1_ENST00000400864.3_RNA	NM_153443.3	NP_703144.2	Q8N743	KI3L3_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 3	184	Ig-like C2-type 2. {ECO:0000305}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P184L(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(3)|prostate(1)|skin(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		TCCATGGGTCCCATGACACCT	0.577																																																	1	Substitution - Missense(1)	kidney(1)											49.0	44.0	46.0					19																	55239272		1954	3357	5311	SO:0001583	missense	100133046			AF352324	CCDS12903.1	19q13.4	2014-05-22			ENSG00000242019	ENSG00000242019		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	16312	protein-coding gene	gene with protein product		610095				11513144	Standard	NM_153443		Approved	KIRC1, KIR3DL7, KIR44, CD158z	uc002qgu.1	Q8N743	OTTHUMG00000065884	ENST00000291860.1:c.551C>T	19.37:g.55239272C>T	ENSP00000291860:p.Pro184Leu	Somatic		WXS	Illumina GAIIx	Phase_I	A9PL62|A9PL64|A9PL65|A9PL66|A9PL67|A9PL68|A9PZV4|A9PZV7|A9PZV8|A9Q066|A9Q0R5|A9Q242|A9Q250|A9Q251|O95056|Q1X775|Q1X777|Q1X778|Q1X779|Q1X780|Q1X781|Q1X782|Q1X783|Q7Z7N4|Q8NHI2|Q8NHI3|Q9UEI4	Missense_Mutation	SNP	ENST00000291860.1	37	CCDS12903.1	.	.	.	.	.	.	.	.	.	.	N	7.948	0.744254	0.15710	.	.	ENSG00000242019	ENST00000291860	T	0.03124	4.04	1.38	0.171	0.15026	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.262225	0.19202	U	0.120151	T	0.11239	0.0274	H	0.95816	3.725	0.09310	N	1	B	0.29766	0.256	B	0.38056	0.264	T	0.12682	-1.0538	10	0.72032	D	0.01	.	4.5453	0.12078	0.3769:0.6231:0.0:0.0	.	184	Q8N743	KI3L3_HUMAN	L	184	ENSP00000291860:P184L	ENSP00000291860:P184L	P	+	2	0	KIR3DL3	59931084	0.001000	0.12720	0.001000	0.08648	0.013000	0.08279	0.957000	0.29215	0.101000	0.17610	0.205000	0.17691	CCC		0.577	KIR3DL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141147.1		NM_153443	
SMG1P5	595101	broad.mit.edu	37	16	30278810	30278811	+	IGR	INS	-	-	A	rs375050412		TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr16:30278810_30278811insA								RP11-347C12.1 (21688 upstream) : snoU13 (11757 downstream)																							aaagcaaaattaaaaaaaAAAA	0.292																																																	0																																										SO:0001628	intergenic_variant	440354																															16.37:g.30278821_30278821dupA		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	INS		37																																																																																				0	0.292									
LONP1	9361	broad.mit.edu;hgsc.bcm.edu	37	19	5699170	5699170	+	Missense_Mutation	SNP	A	A	T			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr19:5699170A>T	ENST00000360614.3	-	10	1710	c.1553T>A	c.(1552-1554)aTc>aAc	p.I518N	LONP1_ENST00000593119.1_Missense_Mutation_p.I454N|LONP1_ENST00000590729.1_Missense_Mutation_p.I388N|LONP1_ENST00000540670.2_Missense_Mutation_p.I322N|LONP1_ENST00000585374.1_Missense_Mutation_p.I404N	NM_004793.2	NP_004784.2			lon peptidase 1, mitochondrial									p.I518N(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GAAGCAGAGGATCTTGCCCTG	0.657																																																	1	Substitution - Missense(1)	kidney(1)											53.0	54.0	53.0					19																	5699170		2203	4300	6503	SO:0001583	missense	9361			U02389	CCDS12148.1, CCDS62507.1, CCDS62508.1	19p13.2	2014-01-28	2006-10-20	2006-10-20	ENSG00000196365	ENSG00000196365		"""ATPases / AAA-type"", ""Serine peptidases / Serine peptidases"""	9479	protein-coding gene	gene with protein product		605490	"""protease, serine, 15"""	PRSS15		8248235, 8119403	Standard	NM_004793		Approved	LonHS, hLON, PIM1	uc002mcx.4	P36776		ENST00000360614.3:c.1553T>A	19.37:g.5699170A>T	ENSP00000353826:p.Ile518Asn	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000360614.3	37	CCDS12148.1	.	.	.	.	.	.	.	.	.	.	A	29.2	4.987367	0.93106	.	.	ENSG00000196365	ENST00000360614;ENST00000358403;ENST00000540670	T;T	0.34472	1.62;1.36	5.08	5.08	0.68730	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.76828	0.4042	H	0.99609	4.655	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.996;0.996	D	0.86531	0.1822	10	0.87932	D	0	-33.3563	12.7987	0.57573	1.0:0.0:0.0:0.0	.	518;454;518	E5KMH8;Q8N8K8;P36776	.;.;LONM_HUMAN	N	518;482;322	ENSP00000353826:I518N;ENSP00000441523:I322N	ENSP00000351177:I482N	I	-	2	0	LONP1	5650170	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.994000	0.93529	1.921000	0.55644	0.448000	0.29417	ATC		0.657	LONP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451662.1		NM_004793	
LONRF1	91694	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	12592860	12592860	+	Missense_Mutation	SNP	T	T	G			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr8:12592860T>G	ENST00000398246.3	-	7	1570	c.1501A>C	c.(1501-1503)Aat>Cat	p.N501H	LONRF1_ENST00000530693.1_5'Flank|LONRF1_ENST00000533751.1_Missense_Mutation_p.N144H	NM_152271.3	NP_689484.3	Q17RB8	LONF1_HUMAN	LON peptidase N-terminal domain and ring finger 1	501							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)	p.N501H(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19				READ - Rectum adenocarcinoma(644;0.236)		TCAAGACAATTCTTACAGAAC	0.358																																																	1	Substitution - Missense(1)	kidney(1)											84.0	75.0	78.0					8																	12592860		1842	4094	5936	SO:0001583	missense	91694			AK074329	CCDS5987.2	8p23.1	2013-01-09			ENSG00000154359	ENSG00000154359		"""RING-type (C3HC4) zinc fingers"""	26302	protein-coding gene	gene with protein product						18253036	Standard	XM_005273685		Approved	FLJ23749, RNF191	uc003wwd.1	Q17RB8	OTTHUMG00000165475	ENST00000398246.3:c.1501A>C	8.37:g.12592860T>G	ENSP00000381298:p.Asn501His	Somatic		WXS	Illumina HiSeq	Phase_I	B4DM29|B4DU84|Q8TEA0|Q9BSV1	Missense_Mutation	SNP	ENST00000398246.3	37	CCDS5987.2	.	.	.	.	.	.	.	.	.	.	T	20.7	4.033732	0.75504	.	.	ENSG00000154359	ENST00000398246;ENST00000533751;ENST00000524526	D;D;D	0.84944	-1.92;-1.92;-1.92	5.17	5.17	0.71159	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type, conserved site (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.255106	0.42682	D	0.000674	T	0.77651	0.4162	N	0.16130	0.375	0.35678	D	0.81388	B;B	0.31413	0.142;0.322	B;B	0.40329	0.089;0.326	T	0.81854	-0.0741	10	0.52906	T	0.07	-15.6593	10.5208	0.44918	0.0:0.0838:0.0:0.9162	.	490;501	Q17RB8-2;Q17RB8	.;LONF1_HUMAN	H	501;144;104	ENSP00000381298:N501H;ENSP00000432130:N144H;ENSP00000433327:N104H	ENSP00000381298:N501H	N	-	1	0	LONRF1	12637231	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.917000	0.69989	2.254000	0.74563	0.460000	0.39030	AAT		0.358	LONRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251693.2		NM_152271	
LRP4	4038	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	46898361	46898361	+	Missense_Mutation	SNP	T	T	G			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr11:46898361T>G	ENST00000378623.1	-	24	3540	c.3298A>C	c.(3298-3300)Agc>Cgc	p.S1100R	LRP4-AS1_ENST00000502049.2_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1100					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)	p.S1100R(1)		breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		TGCAGTGTGCTGTCAGACCAG	0.547																																																	1	Substitution - Missense(1)	kidney(1)											175.0	139.0	151.0					11																	46898361		2201	4299	6500	SO:0001583	missense	4038			AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.3298A>C	11.37:g.46898361T>G	ENSP00000367888:p.Ser1100Arg	Somatic		WXS	Illumina HiSeq	Phase_I	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.343532	0.82022	.	.	ENSG00000134569	ENST00000378623	D	0.96685	-4.09	5.89	5.89	0.94794	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.95551	0.8554	N	0.25426	0.745	0.58432	D	0.999994	D	0.54397	0.966	P	0.58780	0.845	D	0.94545	0.7748	10	0.25106	T	0.35	.	16.3127	0.82898	0.0:0.0:0.0:1.0	.	1100	O75096	LRP4_HUMAN	R	1100	ENSP00000367888:S1100R	ENSP00000367888:S1100R	S	-	1	0	LRP4	46854937	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.065000	0.71176	2.246000	0.74042	0.533000	0.62120	AGC		0.547	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1		NM_002334	
KMT2D	8085	broad.mit.edu;hgsc.bcm.edu	37	12	49444844	49444844	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr12:49444844G>T	ENST00000301067.7	-	10	2621	c.2622C>A	c.(2620-2622)tgC>tgA	p.C874*		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	874	Pro-rich.			Missing (in Ref. 1; AAC51734). {ECO:0000305}.	chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.C874*(1)									CAGGTGCAGGGCATTGGCCTG	0.647																																																	1	Substitution - Nonsense(1)	kidney(1)											47.0	54.0	52.0					12																	49444844		1979	4166	6145	SO:0001587	stop_gained	8085			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.2622C>A	12.37:g.49444844G>T	ENSP00000301067:p.Cys874*	Somatic		WXS	Illumina HiSeq	Phase_I	O14687	Nonsense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.007891	0.93287	.	.	ENSG00000167548	ENST00000301067	.	.	.	3.75	-0.211	0.13172	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	8.0564	0.30608	0.383:0.0:0.617:0.0	.	.	.	.	X	874	.	ENSP00000301067:C874X	C	-	3	2	MLL2	47731111	0.893000	0.30496	0.001000	0.08648	0.719000	0.41307	-0.087000	0.11215	-0.047000	0.13423	0.563000	0.77884	TGC		0.647	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			
MSR1	4481	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	15977930	15977930	+	Missense_Mutation	SNP	G	G	C			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr8:15977930G>C	ENST00000262101.5	-	9	1340	c.1219C>G	c.(1219-1221)Caa>Gaa	p.Q407E	MSR1_ENST00000355282.2_Intron|MSR1_ENST00000445506.2_Missense_Mutation_p.Q425E|MSR1_ENST00000350896.3_Intron			P21757	MSRE_HUMAN	macrophage scavenger receptor 1	407	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				cholesterol transport (GO:0030301)|lipoprotein transport (GO:0042953)|plasma lipoprotein particle clearance (GO:0034381)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)	p.Q407E(1)		haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(7)|lung(14)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	37				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		AAATTACCTTGTCCAAAGTGA	0.507																																																	1	Substitution - Missense(1)	kidney(1)											75.0	75.0	75.0					8																	15977930		2203	4300	6503	SO:0001583	missense	4481			D13263	CCDS5995.1, CCDS5996.1, CCDS5997.1	8p22	2006-02-22			ENSG00000038945	ENSG00000038945		"""CD molecules"""	7376	protein-coding gene	gene with protein product		153622				2251254	Standard	NM_138715		Approved	SCARA1, CD204	uc003wwz.3	P21757	OTTHUMG00000094809	ENST00000262101.5:c.1219C>G	8.37:g.15977930G>C	ENSP00000262101:p.Gln407Glu	Somatic		WXS	Illumina HiSeq	Phase_I	D3DSP3|O60505|P21759|Q45F10	Missense_Mutation	SNP	ENST00000262101.5	37	CCDS5995.1	.	.	.	.	.	.	.	.	.	.	G	13.39	2.223815	0.39300	.	.	ENSG00000038945	ENST00000262101;ENST00000445506	T;T	0.33865	1.39;1.39	4.84	-0.743	0.11105	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	1.085560	0.07220	N	0.860802	T	0.27765	0.0683	L	0.31420	0.93	0.80722	D	1	B;B	0.10296	0.003;0.003	B;B	0.12837	0.008;0.008	T	0.08911	-1.0699	10	0.32370	T	0.25	.	11.947	0.52934	0.0:0.4998:0.3718:0.1284	.	425;407	B4DDJ5;P21757	.;MSRE_HUMAN	E	407;425	ENSP00000262101:Q407E;ENSP00000405453:Q425E	ENSP00000262101:Q407E	Q	-	1	0	MSR1	16022301	1.000000	0.71417	0.984000	0.44739	0.944000	0.59088	0.932000	0.28884	-0.251000	0.09542	0.655000	0.94253	CAA		0.507	MSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211627.2			
