#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_ORegAnno_bin	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
ACTN3	89	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	66322058	66322058	+	RNA	SNP	C	C	T	rs370740496		TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr11:66322058C>T	ENST00000502692.1	+	0	766				ACTN3_ENST00000513398.1_RNA	NM_001258371.1	NP_001245300.1	Q08043	ACTN3_HUMAN	actinin, alpha 3 (gene/pseudogene)						focal adhesion assembly (GO:0048041)|muscle filament sliding (GO:0030049)|regulation of apoptotic process (GO:0042981)	actin filament (GO:0005884)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|pseudopodium (GO:0031143)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.P173L(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(2)	10						AAGACAGCACCGTACCGCAAC	0.587																																																	1	Substitution - Missense(1)	kidney(1)						C	LEU/PRO	1,4265		0,1,2132	67.0	75.0	73.0		521	4.7	0.1	11		73	0,8522		0,0,4261	no	missense	ACTN3	NM_001104.1	98	0,1,6393	TT,TC,CC		0.0,0.0234,0.0078	probably-damaging	174/902	66322058	1,12787	2133	4261	6394			89			M86407		11q13.2	2013-10-02	2012-10-05		ENSG00000248746	ENSG00000248746			165	protein-coding gene	gene with protein product		102574	"""actinin, alpha 3"""			1339456	Standard	NM_001104		Approved		uc031qbp.1	Q08043	OTTHUMG00000160815		11.37:g.66322058C>T			A6NP77|Q4KKV2	Missense_Mutation	SNP	ENST00000502692.1	37																																																																																					0.587	ACTN3-003	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000362465.1		NM_001104	
IGHV3-20	28445	broad.mit.edu	37	14	106667827	106667827	+	RNA	SNP	C	C	A	rs573211863	byFrequency	TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr14:106667827C>A	ENST00000390606.2	-	0	166				AB019440.50_ENST00000605005.1_lincRNA					immunoglobulin heavy variable 3-20																		GTCTCAGGGACCCCCCAGGCC	0.587																																																	0													89.0	83.0	85.0					14																	106667827		1879	4104	5983			8755			M99657		14q32.33	2012-02-08			ENSG00000211946	ENSG00000211946		"""Immunoglobulins / IGH locus"""	5585	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152285		14.37:g.106667827C>A				RNA	SNP	ENST00000390606.2	37																																																																																					0.587	IGHV3-20-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000325673.1		NG_001019	
ALMS1	7840	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	73717074	73717074	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr2:73717074A>G	ENST00000264448.6	+	10	8096	c.7985A>G	c.(7984-7986)aAa>aGa	p.K2662R	AC096546.1_ENST00000408160.1_RNA|ALMS1_ENST00000409009.1_Missense_Mutation_p.K2620R	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2662					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.K2662R(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						GATGAATTCAAAATCAGCAAA	0.393																																																	1	Substitution - Missense(1)	kidney(1)											108.0	102.0	104.0					2																	73717074		1825	4076	5901	SO:0001583	missense	7840			AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.7985A>G	2.37:g.73717074A>G	ENSP00000264448:p.Lys2662Arg		Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	A	10.15	1.269945	0.23221	.	.	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.07567	3.18;3.18	4.45	3.29	0.37713	.	0.382752	0.22672	N	0.057042	T	0.04634	0.0126	N	0.17082	0.46	0.80722	D	1	B;B;B	0.27679	0.185;0.073;0.073	B;B;B	0.22601	0.04;0.04;0.04	T	0.44892	-0.9298	10	0.33141	T	0.24	.	6.2788	0.20995	0.8832:0.0:0.1168:0.0	.	2662;2620;2662	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	R	2620;2662	ENSP00000386627:K2620R;ENSP00000264448:K2662R	ENSP00000264448:K2662R	K	+	2	0	ALMS1	73570582	0.998000	0.40836	0.999000	0.59377	0.836000	0.47400	1.210000	0.32370	1.010000	0.39314	0.528000	0.53228	AAA		0.393	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1		NM_015120	