MTMR4	9110	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	56581545	56581546	+	Frame_Shift_Ins	INS	-	-	GT	rs527839252		TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr17:56581545_56581546insGT	ENST00000323456.5	-	14	1645_1646	c.1521_1522insAC	c.(1519-1524)tacggcfs	p.G508fs	MTMR4_ENST00000579925.1_Intron	NM_004687.4	NP_004678.3	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	508	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(10)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|skin(5)	36	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AGGAAGGTGCCGTAGAGGCAGG	0.559																																																	0																																										SO:0001589	frameshift_variant	9110			AB014547	CCDS11608.1	17q22-q23	2011-06-09				ENSG00000108389		"""Zinc fingers, FYVE domain containing"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7452	protein-coding gene	gene with protein product		603559				9736772	Standard	NM_004687		Approved	KIAA0647, ZFYVE11	uc002iwj.2	Q9NYA4		ENST00000323456.5:c.1520_1521dupAC	17.37:g.56581546_56581547dupGT	ENSP00000325285:p.Gly508fs	Somatic		WXS	Illumina HiSeq	Phase_I	D3DTZ6|Q8IV27|Q9Y4D5	Frame_Shift_Ins	INS	ENST00000323456.5	37	CCDS11608.1																																																																																				0.559	MTMR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444721.1		NM_004687	
NBPF1	55672	broad.mit.edu;hgsc.bcm.edu	37	1	16913638	16913638	+	Missense_Mutation	SNP	T	T	G			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr1:16913638T>G	ENST00000430580.2	-	11	1572	c.685A>C	c.(685-687)Atc>Ctc	p.I229L		NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	229	NBPF 1. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)									UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TCAAAGGTGATGTTGATGTTC	0.463																																																	0													411.0	371.0	384.0					1																	16913638		2195	4294	6489	SO:0001583	missense	55672			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481		"""neuroblastoma breakpoint family"""	26088	protein-coding gene	gene with protein product		610501				11214970, 16079250	Standard	NM_017940		Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.685A>C	1.37:g.16913638T>G	ENSP00000474456:p.Ile229Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q8N4E8|Q9C0H0	Missense_Mutation	SNP	ENST00000430580.2	37																																																																																					0.463	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000106436.3		NM_017940	
NKX2-2	4821	broad.mit.edu	37	20	21493005	21493005	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr20:21493005delG	ENST00000377142.4	-	2	734	c.378delC	c.(376-378)ggcfs	p.G126fs	NKX2-2-AS1_ENST00000549659.1_RNA	NM_002509.3	NP_002500.1	O95096	NKX22_HUMAN	NK2 homeobox 2	126					astrocyte differentiation (GO:0048708)|brain development (GO:0007420)|digestive tract development (GO:0048565)|endocrine pancreas development (GO:0031018)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|oligodendrocyte development (GO:0014003)|optic nerve development (GO:0021554)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell fate commitment (GO:0003327)|ventral spinal cord interneuron fate determination (GO:0060580)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|core promoter proximal region DNA binding (GO:0001159)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21						TTCGCTTCTTGCCGGCGTCCC	0.697																																																	0													13.0	15.0	14.0					20																	21493005		2199	4299	6498	SO:0001589	frameshift_variant	4821			AF019415	CCDS13145.1	20p11.22	2012-03-09	2007-07-09	2002-10-04	ENSG00000125820	ENSG00000125820		"""Homeoboxes / ANTP class : NKL subclass"""	7835	protein-coding gene	gene with protein product		604612	"""NK-2 (Drosophila) homolog B"", ""NK2 transcription factor related, locus 2 (Drosophila)"""	NKX2B		9703340, 1346742	Standard	NM_002509		Approved	NKX2.2	uc002wsi.3	O95096	OTTHUMG00000170524	ENST00000377142.4:c.378delC	20.37:g.21493005delG	ENSP00000366347:p.Gly126fs	Somatic		WXS	Illumina GAIIx	Phase_I		Frame_Shift_Del	DEL	ENST00000377142.4	37	CCDS13145.1																																																																																				0.697	NKX2-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078278.9			
NME2P1	283458	broad.mit.edu	37	12	120720247	120720247	+	IGR	SNP	G	G	A			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr12:120720247G>A								PXN (16673 upstream) : RNU4-2 (9318 downstream)														p.G48R(1)									ATTCTTCCCTGGGCTGGTGAA	0.597																																																	1	Substitution - Missense(1)	kidney(1)																																								SO:0001628	intergenic_variant	283458																															12.37:g.120720247G>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.597									
OR10G4	390264	broad.mit.edu;hgsc.bcm.edu	37	11	123886795	123886795	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr11:123886795C>T	ENST00000320891.4	+	1	514	c.514C>T	c.(514-516)Cag>Tag	p.Q172*		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	172						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q172*(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		TGGACCCAACCAGATCCAGCA	0.557																																																	1	Substitution - Nonsense(1)	kidney(1)											165.0	147.0	153.0					11																	123886795		2201	4287	6488	SO:0001587	stop_gained	390264			AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737		"""GPCR / Class A : Olfactory receptors"""	14809	protein-coding gene	gene with protein product							Standard	NM_001004462		Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.514C>T	11.37:g.123886795C>T	ENSP00000325076:p.Gln172*	Somatic		WXS	Illumina HiSeq	Phase_I	Q6IEW0	Nonsense_Mutation	SNP	ENST00000320891.4	37	CCDS31702.1	.	.	.	.	.	.	.	.	.	.	c	9.576	1.122264	0.20877	.	.	ENSG00000254737	ENST00000320891	.	.	.	3.33	2.39	0.29439	.	0.568844	0.14743	N	0.301047	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	.	7.5405	0.27735	0.1592:0.4265:0.4143:0.0	.	.	.	.	X	172	.	ENSP00000325076:Q172X	Q	+	1	0	OR10G4	123392005	0.000000	0.05858	0.149000	0.22428	0.232000	0.25224	-1.297000	0.02759	0.713000	0.32060	0.580000	0.79431	CAG		0.557	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1		NM_001004462	
PCDHB3	56132	hgsc.bcm.edu	37	5	140481633	140481633	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr5:140481633delC	ENST00000231130.2	+	1	1400	c.1400delC	c.(1399-1401)gccfs	p.A467fs	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	467	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AACAGCCCCGCCCTGCACATC	0.622																																																	0													80.0	81.0	81.0					5																	140481633		2202	4296	6498	SO:0001589	frameshift_variant	56132			AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"""Cadherins / Protocadherins : Clustered"""	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.1400delC	5.37:g.140481633delC	ENSP00000231130:p.Ala467fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2R8P2	Frame_Shift_Del	DEL	ENST00000231130.2	37	CCDS4245.1																																																																																				0.622	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2		NM_018937	
PDE1B	5153	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	54967242	54967242	+	Missense_Mutation	SNP	A	A	T			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr12:54967242A>T	ENST00000243052.3	+	9	1376	c.940A>T	c.(940-942)Aac>Tac	p.N314Y	PDE1B_ENST00000538346.1_Missense_Mutation_p.N273Y|PDE1B_ENST00000394277.3_3'UTR|PDE1B_ENST00000550620.1_Missense_Mutation_p.N294Y	NM_000924.3	NP_000915.1	Q01064	PDE1B_HUMAN	phosphodiesterase 1B, calmodulin-dependent	314	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cGMP catabolic process (GO:0046069)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|monocyte differentiation (GO:0030224)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of dopamine metabolic process (GO:0042053)|regulation of neurotransmitter levels (GO:0001505)|response to amphetamine (GO:0001975)|serotonin metabolic process (GO:0042428)|signal transduction (GO:0007165)|visual learning (GO:0008542)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity (GO:0048101)|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)	p.N314Y(1)		endometrium(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(4)	31					Bepridil(DB01244)|Caffeine(DB00201)|Felodipine(DB01023)|Nicardipine(DB00622)	CATTTTCATCAACCTCACCAA	0.463																																																	1	Substitution - Missense(1)	kidney(1)											131.0	115.0	121.0					12																	54967242		2203	4300	6503	SO:0001583	missense	5153			U56976	CCDS8882.1, CCDS53800.1, CCDS73477.1	12q13	2008-03-18				ENSG00000123360	3.1.4.17	"""Phosphodiesterases"""	8775	protein-coding gene	gene with protein product		171891		PDES1B		8855339, 9419816	Standard	NM_000924		Approved		uc001sgd.2	Q01064	OTTHUMG00000169844	ENST00000243052.3:c.940A>T	12.37:g.54967242A>T	ENSP00000243052:p.Asn314Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	Q92825|Q96KP3	Missense_Mutation	SNP	ENST00000243052.3	37	CCDS8882.1	.	.	.	.	.	.	.	.	.	.	A	19.45	3.830427	0.71258	.	.	ENSG00000123360	ENST00000243052;ENST00000538346;ENST00000550620	D;D;D	0.83992	-1.79;-1.79;-1.79	4.59	4.59	0.56863	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.060637	0.64402	D	0.000009	D	0.91026	0.7177	M	0.85542	2.76	0.54753	D	0.999989	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92218	0.5782	10	0.87932	D	0	.	12.2623	0.54658	1.0:0.0:0.0:0.0	.	294;314	Q01064-2;Q01064	.;PDE1B_HUMAN	Y	314;273;294	ENSP00000243052:N314Y;ENSP00000442559:N273Y;ENSP00000448519:N294Y	ENSP00000243052:N314Y	N	+	1	0	PDE1B	53253509	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.083000	0.76859	2.057000	0.61298	0.528000	0.53228	AAC		0.463	PDE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406203.1			