APBB2	323	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	40829224	40829224	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr4:40829224G>A	ENST00000295974.8	-	14	2283	c.1654C>T	c.(1654-1656)Cgg>Tgg	p.R552W	RP11-632F7.3_ENST00000513127.1_RNA|APBB2_ENST00000506352.1_Missense_Mutation_p.R531W|APBB2_ENST00000508593.1_Missense_Mutation_p.R553W|APBB2_ENST00000513140.1_Missense_Mutation_p.R531W|APBB2_ENST00000543538.1_Missense_Mutation_p.R4W|APBB2_ENST00000502841.1_Missense_Mutation_p.R4W|Y_RNA_ENST00000384466.1_RNA|APBB2_ENST00000504305.1_Missense_Mutation_p.R4W	NM_001166050.1|NM_004307.1	NP_001159522.1|NP_004298.1	Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2	552	PID 1. {ECO:0000255|PROSITE- ProRule:PRU00148}.				axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|extracellular matrix organization (GO:0030198)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|transcription factor binding (GO:0008134)	p.R531W(1)		central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|skin(2)|urinary_tract(1)	34						GCATTCTTCCGTTCAGCCATA	0.507																																					Ovarian(3;20 75 16686 49997)												1	Substitution - Missense(1)	kidney(1)											136.0	137.0	137.0					4																	40829224		1978	4153	6131	SO:0001583	missense	323			U62325	CCDS43224.1, CCDS54760.1, CCDS54761.1, CCDS54762.1	4p13	2011-10-10	2008-07-31		ENSG00000163697	ENSG00000163697			582	protein-coding gene	gene with protein product	"""Fe65-like"""	602710				8955346, 9585438	Standard	NM_173075		Approved	FE65L, FE65L1, MGC35575	uc003gvn.3	Q92870	OTTHUMG00000160416	ENST00000295974.8:c.1654C>T	4.37:g.40829224G>A	ENSP00000295974:p.Arg552Trp		B4DSL4|E9PG87|Q8IUI6	Missense_Mutation	SNP	ENST00000295974.8	37	CCDS54761.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.8|20.8	4.047503|4.047503	0.75846|0.75846	.|.	.|.	ENSG00000163697|ENSG00000163697	ENST00000295974;ENST00000316212;ENST00000543538;ENST00000513140;ENST00000508593;ENST00000502841;ENST00000506352;ENST00000504305;ENST00000512510;ENST00000510670;ENST00000514920;ENST00000513516|ENST00000513611	T;T;T;T;T;T;T;T|.	0.54279|.	2.08;0.58;2.08;2.08;0.58;2.08;0.58;2.08|.	5.89|5.89	4.04|4.04	0.47022|0.47022	Phosphotyrosine interaction domain (3);|.	0.058204|.	0.64402|.	D|.	0.000001|.	T|T	0.72969|0.72969	0.3527|0.3527	M|M	0.76574|0.76574	2.34|2.34	0.58432|0.58432	D|D	0.999996|0.999996	D;D;D|.	0.63046|.	0.986;0.983;0.992|.	P;P;P|.	0.56088|.	0.791;0.686;0.791|.	T|T	0.74553|0.74553	-0.3627|-0.3627	10|5	0.87932|.	D|.	0|.	-22.8575|-22.8575	13.6062|13.6062	0.62048|0.62048	0.0:0.0:0.5999:0.4001|0.0:0.0:0.5999:0.4001	.|.	553;531;552|.	E9PG87;Q92870-2;Q92870|.	.;.;APBB2_HUMAN|.	W|M	552;551;4;531;553;4;531;4;66;4;4;4|521	ENSP00000295974:R552W;ENSP00000439357:R4W;ENSP00000426018:R531W;ENSP00000427211:R553W;ENSP00000425802:R4W;ENSP00000421539:R531W;ENSP00000423765:R4W;ENSP00000426429:R66W|.	ENSP00000295974:R552W|.	R|T	-|-	1|2	2|0	APBB2|APBB2	40523981|40523981	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.841000|0.841000	0.47740|0.47740	2.511000|2.511000	0.45476|0.45476	1.460000|1.460000	0.47911|0.47911	0.563000|0.563000	0.77884|0.77884	CGG|ACG		0.507	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360523.3		NM_173075	
CCT6B	10693	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	33269618	33269618	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr17:33269618T>A	ENST00000314144.5	-	7	885	c.770A>T	c.(769-771)gAg>gTg	p.E257V	CCT6B_ENST00000421975.3_Missense_Mutation_p.E220V|CCT6B_ENST00000436961.3_Missense_Mutation_p.E212V	NM_006584.3	NP_006575.2	Q92526	TCPW_HUMAN	chaperonin containing TCP1, subunit 6B (zeta 2)	257					chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	chaperonin-containing T-complex (GO:0005832)	ATP binding (GO:0005524)|protein transporter activity (GO:0008565)|unfolded protein binding (GO:0051082)	p.E257V(1)		NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	20		Ovarian(249;0.17)				TACCAATTTCTCTTTCTCTTC	0.323																																																	1	Substitution - Missense(1)	kidney(1)											64.0	61.0	62.0					17																	33269618		2203	4297	6500	SO:0001583	missense	10693			D78333	CCDS32617.1, CCDS54105.1, CCDS54106.1	17q	2011-09-02			ENSG00000132141	ENSG00000132141		"""Heat Shock Proteins / Chaperonins"""	1621	protein-coding gene	gene with protein product		610730				8812458, 9013858	Standard	NM_006584		Approved	Cctz2, TSA303	uc002hig.3	Q92526		ENST00000314144.5:c.770A>T	17.37:g.33269618T>A	ENSP00000327191:p.Glu257Val		B4DX20|B4DYB0|Q8TC34	Missense_Mutation	SNP	ENST00000314144.5	37	CCDS32617.1	.	