POLD3	10714	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	74340306	74340306	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr11:74340306delA	ENST00000263681.2	+	9	1073	c.944delA	c.(943-945)gaafs	p.E315fs	POLD3_ENST00000527458.1_Frame_Shift_Del_p.E276fs|POLD3_ENST00000532497.1_Frame_Shift_Del_p.E209fs	NM_006591.2	NP_006582.1	Q15054	DPOD3_HUMAN	polymerase (DNA-directed), delta 3, accessory subunit	315					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	delta DNA polymerase complex (GO:0043625)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|stomach(1)	18	Breast(11;3.21e-06)					AAGGAAACTGAAAACATGAGG	0.388																																																	0													154.0	151.0	152.0					11																	74340306		2200	4293	6493	SO:0001589	frameshift_variant	10714			D26018	CCDS8233.1	11q14	2014-06-13			ENSG00000077514	ENSG00000077514		"""DNA polymerases"""	20932	protein-coding gene	gene with protein product	"""DNA polymerase delta subunit p66"", ""Pol delta C subunit (p66)"", ""protein phosphatase 1, regulatory subunit 128"""	611415				10219083	Standard	NM_006591		Approved	P66, KIAA0039, P68, PPP1R128	uc001ovf.2	Q15054	OTTHUMG00000165621	ENST00000263681.2:c.944delA	11.37:g.74340306delA	ENSP00000263681:p.Glu315fs	Somatic		WXS	Illumina HiSeq	Phase_I	B7ZAI6|Q32MZ9|Q32N00	Frame_Shift_Del	DEL	ENST00000263681.2	37	CCDS8233.1																																																																																				0.388	POLD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385376.1		NM_006591	
PPARGC1B	133522	broad.mit.edu;hgsc.bcm.edu	37	5	149212567	149212567	+	Missense_Mutation	SNP	C	C	T			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr5:149212567C>T	ENST00000309241.5	+	5	963	c.931C>T	c.(931-933)Cca>Tca	p.P311S	PPARGC1B_ENST00000360453.4_Missense_Mutation_p.P272S|PPARGC1B_ENST00000403750.1_Missense_Mutation_p.P247S|PPARGC1B_ENST00000394320.3_Missense_Mutation_p.P311S	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	311					actin filament organization (GO:0007015)|bone trabecula formation (GO:0060346)|cellular lipid metabolic process (GO:0044255)|cellular response to reactive oxygen species (GO:0034614)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of phosphorylation (GO:0042327)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transcription from mitochondrial promoter (GO:0006390)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-2 domain binding (GO:0050682)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|receptor activator activity (GO:0030546)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)	p.P311S(1)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			GACCCCTGAGCCACTCCCCAA	0.632																																																	1	Substitution - Missense(1)	kidney(1)											40.0	47.0	44.0					5																	149212567		2203	4300	6503	SO:0001583	missense	133522			AF468496	CCDS4298.1, CCDS54933.1, CCDS54934.1	5q33.1	2013-02-12	2006-10-17		ENSG00000155846	ENSG00000155846		"""RNA binding motif (RRM) containing"""	30022	protein-coding gene	gene with protein product		608886	"""peroxisome proliferative activated receptor, gamma, coactivator 1, beta"""			11793024, 11854298	Standard	NM_133263		Approved	PERC, PGC1B	uc003lrc.3	Q86YN6	OTTHUMG00000130055	ENST00000309241.5:c.931C>T	5.37:g.149212567C>T	ENSP00000312649:p.Pro311Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Missense_Mutation	SNP	ENST00000309241.5	37	CCDS4298.1	.	.	.	.	.	.	.	.	.	.	C	7.348	0.622335	0.14193	.	.	ENSG00000155846	ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750	T;T;T;T	0.08458	3.16;3.09;3.1;3.16	5.61	3.64	0.41730	.	0.364252	0.26590	N	0.023529	T	0.05456	0.0144	L	0.29908	0.895	0.09310	N	1	B;P;B;B;B	0.38078	0.053;0.617;0.053;0.031;0.066	B;B;B;B;B	0.37144	0.019;0.242;0.032;0.009;0.018	T	0.30001	-0.9993	10	0.44086	T	0.13	-5.4821	2.4314	0.04472	0.2035:0.4628:0.1787:0.1549	.	290;290;272;311;311	Q86YN6-2;Q86YN6-4;Q86YN6-5;Q86YN6;Q86YN6-3	.;.;.;PRGC2_HUMAN;.	S	272;311;311;247	ENSP00000353638:P272S;ENSP00000377855:P311S;ENSP00000312649:P311S;ENSP00000384403:P247S	ENSP00000312649:P311S	P	+	1	0	PPARGC1B	149192760	0.018000	0.18449	0.932000	0.37286	0.290000	0.27261	0.356000	0.20181	1.369000	0.46134	0.655000	0.94253	CCA		0.632	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1		NM_133263	
PRKD1	5587	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	30132916	30132916	+	Missense_Mutation	SNP	C	C	T			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr14:30132916C>T	ENST00000331968.5	-	4	914	c.685G>A	c.(685-687)Gag>Aag	p.E229K	PRKD1_ENST00000415220.2_Missense_Mutation_p.E229K	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	229					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.E229K(2)		NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		AGAAGGGGCTCATCAGGGGCA	0.527																																																	2	Substitution - Missense(2)	kidney(2)											154.0	147.0	149.0					14																	30132916		2203	4300	6503	SO:0001583	missense	5587				CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	9407	protein-coding gene	gene with protein product		605435	"""protein kinase C, mu"""	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.685G>A	14.37:g.30132916C>T	ENSP00000333568:p.Glu229Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A6NL64|B2RAF6	Missense_Mutation	SNP	ENST00000331968.5	37	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	C	19.78	3.891852	0.72524	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	T;T	0.66099	-0.19;-0.16	5.93	5.93	0.95920	.	0.054186	0.64402	D	0.000001	T	0.64011	0.2560	M	0.66939	2.045	0.80722	D	1	P	0.37548	0.599	B	0.35607	0.206	T	0.63346	-0.6658	10	0.38643	T	0.18	-12.3313	20.3368	0.98748	0.0:1.0:0.0:0.0	.	229	Q15139	KPCD1_HUMAN	K	229	ENSP00000333568:E229K;ENSP00000390535:E229K	ENSP00000333568:E229K	E	-	1	0	PRKD1	29202667	1.000000	0.71417	0.999000	0.59377	0.984000	0.73092	7.307000	0.78920	2.805000	0.96524	0.655000	0.94253	GAG		0.527	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2		NM_002742	
PTPN12	5782	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	77256021	77256021	+	Splice_Site	SNP	G	G	A			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr7:77256021G>A	ENST00000248594.6	+	13	1297		c.e13-1		PTPN12_ENST00000435495.2_Splice_Site|PTPN12_ENST00000415482.2_Splice_Site	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12						protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)	p.?(1)		breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						TTGTTTTTCAGTTGCCTTGTT	0.408																																																	1	Unknown(1)	kidney(1)											58.0	56.0	57.0					7																	77256021		2203	4300	6503	SO:0001630	splice_region_variant	5782				CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.1026-1G>A	7.37:g.77256021G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Splice_Site	SNP	ENST00000248594.6	37	CCDS5592.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.944494	0.73672	.	.	ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000543073;ENST00000435495	.	.	.	6.17	6.17	0.99709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PTPN12	77093957	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	8.902000	0.92568	2.941000	0.99782	0.655000	0.94253	.		0.408	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3			Intron
PTPRC	5788	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	198723495	198723495	+	Missense_Mutation	SNP	G	G	T			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr1:198723495G>T	ENST00000367376.2	+	32	3772	c.3601G>T	c.(3601-3603)Gct>Tct	p.A1201S	PTPRC_ENST00000352140.3_Missense_Mutation_p.A1153S|PTPRC_ENST00000594404.1_Missense_Mutation_p.A1040S|PTPRC_ENST00000442510.2_Missense_Mutation_p.A1203S|PTPRC_ENST00000348564.6_Missense_Mutation_p.A1042S	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	1201	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.A1201S(1)		breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						AGTGGTAAAAGCTCTACGCAA	0.388																																																	1	Substitution - Missense(1)	kidney(1)											128.0	127.0	127.0					1																	198723495		2203	4300	6503	SO:0001583	missense	5788			Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.3601G>T	1.37:g.198723495G>T	ENSP00000356346:p.Ala1201Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	37		.	.	.	.	.	.	.	.	.	.	G	2.753	-0.259619	0.05791	.	.	ENSG00000081237	ENST00000367376;ENST00000352140;ENST00000442510;ENST00000348564	D	0.82893	-1.66	6.02	3.69	0.42338	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.307027	0.23698	N	0.045443	T	0.60248	0.2254	N	0.02916	-0.46	0.27843	N	0.941048	B;B;B	0.10296	0.003;0.003;0.003	B;B;B	0.15052	0.012;0.012;0.012	T	0.42699	-0.9436	10	0.02654	T	1	.	14.0661	0.64831	0.0:0.0:0.477:0.523	.	1042;1153;1201	B1ALS3;E9PC28;P08575	.;.;PTPRC_HUMAN	S	1203;1153;1201;1040	ENSP00000193532:A1153S	ENSP00000306782:A1040S	A	+	1	0	PTPRC	196990118	1.000000	0.71417	0.918000	0.36340	0.950000	0.60333	1.432000	0.34936	0.518000	0.28383	-1.075000	0.02238	GCT		0.388	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				
RAB11FIP4	84440	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	29857420	29857420	+	Missense_Mutation	SNP	A	A	G			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr17:29857420A>G	ENST00000325874.8	+	14	1959	c.1730A>G	c.(1729-1731)aAc>aGc	p.N577S	RAB11FIP4_ENST00000394744.2_Missense_Mutation_p.N475S	NM_032932.3	NP_116321.2	Q86YS3	RFIP4_HUMAN	RAB11 family interacting protein 4 (class II)	577	FIP-RBD. {ECO:0000255|PROSITE- ProRule:PRU00844}.|Necessary for interaction with RAB11A, subcellular location, homo- or heterooligomerization.				cytokinesis (GO:0000910)|transport (GO:0006810)|viral process (GO:0016032)	cleavage furrow (GO:0032154)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|midbody (GO:0030496)|recycling endosome membrane (GO:0055038)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)	p.N577S(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(10;3.62e-13)|all_epithelial(10;0.000387)|all_lung(9;0.0132)|Breast(31;0.014)|all_hematologic(16;0.015)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0259)|Ovarian(249;0.0423)|Lung NSC(157;0.066)				GAAGCAAAAAACCTCTTTGCT	0.542																																																	1	Substitution - Missense(1)	kidney(1)											103.0	104.0	104.0					17																	29857420		2203	4300	6503	SO:0001583	missense	84440			AB058724	CCDS11267.1	17q11.2	2013-01-10			ENSG00000131242	ENSG00000131242		"""EF-hand domain containing"""	30267	protein-coding gene	gene with protein product		611999				11347906, 11468690	Standard	NM_032932		Approved	RAB11-FIP4, KIAA1821, MGC11316, FLJ00131	uc002hgn.1	Q86YS3	OTTHUMG00000132787	ENST00000325874.8:c.1730A>G	17.37:g.29857420A>G	ENSP00000312837:p.Asn577Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q52LI1|Q8N829|Q8NDT7|Q969D8	Missense_Mutation	SNP	ENST00000325874.8	37	CCDS11267.1	.	.	.	.	.	.	.	.	.	.	A	13.61	2.287310	0.40494	.	.	ENSG00000131242	ENST00000325874;ENST00000394744	.	.	.	5.8	5.8	0.92144	Rab-binding domain FIP-RBD (1);	0.045491	0.85682	D	0.000000	T	0.48390	0.1497	L	0.36672	1.1	0.53688	D	0.999975	B;B	0.25312	0.123;0.006	B;B	0.29862	0.108;0.013	T	0.41610	-0.9499	8	.	.	.	-54.9815	12.5402	0.56165	1.0:0.0:0.0:0.0	.	475;577	Q86YS3-2;Q86YS3	.;RFIP4_HUMAN	S	577	.	.	N	+	2	0	RAB11FIP4	26881540	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	4.960000	0.63673	2.226000	0.72624	0.459000	0.35465	AAC		0.542	RAB11FIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256195.2		NM_032932	
RAB39B	116442	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	154490261	154490261	+	Missense_Mutation	SNP	C	C	T			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chrX:154490261C>T	ENST00000369454.3	-	2	769	c.469G>A	c.(469-471)Gcc>Acc	p.A157T		NM_171998.2	NP_741995.1	Q96DA2	RB39B_HUMAN	RAB39B, member RAS oncogene family	157					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|synapse organization (GO:0050808)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	GTP binding (GO:0005525)|myosin V binding (GO:0031489)	p.A157T(1)		breast(1)|central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(12)	19	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					ACATTAATGGCATCTCGGGCT	0.512																																																	1	Substitution - Missense(1)	kidney(1)											108.0	86.0	94.0					X																	154490261		2203	4300	6503	SO:0001583	missense	116442			AY052478	CCDS14766.1	Xq28	2014-01-31			ENSG00000155961	ENSG00000155961		"""RAB, member RAS oncogene"""	16499	protein-coding gene	gene with protein product		300774	"""mental retardation, X-linked 72"""	MRX72		12438742, 20159109	Standard	NM_171998		Approved		uc004fne.3	Q96DA2	OTTHUMG00000022659	ENST00000369454.3:c.469G>A	X.37:g.154490261C>T	ENSP00000358466:p.Ala157Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q5JT79|Q8NEX3	Missense_Mutation	SNP	ENST00000369454.3	37	CCDS14766.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.692578	0.88735	.	.	ENSG00000155961	ENST00000369454	T	0.79845	-1.31	5.17	5.17	0.71159	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.78805	0.4341	L	0.41710	1.295	0.58432	D	0.999994	P	0.41366	0.747	P	0.45232	0.474	T	0.81782	-0.0775	10	0.87932	D	0	.	15.2574	0.73596	0.0:1.0:0.0:0.0	.	157	Q96DA2	RB39B_HUMAN	T	157	ENSP00000358466:A157T	ENSP00000358466:A157T	A	-	1	0	RAB39B	154143455	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.420000	0.80191	2.280000	0.76307	0.513000	0.50165	GCC		0.512	RAB39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058792.1		NM_171998	
RASSF9	9182	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	86199472	86199472	+	Nonsense_Mutation	SNP	C	C	A	rs562341468		TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr12:86199472C>A	ENST00000361228.3	-	2	684	c.316G>T	c.(316-318)Gag>Tag	p.E106*		NM_005447.3	NP_005438.2	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	106	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				endosomal transport (GO:0016197)|protein targeting (GO:0006605)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|trans-Golgi network transport vesicle membrane (GO:0012510)	transporter activity (GO:0005215)	p.E106*(2)		endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TTGGGCTGCTCATCTCCCCAC	0.453																																																	2	Substitution - Nonsense(2)	kidney(2)											119.0	120.0	120.0					12																	86199472		1915	4136	6051	SO:0001587	stop_gained	9182				CCDS44950.1	12q21.31	2008-02-22	2008-02-22	2008-02-22		ENSG00000198774			15739	protein-coding gene	gene with protein product		610383	"""peptidylglycine alpha-amidating monooxygenase COOH-terminal interactor"""	PAMCI		9837933, 18272789	Standard	NM_005447		Approved	P-CIP1	uc001taf.1	O75901	OTTHUMG00000169831	ENST00000361228.3:c.316G>T	12.37:g.86199472C>A	ENSP00000354884:p.Glu106*	Somatic		WXS	Illumina HiSeq	Phase_I	B3KMQ4|Q8N5U8	Nonsense_Mutation	SNP	ENST00000361228.3	37	CCDS44950.1	.	.	.	.	.	.	.	.	.	.	C	37	6.447107	0.97572	.	.	ENSG00000198774	ENST00000361228	.	.	.	4.96	4.96	0.65561	.	0.064498	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-19.6655	18.5686	0.91126	0.0:1.0:0.0:0.0	.	.	.	.	X	106	.	ENSP00000354884:E106X	E	-	1	0	RASSF9	84723603	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	4.779000	0.62375	2.471000	0.83476	0.609000	0.83330	GAG		0.453	RASSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406109.1			
RBMXL1	494115	hgsc.bcm.edu	37	1	89449509	89449509	+	Start_Codon_Del	DEL	T	T	-	rs78548172	byFrequency	TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr1:89449509delT	ENST00000321792.5	-	0	428				CCBL2_ENST00000446900.2_Intron|RBMXL1_ENST00000399794.2_Start_Codon_Del|CCBL2_ENST00000370485.2_Intron|CCBL2_ENST00000260508.4_Intron|CCBL2_ENST00000370491.3_Intron|RBMXL1_ENST00000413769.1_5'UTR	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1						mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										GCTTCAACCATTTTTTTTTTT	0.498											OREG0013593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					0													105.0	108.0	107.0					1																	89449509		2203	4300	6503	SO:0001582	initiator_codon_variant	494115			BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661		1.37:g.89449509delT		Somatic	1267	WXS	Illumina HiSeq	Phase_I		Frame_Shift_Del	DEL	ENST00000321792.5	37	CCDS716.1																																																																																				0.498	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3		NM_019610	
LAMTOR2	28956	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	156025137	156025137	+	Missense_Mutation	SNP	A	A	C			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr1:156025137A>C	ENST00000368305.4	+	2	290	c.152A>C	c.(151-153)aAc>aCc	p.N51T	UBQLN4_ENST00000472638.1_5'Flank|LAMTOR2_ENST00000368304.5_Missense_Mutation_p.N51T|LAMTOR2_ENST00000368302.3_Missense_Mutation_p.N51T|UBQLN4_ENST00000368309.3_5'Flank|LAMTOR2_ENST00000489664.1_3'UTR	NM_014017.3	NP_054736.1	Q9Y2Q5	LTOR2_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 2	51					activation of MAPKK activity (GO:0000186)|cell growth (GO:0016049)|cellular protein localization (GO:0034613)|cellular response to amino acid stimulus (GO:0071230)|positive regulation of GTPase activity (GO:0043547)|positive regulation of TOR signaling (GO:0032008)	extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|Ragulator complex (GO:0071986)		p.N51T(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	7						ATAGCCAGTAACATCTGGGCC	0.577																																																	1	Substitution - Missense(1)	kidney(1)											98.0	100.0	99.0					1																	156025137		2203	4300	6503	SO:0001583	missense	0			BC024190	CCDS1128.1, CCDS44243.1	1q22	2014-09-17	2011-02-15	2011-02-15	ENSG00000116586	ENSG00000116586			29796	protein-coding gene	gene with protein product	"""mitogen activated protein binding protein interacting protein"", ""MAPKSP1 adaptor protein"", ""endosomal adaptor protein"""	610389	"""roadblock domain containing 3"""	ROBLD3		11042152	Standard	NM_014017		Approved	MAPBPIP, MAPKSP1AP, p14, ENDAP, Ragulator2	uc001fnb.3	Q9Y2Q5	OTTHUMG00000017462	ENST00000368305.4:c.152A>C	1.37:g.156025137A>C	ENSP00000357288:p.Asn51Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VY97|Q5VY98|Q5VY99	Missense_Mutation	SNP	ENST00000368305.4	37	CCDS1128.1	.	.	.	.	.	.	.	.	.	.	A	34	5.312518	0.95655	.	.	ENSG00000116586	ENST00000368305;ENST00000368304;ENST00000368302	T;T;T	0.20738	2.05;2.05;2.05	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.37489	0.1005	M	0.85945	2.785	0.80722	D	1	P;P	0.45827	0.47;0.867	P;P	0.56278	0.524;0.795	T	0.36286	-0.9754	10	0.72032	D	0.01	-15.5034	14.8012	0.69916	1.0:0.0:0.0:0.0	.	51;51	Q5VY98;Q9Y2Q5	.;LTOR2_HUMAN	T	51	ENSP00000357288:N51T;ENSP00000357287:N51T;ENSP00000357285:N51T	ENSP00000357285:N51T	N	+	2	0	LAMTOR2	154291761	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.677000	0.91203	2.170000	0.68504	0.533000	0.62120	AAC		0.577	LAMTOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046197.1		NM_014017	
RPGRIP1	57096	hgsc.bcm.edu;ucsc.edu	37	14	21793467	21793467	+	Silent	SNP	G	G	A	rs35207255	byFrequency	TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr14:21793467G>A	ENST00000400017.2	+	15	2292	c.2292G>A	c.(2290-2292)gcG>gcA	p.A764A	RPGRIP1_ENST00000307974.4_Silent_p.A123A|RPGRIP1_ENST00000557771.1_Silent_p.A726A|RPGRIP1_ENST00000206660.6_Silent_p.A764A|RPGRIP1_ENST00000556336.1_Intron|RPGRIP1_ENST00000382933.4_Intron|RPGRIP1_ENST00000553500.1_3'UTR	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	764			A -> V (does not affect the interaction with NPHP4). {ECO:0000269|PubMed:21224891}.		eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)				breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		GCCTACAGGCGTGCAATAAAC	0.537													A|||	30	0.00599042	0.0212	0.0029	5008	,	,		20160	0.0		0.0	False		,,,				2504	0.0																0								A		73,3693		1,71,1811	40.0	40.0	40.0		2292	4.2	1.0	14	dbSNP_126	40	4,8206		0,4,4101	no	coding-synonymous	RPGRIP1	NM_020366.3		1,75,5912	AA,AG,GG		0.0487,1.9384,0.643		764/1287	21793467	77,11899	1883	4105	5988	SO:0001819	synonymous_variant	57096			AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.2292G>A	14.37:g.21793467G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Silent	SNP	ENST00000400017.2	37	CCDS45080.1																																																																																				0.537	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1		NM_020366	
RRAD	6236	broad.mit.edu	37	16	66956073	66956073	+	Missense_Mutation	SNP	G	G	T			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr16:66956073G>T	ENST00000299759.6	-	5	1083	c.833C>A	c.(832-834)gCg>gAg	p.A278E	RRAD_ENST00000420652.1_Missense_Mutation_p.A278E			P55042	RAD_HUMAN	Ras-related associated with diabetes	278	Calmodulin-binding.				small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.A278E(6)		endometrium(2)|kidney(4)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|urinary_tract(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0862)|Epithelial(162;0.198)		GAAGCGCTTCGCCTTTTTGCC	0.612																																																	6	Substitution - Missense(6)	kidney(4)|prostate(1)|endometrium(1)											94.0	75.0	81.0					16																	66956073		2200	4300	6500	SO:0001583	missense	6236			L24564	CCDS10824.1	16q22	2014-05-09			ENSG00000166592	ENSG00000166592			10446	protein-coding gene	gene with protein product		179503				7859947	Standard	NM_004165		Approved	REM3, RAD	uc002eqo.2	P55042	OTTHUMG00000137511	ENST00000299759.6:c.833C>A	16.37:g.66956073G>T	ENSP00000299759:p.Ala278Glu	Somatic		WXS	Illumina GAIIx	Phase_I	Q96F39	Missense_Mutation	SNP	ENST00000299759.6	37	CCDS10824.1	.	.	.	.	.	.	.	.	.	.	G	36	5.625454	0.96671	.	.	ENSG00000166592	ENST00000420652;ENST00000299759	T;T	0.68181	-0.31;-0.31	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.83524	0.5273	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84232	0.0467	10	0.87932	D	0	.	20.328	0.98708	0.0:0.0:1.0:0.0	.	278	P55042	RAD_HUMAN	E	278	ENSP00000388744:A278E;ENSP00000299759:A278E	ENSP00000299759:A278E	A	-	2	0	RRAD	65513574	1.000000	0.71417	0.969000	0.41365	0.983000	0.72400	9.471000	0.97696	2.802000	0.96397	0.561000	0.74099	GCG		0.612	RRAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268830.1		NM_004165	
SGIP1	84251	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	67147913	67147913	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr1:67147913delT	ENST00000371037.4	+	15	1253	c.1176delT	c.(1174-1176)gatfs	p.D392fs	SGIP1_ENST00000237247.6_Frame_Shift_Del_p.D396fs|SGIP1_ENST00000371039.1_Intron|SGIP1_ENST00000371035.3_Intron|SGIP1_ENST00000371036.3_Intron	NM_032291.2	NP_115667.2	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting protein 1	392	Pro-rich.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of feeding behavior (GO:2000253)|positive regulation of receptor-mediated endocytosis (GO:0048260)|response to dietary excess (GO:0002021)	AP-2 adaptor complex (GO:0030122)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	microtubule binding (GO:0008017)|phospholipid binding (GO:0005543)|SH3 domain binding (GO:0017124)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(43)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	71						TTAAAGATGATTACTTAGAAA	0.512																																																	0													77.0	87.0	84.0					1																	67147913		2203	4300	6503	SO:0001589	frameshift_variant	84251			AL136561	CCDS30744.1	1p31.3	2008-02-05			ENSG00000118473	ENSG00000118473			25412	protein-coding gene	gene with protein product		611540				11230166	Standard	NM_032291		Approved	DKFZp761D221	uc001dcr.3	Q9BQI5	OTTHUMG00000009161	ENST00000371037.4:c.1176delT	1.37:g.67147913delT	ENSP00000360076:p.Asp392fs	Somatic		WXS	Illumina HiSeq	Phase_I	A6NL81|A6NLD1|Q4LE32|Q5VYE2|Q5VYE3|Q5VYE4|Q68D76|Q6MZY6|Q8IWC2	Frame_Shift_Del	DEL	ENST00000371037.4	37	CCDS30744.1																																																																																				0.512	SGIP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025395.4		NM_032291	
SGSM1	129049	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	25282686	25282686	+	Missense_Mutation	SNP	A	A	C			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr22:25282686A>C	ENST00000400359.4	+	17	1933	c.1926A>C	c.(1924-1926)gaA>gaC	p.E642D	SGSM1_ENST00000400358.4_Missense_Mutation_p.E587D	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	642	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.					Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)	p.E642D(1)|p.E587D(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						CGGAAACAGAAAGGAAAGAGG	0.592																																																	2	Substitution - Missense(2)	kidney(2)											21.0	20.0	20.0					22																	25282686		1983	4148	6131	SO:0001583	missense	129049			AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"""Small G protein signaling modulators"""	29410	protein-coding gene	gene with protein product		611417	"""RUN and TBC1 domain containing 2"""	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.1926A>C	22.37:g.25282686A>C	ENSP00000383212:p.Glu642Asp	Somatic		WXS	Illumina HiSeq	Phase_I	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Missense_Mutation	SNP	ENST00000400359.4	37	CCDS46674.1	.	.	.	.	.	.	.	.	.	.	A	14.82	2.649922	0.47362	.	.	ENSG00000167037	ENST00000403206;ENST00000400358;ENST00000400359	T;T	0.04809	3.55;3.55	5.85	-11.7	0.00046	Rab-GAP/TBC domain (2);	0.390997	0.32852	N	0.005573	T	0.02455	0.0075	L	0.31294	0.92	0.43399	D	0.995528	B;B;B;B	0.14438	0.01;0.003;0.007;0.0	B;B;B;B	0.15484	0.004;0.006;0.013;0.001	T	0.46091	-0.9216	10	0.36615	T	0.2	-5.3417	8.7397	0.34550	0.1377:0.1794:0.618:0.0648	.	587;703;720;642	Q2NKQ1-4;C9J7S8;Q2NKQ1-3;Q2NKQ1	.;.;.;SGSM1_HUMAN	D	703;587;642	ENSP00000383211:E587D;ENSP00000383212:E642D	ENSP00000383211:E587D	E	+	3	2	SGSM1	23612686	0.213000	0.23551	0.094000	0.20943	0.746000	0.42486	-0.542000	0.06091	-2.563000	0.00472	-0.290000	0.09829	GAA		0.592	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1		XM_059318	
SHROOM1	134549	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	132160424	132160424	+	Missense_Mutation	SNP	G	G	A	rs201446106		TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr5:132160424G>A	ENST00000378679.3	-	6	1928	c.1124C>T	c.(1123-1125)aCc>aTc	p.T375I	SHROOM1_ENST00000378676.1_Intron|SHROOM1_ENST00000319854.3_Missense_Mutation_p.T375I|SHROOM1_ENST00000488072.1_5'Flank	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	375					actin filament bundle assembly (GO:0051017)|cell morphogenesis (GO:0000902)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|myosin II complex (GO:0016460)	actin filament binding (GO:0051015)	p.T375I(1)		endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CACAATGCAGGTCTCTGAGAC	0.582																																																	1	Substitution - Missense(1)	kidney(1)											76.0	82.0	80.0					5																	132160424		2203	4300	6503	SO:0001583	missense	134549			AF314142	CCDS4161.1, CCDS54902.1	5q31.1	2007-05-03			ENSG00000164403	ENSG00000164403			24084	protein-coding gene	gene with protein product		611179				11853319, 16615870	Standard	NM_133456		Approved	APXL2, KIAA1960	uc003kxy.2	Q2M3G4	OTTHUMG00000059835	ENST00000378679.3:c.1124C>T	5.37:g.132160424G>A	ENSP00000367950:p.Thr375Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B7WP40|B7ZL01|Q8TDP0|Q8TF41	Missense_Mutation	SNP	ENST00000378679.3	37	CCDS54902.1	.	.	.	.	.	.	.	.	.	.	G	14.35	2.508299	0.44660	.	.	ENSG00000164403	ENST00000378679;ENST00000319854	T;T	0.24723	1.84;1.84	3.49	1.66	0.24008	.	1.199520	0.05799	N	0.611848	T	0.15522	0.0374	N	0.24115	0.695	0.24187	N	0.99557	P;B	0.35348	0.496;0.363	B;B	0.31245	0.126;0.059	T	0.24012	-1.0172	10	0.39692	T	0.17	-7.7636	4.1079	0.10045	0.1235:0.0:0.6315:0.245	.	375;375	Q2M3G4-2;Q2M3G4	.;SHRM1_HUMAN	I	375	ENSP00000367950:T375I;ENSP00000324245:T375I	ENSP00000324245:T375I	T	-	2	0	SHROOM1	132188323	0.002000	0.14202	0.251000	0.24312	0.569000	0.35902	0.664000	0.25068	0.450000	0.26774	0.561000	0.74099	ACC		0.582	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1		NM_133456	
SHROOM4	57477	hgsc.bcm.edu	37	X	50350758	50350759	+	In_Frame_Ins	INS	-	-	TGCTGCTGCTGT	rs201922875|rs553160982		TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chrX:50350758_50350759insTGCTGCTGCTGT	ENST00000289292.7	-	6	3666_3667	c.3383_3384insACAGCAGCAGCA	c.(3382-3384)cag>caACAGCAGCAGCAg	p.1128_1128Q>QQQQQ	SHROOM4_ENST00000460112.3_In_Frame_Ins_p.1012_1012Q>QQQQQ|SHROOM4_ENST00000376020.2_In_Frame_Ins_p.1128_1128Q>QQQQQ			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1128	Gln-rich.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					cctgttgcttctgctgctgctg	0.589																																																	0										12,1892,1813		0,4,5,3,450,721,267,412,263						-6.4	0.0			16	21,2147,4298		1,7,3,9,306,942,586,1095,1163	no	codingComplex	SHROOM4	NM_020717.3		1,11,8,12,756,1663,853,1507,1426	A1A1,A1A2,A1R,A1,A2A2,A2R,A2,RR,R		33.5292,49.0987,39.9882				33,4039,6111				SO:0001652	inframe_insertion	57477			AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3372_3383dupACAGCAGCAGCA	X.37:g.50350758_50350759insTGCTGCTGCTGT	ENSP00000289292:p.GlnGlnGlnGln1128dup	Somatic		WXS	Illumina HiSeq	Phase_I	A7E2X9|D6RFW0|Q96LA0	In_Frame_Ins	INS	ENST00000289292.7	37	CCDS35277.1																																																																																				0.589	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4		NM_020717	
SIGLEC12	89858	hgsc.bcm.edu	37	19	52004791	52004792	+	Frame_Shift_Ins	INS	-	-	C	rs66949844	byFrequency	TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr19:52004791_52004792insC	ENST00000291707.3	-	1	251_252	c.196_197insG	c.(196-198)gcafs	p.A66fs	SIGLEC12_ENST00000598614.1_5'Flank	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	66	Ig-like V-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.A66V(1)|p.A66fs*50(1)		NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		ATGGTCCCCTGCCCGGAACCAG	0.599													?|CCC|CCCC|unsure	2969	0.592851	0.5953	0.745	5008	,	,		16981	0.369		0.67	False		,,,				2504	0.6329																2	Substitution - Missense(1)|Insertion - Frameshift(1)	biliary_tract(1)|liver(1)								2597,1667		799,999,334						1.2	0.0		dbSNP_130	79	5544,2710		1845,1854,428	no	frameshift	SIGLEC12	NM_053003.2		2644,2853,762	A1A1,A1R,RR		32.8326,39.0947,34.9656				8141,4377				SO:0001589	frameshift_variant	89858			AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15482	protein-coding gene	gene with protein product		606094	"""SIGLEC-like 1"", ""sialic acid binding Ig-like lectin 12"""	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.197dupG	19.37:g.52004794_52004794dupC	ENSP00000291707:p.Ala66fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q8IYH7	Frame_Shift_Ins	INS	ENST00000291707.3	37	CCDS12833.1																																																																																				0.599	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2		NM_053003	
SLC17A3	10786	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	25850134	25850134	+	Silent	SNP	A	A	G			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr6:25850134A>G	ENST00000360657.3	-	9	1221	c.936T>C	c.(934-936)aaT>aaC	p.N312N	SLC17A3_ENST00000361703.6_Silent_p.N312N|SLC17A3_ENST00000397060.4_Silent_p.N390N			O00476	NPT4_HUMAN	solute carrier family 17 (organic anion transporter), member 3	312					drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|glucose-6-phosphate transport (GO:0015760)|ion transmembrane transport (GO:0034220)|organic acid transport (GO:0015849)|organic anion transport (GO:0015711)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|regulation of anion transport (GO:0044070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|efflux transmembrane transporter activity (GO:0015562)|organic anion transmembrane transporter activity (GO:0008514)|sodium:phosphate symporter activity (GO:0005436)|toxin transporter activity (GO:0019534)|urate transmembrane transporter activity (GO:0015143)|voltage-gated anion channel activity (GO:0008308)	p.N312N(1)|p.N390N(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)	20						TATAGCCGGAATTGAGGTAAG	0.433																																																	2	Substitution - coding silent(2)	kidney(2)											97.0	97.0	97.0					6																	25850134		2203	4300	6503	SO:0001819	synonymous_variant	10786			U90545	CCDS4566.2, CCDS47385.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124564	ENSG00000124564		"""Solute carriers"""	10931	protein-coding gene	gene with protein product		611034	"""solute carrier family 17 (sodium phosphate), member 3"""			9149941	Standard	NM_006632		Approved	NPT4	uc003nfk.4	O00476	OTTHUMG00000014412	ENST00000360657.3:c.936T>C	6.37:g.25850134A>G		Somatic		WXS	Illumina HiSeq	Phase_I	B7WNJ5|B7Z511|Q8WWC7|Q9H533	Silent	SNP	ENST00000360657.3	37	CCDS4566.2																																																																																				0.433	SLC17A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040070.2			
SLCO2B1	11309	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	74876867	74876867	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr11:74876867delT	ENST00000289575.5	+	4	716	c.321delT	c.(319-321)tatfs	p.Y107fs	SLCO2B1_ENST00000525650.1_Intron|SLCO2B1_ENST00000341411.4_5'UTR|SLCO2B1_ENST00000526660.1_Intron|SLCO2B1_ENST00000532236.1_5'UTR|SLCO2B1_ENST00000428359.2_Frame_Shift_Del_p.Y85fs|SLCO2B1_ENST00000454962.2_5'UTR|SLCO2B1_ENST00000531756.1_Intron	NM_007256.4	NP_009187	O94956	SO2B1_HUMAN	solute carrier organic anion transporter family, member 2B1	107					liver development (GO:0001889)|sodium-independent icosanoid transport (GO:0071718)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid transmembrane transporter activity (GO:0015125)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(2)|endometrium(1)|large_intestine(7)|lung(20)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	39					Acetic acid(DB03166)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)|Ergoloid mesylate(DB01049)|Estradiol(DB00783)|Estrone(DB00655)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Glyburide(DB01016)|Ibuprofen(DB01050)|Iloprost(DB01088)|Latanoprost(DB00654)|Montelukast(DB00471)|Niacin(DB00627)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Tolbutamide(DB01124)	TTGTGAGCTATTTTGGCAGCC	0.587																																																	0													178.0	156.0	164.0					11																	74876867		2200	4293	6493	SO:0001589	frameshift_variant	11309			AB026256	CCDS8235.1, CCDS44683.1, CCDS53679.1	11q13	2013-05-22	2003-11-25	2003-11-26				"""Solute carriers"""	10962	protein-coding gene	gene with protein product		604988	"""solute carrier family 21 (organic anion transporter), member 9"""	SLC21A9			Standard	NM_007256		Approved	OATP-B, OATP2B1	uc001owb.3	O94956		ENST00000289575.5:c.321delT	11.37:g.74876867delT	ENSP00000289575:p.Tyr107fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8K2G9|B4DGA9|B4DTB0|E7ERN5|E9PPU8|Q9H2Z0|Q9UFU1	Frame_Shift_Del	DEL	ENST00000289575.5	37	CCDS8235.1																																																																																				0.587	SLCO2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383933.1		NM_007256	
STON2	85439	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	81736986	81736987	+	Missense_Mutation	DNP	GC	GC	AT			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr14:81736986_81736987GC>AT	ENST00000267540.2	-	5	2840_2841	c.2640_2641GC>AT	c.(2638-2643)atGCtt>atATtt	p.880_881ML>IF	STON2_ENST00000555447.1_Intron	NM_033104.3	NP_149095.2	Q8WXE9	STON2_HUMAN	stonin 2	880					hematopoietic progenitor cell differentiation (GO:0002244)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|synaptic vesicle (GO:0008021)		p.L881F(1)|p.M880I(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|pancreas(2)|prostate(1)|skin(5)	34				BRCA - Breast invasive adenocarcinoma(234;0.0348)		GGAGTTGGAAGCATTAGCCAGA	0.47																																																	2	Substitution - Missense(2)	kidney(2)																																								SO:0001583	missense	85439			AB208948	CCDS9875.1, CCDS58332.1	14q31.1	2007-08-01				ENSG00000140022			30652	protein-coding gene	gene with protein product	"""stoned B homolog 2 (Drosophila)"""	608467				11381094, 11454741	Standard	NM_033104		Approved	STNB2, STN2	uc001xvk.2	Q8WXE9		ENST00000267540.2:c.2640_2641delinsAT	14.37:g.81736986_81736987delinsAT	ENSP00000267540:p.M880_L881delinsIF	Somatic		WXS	Illumina HiSeq	Phase_I	G3V2T7|Q17R24|Q59H11|Q6NT47|Q96RI7|Q96RU6	Missense_Mutation	SNP	ENST00000267540.2	37	CCDS9875.1																																																																																				0.470	STON2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413317.1		NM_033104	
SYBU	55638	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	110587762	110587762	+	Silent	SNP	G	G	A			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr8:110587762G>A	ENST00000422135.1	-	8	1880	c.1365C>T	c.(1363-1365)gaC>gaT	p.D455D	SYBU_ENST00000533895.1_Silent_p.D454D|SYBU_ENST00000533065.1_Silent_p.D336D|SYBU_ENST00000533171.1_Silent_p.D455D|SYBU_ENST00000529690.1_Silent_p.D325D|SYBU_ENST00000527707.1_5'Flank|SYBU_ENST00000532779.1_Silent_p.D387D|SYBU_ENST00000529175.1_Silent_p.D249D|SYBU_ENST00000440310.1_Silent_p.D455D|SYBU_ENST00000446070.2_Silent_p.D454D|SYBU_ENST00000528331.1_Silent_p.D336D|SYBU_ENST00000408889.3_Silent_p.D336D|SYBU_ENST00000419099.1_Silent_p.D454D|SYBU_ENST00000528647.1_Silent_p.D454D|SYBU_ENST00000276646.9_Silent_p.D455D|SYBU_ENST00000433638.1_Silent_p.D455D|SYBU_ENST00000424158.2_Silent_p.D460D|SYBU_ENST00000408908.2_Silent_p.D455D|SYBU_ENST00000399066.3_Silent_p.D452D	NM_001099744.1	NP_001093214.1	Q9NX95	SYBU_HUMAN	syntabulin (syntaxin-interacting)	455					regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|dense body (GO:0097433)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.D452D(1)		NS(1)|breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	30						CAAGCTCCAGGTCACCAGATT	0.577																																																	1	Substitution - coding silent(1)	kidney(1)											133.0	137.0	136.0					8																	110587762		2103	4215	6318	SO:0001819	synonymous_variant	55638			AB040905	CCDS43763.1, CCDS43764.1, CCDS47912.1, CCDS55271.1	8q23.2	2010-08-27				ENSG00000147642			26011	protein-coding gene	gene with protein product	"""syntaphilin-like"""	611568				17611281, 16750881, 16157705, 15656992, 15459722	Standard	NM_001099743		Approved	FLJ20366, GOLSYN, KIAA1472, OCSYN, SNPHL	uc003ynj.4	Q9NX95		ENST00000422135.1:c.1365C>T	8.37:g.110587762G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A8K354|B3KQX3|B3KU61|Q5R1T1|Q5R1T2|Q5R1T3|Q5Y2M6|Q8ND49|Q8TCR6|Q96D80|Q9P256	Silent	SNP	ENST00000422135.1	37	CCDS47912.1																																																																																				0.577	SYBU-204	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385501.1		NM_017786	
TDRD5	163589	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	179620176	179620176	+	Missense_Mutation	SNP	G	G	C			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr1:179620176G>C	ENST00000367614.1	+	12	2334	c.1975G>C	c.(1975-1977)Gta>Cta	p.V659L	TDRD5_ENST00000294848.8_Missense_Mutation_p.V659L|TDRD5_ENST00000444136.1_Missense_Mutation_p.V659L	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	659					DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)		p.V659L(1)		NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						CCATGCTATTGTATGCCGAGA	0.338																																																	1	Substitution - Missense(1)	kidney(1)											133.0	125.0	128.0					1																	179620176		2203	4300	6503	SO:0001583	missense	163589			AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"""Tudor domain containing"""	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.1975G>C	1.37:g.179620176G>C	ENSP00000356586:p.Val659Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	37	CCDS1332.1	.	.	.	.	.	.	.	.	.	.	G	19.15	3.771104	0.69992	.	.	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136;ENST00000417329	T;T;T;T	0.32023	2.72;2.72;2.9;1.47	5.91	5.0	0.66597	.	0.990599	0.08217	N	0.979820	T	0.44265	0.1285	L	0.57536	1.79	0.27096	N	0.96272	D;P	0.56521	0.976;0.915	P;P	0.59012	0.85;0.542	T	0.15492	-1.0435	10	0.11485	T	0.65	-16.8825	9.0627	0.36444	0.1648:0.0:0.8352:0.0	.	659;659	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	L	659;659;659;115	ENSP00000356586:V659L;ENSP00000294848:V659L;ENSP00000406052:V659L;ENSP00000410744:V115L	ENSP00000294848:V659L	V	+	1	0	TDRD5	177886799	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.925000	0.48884	1.500000	0.48636	0.655000	0.94253	GTA		0.338	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1		NM_173533	
TMEM145	284339	hgsc.bcm.edu;ucsc.edu	37	19	42821885	42821886	+	Frame_Shift_Ins	INS	-	-	AC			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr19:42821885_42821886insAC	ENST00000301204.3	+	12	966_967	c.925_926insAC	c.(925-927)tacfs	p.Y309fs	TMEM145_ENST00000598766.1_Frame_Shift_Ins_p.Y333fs	NM_173633.2	NP_775904.2	Q8NBT3	TM145_HUMAN	transmembrane protein 145	309					G-protein coupled receptor signaling pathway (GO:0007186)|response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	27		Prostate(69;0.00682)				CCAGGTACTGTACACGTATGAG	0.619																																																	0																																										SO:0001589	frameshift_variant	284339			AK075286	CCDS12603.1	19q13.2	2008-02-05				ENSG00000167619			26912	protein-coding gene	gene with protein product							Standard	NM_173633		Approved	FLJ90805	uc002otk.1	Q8NBT3		ENST00000301204.3:c.928_929dupAC	19.37:g.42821888_42821889dupAC	ENSP00000301204:p.Tyr309fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Ins	INS	ENST00000301204.3	37	CCDS12603.1																																																																																				0.619	TMEM145-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463737.1		NM_173633	
TMPRSS15	5651	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	21	19725219	19725219	+	Splice_Site	SNP	C	C	A			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr21:19725219C>A	ENST00000284885.3	-	10	1205		c.e10+1			NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15							brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.?(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						ATGAATTATACCTGAAGCATT	0.348																																																	1	Unknown(1)	kidney(1)											97.0	109.0	105.0					21																	19725219		2203	4299	6502	SO:0001630	splice_region_variant	5651				CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"""Serine peptidases / Transmembrane"""	9490	protein-coding gene	gene with protein product	"""proenterokinase"", ""enteropeptidase"""	606635	"""protease, serine, 7 (enterokinase)"""	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1171+1G>T	21.37:g.19725219C>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q2NKL7	Splice_Site	SNP	ENST00000284885.3	37	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	C	18.87	3.715378	0.68844	.	.	ENSG00000154646	ENST00000284885	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1108	0.89534	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMPRSS15	18647090	1.000000	0.71417	0.999000	0.59377	0.795000	0.44927	4.410000	0.59774	2.575000	0.86900	0.655000	0.94253	.		0.348	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2		NM_002772	Intron
TPP2	7174	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	103275378	103275378	+	Missense_Mutation	SNP	G	G	T			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr13:103275378G>T	ENST00000376065.4	+	6	808	c.772G>T	c.(772-774)Gtg>Ttg	p.V258L	TPP2_ENST00000376052.3_Missense_Mutation_p.V258L	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II	258	Peptidase S8.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)|tripeptidyl-peptidase activity (GO:0008240)	p.V258L(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	52	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GCTCTCCATTGTGACCAGTGG	0.413																																																	1	Substitution - Missense(1)	kidney(1)											149.0	154.0	152.0					13																	103275378		2203	4300	6503	SO:0001583	missense	7174			M55169	CCDS9502.1	13q32-q33	2008-02-05			ENSG00000134900	ENSG00000134900	3.4.14.10		12016	protein-coding gene	gene with protein product		190470				1670990	Standard	NM_003291		Approved		uc001vpi.4	P29144	OTTHUMG00000017305	ENST00000376065.4:c.772G>T	13.37:g.103275378G>T	ENSP00000365233:p.Val258Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VZU8	Missense_Mutation	SNP	ENST00000376065.4	37	CCDS9502.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.359867	0.82353	.	.	ENSG00000134900	ENST00000376065;ENST00000376052	.	.	.	5.75	5.75	0.90469	Peptidase S8/S53, subtilisin/kexin/sedolisin (2);	0.000000	0.85682	D	0.000000	T	0.63271	0.2497	L	0.55990	1.75	0.80722	D	1	P	0.38110	0.618	B	0.38428	0.273	T	0.66244	-0.5972	9	0.66056	D	0.02	.	19.9503	0.97197	0.0:0.0:1.0:0.0	.	258	P29144	TPP2_HUMAN	L	258	.	ENSP00000365220:V258L	V	+	1	0	TPP2	102073379	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	9.192000	0.94947	2.726000	0.93360	0.585000	0.79938	GTG		0.413	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2			
TUBBP5	643224	broad.mit.edu	37	9	141071078	141071078	+	RNA	SNP	A	A	G	rs201043758	byFrequency	TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr9:141071078A>G	ENST00000503395.1	+	0	1735									tubulin, beta pseudogene 5									p.M233V(7)									GTCTGCTACCATGAGTGGGGT	0.552																																																	7	Substitution - Missense(7)	endometrium(4)|kidney(2)|ovary(1)																																										643224			AF355123		9q34.3	2012-03-06	2005-11-15		ENSG00000159247	ENSG00000159247			23674	pseudogene	pseudogene			"""tubulin, beta polypeptide pseudogene 5"""			11731935	Standard	NR_027156		Approved		uc010ncq.3		OTTHUMG00000021001		9.37:g.141071078A>G		Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000503395.1	37																																																																																					0.552	TUBBP5-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000373087.1		NR_027156	
UBLCP1	134510	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	158710292	158710292	+	Missense_Mutation	SNP	A	A	C			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr5:158710292A>C	ENST00000296786.6	+	10	1200	c.874A>C	c.(874-876)Aag>Cag	p.K292Q		NM_145049.3	NP_659486.2	Q8WVY7	UBCP1_HUMAN	ubiquitin-like domain containing CTD phosphatase 1	292	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.|Phosphatase.					nucleolus (GO:0005730)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)	p.K292Q(1)		endometrium(1)|kidney(3)|large_intestine(4)|ovary(1)	9	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCAGTACCTCAAGGAGATAGC	0.299																																																	1	Substitution - Missense(1)	kidney(1)											95.0	102.0	99.0					5																	158710292		2203	4293	6496	SO:0001583	missense	134510			AK057996	CCDS4345.1	5q33.3	2010-06-21			ENSG00000164332	ENSG00000164332	3.1.3.16	"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	28110	protein-coding gene	gene with protein product	"""CTD phosphatase-like with ubiquitin domain 1"""	609867				15883030	Standard	NM_145049		Approved	MGC10067, CPUB1	uc003lxq.2	Q8WVY7	OTTHUMG00000130305	ENST00000296786.6:c.874A>C	5.37:g.158710292A>C	ENSP00000296786:p.Lys292Gln	Somatic		WXS	Illumina HiSeq	Phase_I	D3DQJ7|Q96DK5	Missense_Mutation	SNP	ENST00000296786.6	37	CCDS4345.1	.	.	.	.	.	.	.	.	.	.	A	15.85	2.955039	0.53293	.	.	ENSG00000164332	ENST00000296786	T	0.18174	2.23	5.37	5.37	0.77165	HAD-superfamily hydrolase, subfamily IIID (1);NLI interacting factor (2);HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.21347	0.0514	L	0.56199	1.76	0.58432	D	0.999999	P	0.48998	0.918	P	0.46585	0.521	T	0.03662	-1.1015	10	0.13853	T	0.58	-21.4226	14.2388	0.65943	1.0:0.0:0.0:0.0	.	292	Q8WVY7	UBCP1_HUMAN	Q	292	ENSP00000296786:K292Q	ENSP00000296786:K292Q	K	+	1	0	UBLCP1	158642870	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	8.910000	0.92685	2.154000	0.67381	0.533000	0.62120	AAG		0.299	UBLCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252650.2		NM_145049	
UBR4	23352	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	19499967	19499967	+	Missense_Mutation	SNP	C	C	A			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr1:19499967C>A	ENST00000375254.3	-	23	3158	c.3131G>T	c.(3130-3132)cGg>cTg	p.R1044L	UBR4_ENST00000375226.2_Missense_Mutation_p.R1044L|UBR4_ENST00000375217.2_Missense_Mutation_p.R1044L|UBR4_ENST00000375267.2_Missense_Mutation_p.R1044L	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1044					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R1044L(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		GATCCGGAGCCGAGAAGACCA	0.443																																																	1	Substitution - Missense(1)	kidney(1)											74.0	71.0	72.0					1																	19499967		2203	4300	6503	SO:0001583	missense	23352			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.3131G>T	1.37:g.19499967C>A	ENSP00000364403:p.Arg1044Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	C	32	5.105494	0.94245	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000419533	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.61388	0.2343	L	0.54323	1.7	0.80722	D	1	D	0.60160	0.987	D	0.67725	0.953	T	0.62793	-0.6779	10	0.87932	D	0	.	19.1194	0.93357	0.0:1.0:0.0:0.0	.	1044	Q5T4S7	UBR4_HUMAN	L	1044;1044;1044;1044;260	ENSP00000364403:R1044L;ENSP00000364416:R1044L;ENSP00000364365:R1044L;ENSP00000364374:R1044L	ENSP00000364365:R1044L	R	-	2	0	UBR4	19372554	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.484000	0.81180	2.605000	0.88082	0.655000	0.94253	CGG		0.443	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1		NM_020765	
UPK3A	7380	hgsc.bcm.edu	37	22	45691552	45691553	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr22:45691552_45691553insC	ENST00000216211.4	+	6	848_849	c.816_817insC	c.(817-819)ccgfs	p.P273fs	UPK3A_ENST00000396082.2_Frame_Shift_Ins_p.P152fs	NM_006953.3	NP_008884.1	O75631	UPK3A_HUMAN	uroplakin 3A	273			P -> L (found in patients with renal adysplasia; unknown pathological significance; normal targeting to the cell surface; dbSNP:rs121918186). {ECO:0000269|PubMed:15888565}.		cell morphogenesis (GO:0000902)|epithelial cell differentiation (GO:0030855)|kidney development (GO:0001822)|potassium ion homeostasis (GO:0055075)|sodium ion homeostasis (GO:0055078)|urea transport (GO:0015840)|urinary bladder development (GO:0060157)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(2)|skin(1)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		TGAACCGGGGGCCGCCACTGGA	0.629																																																	0																																										SO:0001589	frameshift_variant	7380			AB010637	CCDS14064.1, CCDS54539.1	22q13.31	2005-11-14	2003-07-29	2003-07-30	ENSG00000100373	ENSG00000100373			12580	protein-coding gene	gene with protein product		611559	"""uroplakin 3"""	UPK3		9818021	Standard	NM_006953		Approved		uc003bfy.3	O75631	OTTHUMG00000151339	ENST00000216211.4:c.818dupC	22.37:g.45691554_45691554dupC	ENSP00000216211:p.Pro273fs	Somatic		WXS	Illumina HiSeq	Phase_I	B0QY25|O60261|Q32N05|Q5TII6	Frame_Shift_Ins	INS	ENST00000216211.4	37	CCDS14064.1																																																																																				0.629	UPK3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000322276.1		NM_006953	
USH2A	7399	hgsc.bcm.edu;ucsc.edu	37	1	215823997	215823998	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr1:215823997_215823998insT	ENST00000307340.3	-	65	14665_14666	c.14279_14280insA	c.(14278-14280)aagfs	p.K4760fs	USH2A_ENST00000366943.2_Frame_Shift_Ins_p.K4760fs	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4760	Fibronectin type-III 33. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TCCCGTTGGGCTTCCCAGGGGC	0.584										HNSCC(13;0.011)																																							0																																										SO:0001589	frameshift_variant	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.14280dupA	1.37:g.215823999_215823999dupT	ENSP00000305941:p.Lys4760fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VVM9|Q6S362|Q9NS27	Frame_Shift_Ins	INS	ENST00000307340.3	37	CCDS31025.1																																																																																				0.584	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1		NM_007123	
VHL	7428	hgsc.bcm.edu	37	3	10183746	10183746	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AK-3430-01A-01W-1244-10	TCGA-AK-3430-10A-01W-1244-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PacBio	.		Illumina GAIIx	e06607ae-d7b1-4109-9e18-f42b3cc518e2	012aa7b4-8d61-4f85-9a3a-64cdb9f62ac0	g.chr3:10183746delC	ENST00000256474.2	+	1	1055	c.215delC	c.(214-216)tccfs	p.S72fs	snoU13_ENST00000458986.1_RNA|VHL_ENST00000345392.2_Frame_Shift_Del_p.S72fs	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	72			Missing (in VHLD; type I).		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.E70fs*85(1)|p.S72_V87>L(1)|p.P71fs*84(1)|p.Q73fs*86(1)|p.R60fs*35(1)|p.N67_V74del(1)|p.P71fs*56(1)|p.V74fs*51(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)		CGCGAGCCCTCCCAGGTCATC	0.721		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"""	8	Deletion - Frameshift(6)|Complex - deletion inframe(1)|Deletion - In frame(1)	kidney(7)|soft_tissue(1)											10.0	13.0	12.0					3																	10183746		2151	4223	6374	SO:0001589	frameshift_variant	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.215delC	3.37:g.10183746delC	ENSP00000256474:p.Ser72fs	Somatic		WXS	Illumina MiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Frame_Shift_Del	DEL	ENST00000256474.2	37	CCDS2597.1																																																																																				0.721	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
ZCCHC17	51538	hgsc.bcm.edu;ucsc.edu	37	1	31836865	31836884	+	Splice_Site	DEL	AATTTTCTTTTCAGGAGAAG	AATTTTCTTTTCAGGAGAAG	-	rs576307561		TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	AATTTTCTTTTCAGGAGAAG	AATTTTCTTTTCAGGAGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr1:31836865_31836884delAATTTTCTTTTCAGGAGAAG	ENST00000373714.1	+	8	825_831	c.564_570delAATTTTCTTTTCAGGAGAAG	c.(562-570)aaaattttc>aa	p.KIF188fs	ZCCHC17_ENST00000422613.2_Splice_Site_p.KIF190fs|FABP3_ENST00000497275.1_5'Flank|ZCCHC17_ENST00000344147.5_Splice_Site_p.KIF188fs|ZCCHC17_ENST00000546109.1_Splice_Site_p.KIF180fs	NM_001282568.1|NM_001282570.1	NP_001269497.1|NP_001269499.1	Q9NP64	NO40_HUMAN	zinc finger, CCHC domain containing 17	188	Lys-rich.					cytosolic large ribosomal subunit (GO:0022625)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(2)|ovary(1)|skin(1)	6		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)|all_neural(195;0.146)|Medulloblastoma(700;0.151)|Breast(348;0.222)		STAD - Stomach adenocarcinoma(196;0.0215)|READ - Rectum adenocarcinoma(331;0.168)		TGATTTTTAAAATTTTCTTTTCAGGAGAAGAAGAAAAAGA	0.395																																																	0																																										SO:0001630	splice_region_variant	51538			AF151085	CCDS341.1, CCDS60061.1, CCDS72741.1, CCDS72742.1, CCDS72743.1, CCDS72744.1	1p35.2	2008-05-02			ENSG00000121766	ENSG00000121766		"""Zinc fingers, CCHC domain containing"""	30246	protein-coding gene	gene with protein product						12202495, 12893261	Standard	NM_001282572		Approved	PS1D, HSPC251, pNO40	uc001bsp.1	Q9NP64	OTTHUMG00000003791	ENST00000373714.1:c.565-1AATTTTCTTTTCAGGAGAAG>-	1.37:g.31836865_31836884delAATTTTCTTTTCAGGAGAAG		Somatic		WXS	Illumina HiSeq	Phase_I	B4DY38|D3DPN4|Q6PKH4|Q9NYG4|Q9P0M8	Frame_Shift_Del	DEL	ENST00000373714.1	37	CCDS341.1																																																																																				0.395	ZCCHC17-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010665.1		NM_016505	Frame_Shift_Del
WDR77	79084	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	111990200	111990200	+	Splice_Site	SNP	T	T	A			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr1:111990200T>A	ENST00000235090.5	-	3	508		c.e3-2		WDR77_ENST00000411751.2_Intron|WDR77_ENST00000497278.1_5'Flank|Y_RNA_ENST00000363020.1_RNA|ATP5F1_ENST00000369722.3_5'Flank|ATP5F1_ENST00000483994.1_5'Flank	NM_024102.2	NP_077007.1	Q9BQA1	MEP50_HUMAN	WD repeat domain 77						gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA metabolic process (GO:0016070)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|methylosome (GO:0034709)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)	p.?(1)		NS(2)|endometrium(2)|kidney(2)|large_intestine(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		all_cancers(81;0.000902)|all_epithelial(167;0.00056)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0238)|Colorectal(144;0.0296)|all cancers(265;0.0488)|Epithelial(280;0.0732)|COAD - Colon adenocarcinoma(174;0.114)|LUSC - Lung squamous cell carcinoma(189;0.135)		CAACAGCACCTGTTGGGGGTA	0.403																																																	1	Unknown(1)	kidney(1)											109.0	93.0	98.0					1																	111990200		2203	4300	6503	SO:0001630	splice_region_variant	79084			BC016946	CCDS835.1	1p13.2	2013-01-09		2005-08-09	ENSG00000116455	ENSG00000116455		"""WD repeat domain containing"""	29652	protein-coding gene	gene with protein product		611734				11756452, 8619474	Standard	NM_024102		Approved	MEP50	uc001ebb.3	Q9BQA1	OTTHUMG00000011748	ENST00000235090.5:c.302-2A>T	1.37:g.111990200T>A		Somatic		WXS	Illumina HiSeq	Phase_I	B3KMW6|B4DP38|Q3LID2|Q53FU2|Q6JZZ5|Q96GK4|Q9BWY3	Splice_Site	SNP	ENST00000235090.5	37	CCDS835.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.113973	0.77210	.	.	ENSG00000116455	ENST00000235090;ENST00000449340	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7264	0.77763	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	WDR77	111791723	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	7.387000	0.79785	2.202000	0.70862	0.379000	0.24179	.		0.403	WDR77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032465.1		NM_024102	Intron
ZFP91	80829	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	58381764	58381764	+	Silent	SNP	A	A	G			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr11:58381764A>G	ENST00000316059.6	+	9	1221	c.1050A>G	c.(1048-1050)ggA>ggG	p.G350G	ZFP91-CNTF_ENST00000389919.4_Silent_p.G350G	NM_001197051.1|NM_053023.4	NP_001183980.1|NP_444251.1	Q96JP5	ZFP91_HUMAN	ZFP91 zinc finger protein	350	Interaction with MAP3K14/NIK.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein K63-linked ubiquitination (GO:0070534)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)	p.G350G(2)		cervix(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	26		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				CCTCCTGTGGACGACTCTTCA	0.393																																																	2	Substitution - coding silent(2)	kidney(2)											98.0	90.0	93.0					11																	58381764		2201	4295	6496	SO:0001819	synonymous_variant	80829			AB056107	CCDS31553.1	11q12	2012-11-27	2012-11-27		ENSG00000186660	ENSG00000186660		"""Zinc fingers, C2H2-type"""	14983	protein-coding gene	gene with protein product			"""zinc finger protein homologous to Zfp91 in mouse"", ""zinc finger protein 91 homolog (mouse)"""			12738986, 20682767	Standard	NM_053023		Approved	PZF, ZNF757	uc001nmx.4	Q96JP5	OTTHUMG00000137391	ENST00000316059.6:c.1050A>G	11.37:g.58381764A>G		Somatic		WXS	Illumina HiSeq	Phase_I	A6NHC4|A8MSG7|Q86V47|Q96JP4|Q96QA3	Silent	SNP	ENST00000316059.6	37	CCDS31553.1																																																																																				0.393	ZFP91-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268674.1		NM_053023	
ZMYND11	10771	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	225962	225962	+	Silent	SNP	T	T	C			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr10:225962T>C	ENST00000397962.3	+	2	438	c.10T>C	c.(10-12)Tta>Cta	p.L4L	ZMYND11_ENST00000309776.4_5'UTR|ZMYND11_ENST00000602682.1_Silent_p.L4L|ZMYND11_ENST00000402736.1_Silent_p.L4L|ZMYND11_ENST00000403354.1_Silent_p.L4L|ZMYND11_ENST00000509513.2_Silent_p.L4L|ZMYND11_ENST00000558098.2_Silent_p.L4L|ZMYND11_ENST00000381602.4_5'UTR|ZMYND11_ENST00000381604.4_5'UTR|ZMYND11_ENST00000381607.4_5'UTR|ZMYND11_ENST00000381591.1_Silent_p.L4L|ZMYND11_ENST00000397959.3_Silent_p.L4L|ZMYND11_ENST00000381584.1_5'UTR			Q15326	ZMY11_HUMAN	zinc finger, MYND-type containing 11	4					cell cycle (GO:0007049)|cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription elongation from RNA polymerase II promoter (GO:0034243)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.L4L(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	24		all_cancers(4;1.32e-05)|all_lung(4;3.67e-05)|Lung NSC(4;0.000301)|all_epithelial(10;0.000416)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.132)	Epithelial(11;0.00289)|all cancers(11;0.0108)|Lung(33;0.0689)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		CATGGCACGTTTAACAAAAAG	0.373																																																	2	Substitution - coding silent(2)	kidney(2)											100.0	90.0	93.0					10																	225962		1568	3582	5150	SO:0001819	synonymous_variant	10771			X86098	CCDS7052.1, CCDS7053.1, CCDS7052.2, CCDS55696.1, CCDS55697.1, CCDS7053.2, CCDS73060.1, CCDS73061.1	10p14	2011-01-26	2011-01-26		ENSG00000015171	ENSG00000015171		"""Zinc fingers, MYND-type"""	16966	protein-coding gene	gene with protein product		608668	"""zinc finger, MYND domain containing 11"""			7621829, 10734313	Standard	NM_006624		Approved	BS69	uc010pzx.2	Q15326	OTTHUMG00000017526	ENST00000397962.3:c.10T>C	10.37:g.225962T>C		Somatic		WXS	Illumina HiSeq	Phase_I	B2R6G8|B7Z293|F6UH50|Q2LD45|Q2LD46|Q2LD47|Q2LD48|Q5VUI1|Q8N4B3	Silent	SNP	ENST00000397962.3	37	CCDS7052.2																																																																																				0.373	ZMYND11-206	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046382.4		NM_006624	
ZNF343	79175	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	2464292	2464292	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr20:2464292delA	ENST00000278772.4	-	6	1802	c.1315delT	c.(1315-1317)tgcfs	p.C439fs	RP4-734P14.4_ENST00000461548.1_Intron	NM_001282495.1|NM_001282496.1|NM_024325.4	NP_001269424.1|NP_001269425.1|NP_077301.4	Q6P1L6	ZN343_HUMAN	zinc finger protein 343	439					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|skin(4)|upper_aerodigestive_tract(1)	25						CACTCCCTGCAAACATAAGGC	0.527																																																	0													110.0	94.0	100.0					20																	2464292		2203	4300	6503	SO:0001589	frameshift_variant	79175			AK096911	CCDS13028.1, CCDS74692.1, CCDS74693.1, CCDS74694.1	20p13	2013-01-08			ENSG00000088876	ENSG00000088876		"""Zinc fingers, C2H2-type"", ""-"""	16017	protein-coding gene	gene with protein product							Standard	NM_001282498		Approved	MGC10715	uc002wge.1	Q6P1L6	OTTHUMG00000031701	ENST00000278772.4:c.1315delT	20.37:g.2464292delA	ENSP00000278772:p.Cys439fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q5JXU8|Q5JXU9|Q8N8F2|Q96EX8|Q96NA5|Q9BQB0	Frame_Shift_Del	DEL	ENST00000278772.4	37	CCDS13028.1																																																																																				0.527	ZNF343-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077617.1		NM_024325	
ZNF548	147694	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	57910589	57910590	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AK-3430-01A-01D-1251-10	TCGA-AK-3430-10A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9d9a311d-7ca1-4021-95dc-0d6716917938	239a2754-4a2e-48d1-89eb-3c91161fb67e	g.chr19:57910589_57910590insT	ENST00000366197.5	+	3	1184_1185	c.934_935insT	c.(934-936)aggfs	p.R312fs	AC003002.6_ENST00000600421.1_Intron|AC003002.6_ENST00000596400.1_Intron|ZNF548_ENST00000336128.7_Frame_Shift_Ins_p.R324fs|AC004076.7_ENST00000597410.1_Intron	NM_152909.3	NP_690873.2	Q8NEK5	ZN548_HUMAN	zinc finger protein 548	312					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GTATGAGTGCAGGGAATGTGGG	0.436																																																	0																																										SO:0001589	frameshift_variant	147694			AK057494	CCDS46209.1, CCDS54324.1	19q13.43	2013-01-08				ENSG00000188785		"""Zinc fingers, C2H2-type"", ""-"""	26561	protein-coding gene	gene with protein product						12477932	Standard	NM_152909		Approved	FLJ32932	uc002qon.3	Q8NEK5		Exception_encountered	19.37:g.57910589_57910590insT	ENSP00000379482:p.Arg312fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q96M05	Frame_Shift_Ins	INS	ENST00000366197.5	37	CCDS46209.1																																																																																				0.436	ZNF548-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465937.1		NM_152909	