.	.	.	.	.	.	.	.	.	T	17.18	3.324065	0.60634	.	.	ENSG00000132141	ENST00000421975;ENST00000314144;ENST00000436961	T;T;T	0.80033	-1.33;-1.33;-1.33	4.06	4.06	0.47325	.	0.094349	0.64402	D	0.000001	D	0.92133	0.7506	H	0.97611	4.04	0.80722	D	1	P;P;P	0.52061	0.925;0.927;0.95	P;P;D	0.64410	0.865;0.905;0.925	D	0.93697	0.7012	10	0.72032	D	0.01	-8.4011	11.2674	0.49118	0.0:0.0:0.0:1.0	.	212;220;257	B4DYB0;B4DX20;Q92526	.;.;TCPW_HUMAN	V	220;257;212	ENSP00000398044:E220V;ENSP00000327191:E257V;ENSP00000400917:E212V	ENSP00000327191:E257V	E	-	2	0	CCT6B	30293731	1.000000	0.71417	1.000000	0.80357	0.550000	0.35303	7.230000	0.78097	1.801000	0.52704	0.482000	0.46254	GAG		0.323	CCT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448014.1		NM_006584	
APOH	350	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	64216834	64216834	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr17:64216834G>T	ENST00000205948.6	-	5	479	c.442C>A	c.(442-444)Cct>Act	p.P148T		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	148	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)	p.P148T(1)		central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			GCAAACGTAGGTATGGATGGT	0.383																																					Melanoma(155;624 1882 16869 48804 51309)												1	Substitution - Missense(1)	kidney(1)											99.0	98.0	98.0					17																	64216834		2203	4300	6503	SO:0001583	missense	350				CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"""Apolipoproteins"""	616	protein-coding gene	gene with protein product	"""beta-2-glycoprotein I"""	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.442C>A	17.37:g.64216834G>T	ENSP00000205948:p.Pro148Thr		B2R9M3|Q9UCN7	Missense_Mutation	SNP	ENST00000205948.6	37	CCDS11663.1	.	.	.	.	.	.	.	.	.	.	g	3.353	-0.132105	0.06753	.	.	ENSG00000091583	ENST00000205948	T	0.64803	-0.12	5.42	5.42	0.78866	Complement control module (2);Sushi/SCR/CCP (3);	0.051779	0.85682	D	0.000000	T	0.79828	0.4513	M	0.90650	3.135	0.41720	D	0.989508	D	0.71674	0.998	D	0.66716	0.946	T	0.80034	-0.1551	10	0.27785	T	0.31	.	12.1587	0.54091	0.0833:0.0:0.9167:0.0	.	148	P02749	APOH_HUMAN	T	148	ENSP00000205948:P148T	ENSP00000205948:P148T	P	-	1	0	APOH	61647296	0.998000	0.40836	0.179000	0.23059	0.004000	0.04260	3.065000	0.49994	2.543000	0.85770	0.563000	0.77884	CCT		0.383	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1		NM_000042	
CD84	8832	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	160523749	160523749	+	Silent	SNP	C	C	T			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr1:160523749C>T	ENST00000311224.4	-	3	642	c.576G>A	c.(574-576)acG>acA	p.T192T	CD84_ENST00000368051.3_Silent_p.T192T|CD84_ENST00000368054.3_Silent_p.T192T|CD84_ENST00000368048.3_Silent_p.T192T|CD84_ENST00000534968.1_Silent_p.T78T|CD84_ENST00000368047.3_5'UTR|RP11-528G1.2_ENST00000446952.1_RNA	NM_001184879.1	NP_001171808.1	Q9UIB8	SLAF5_HUMAN	CD84 molecule	192	Ig-like C2-type.				blood coagulation (GO:0007596)|defense response (GO:0006952)|homophilic cell adhesion (GO:0007156)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.T192T(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(1)	24	all_cancers(52;3.62e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			GGGCTGTACACGTGTAAGTCA	0.507																																																	1	Substitution - coding silent(1)	kidney(1)											177.0	162.0	167.0					1																	160523749		2203	4300	6503	SO:0001819	synonymous_variant	8832			AF054816	CCDS1206.1, CCDS53395.1, CCDS53396.1, CCDS53397.1	1q24	2013-01-11	2006-03-31		ENSG00000066294	ENSG00000066294		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1704	protein-coding gene	gene with protein product		604513	"""CD84 antigen (leukocyte antigen)"", ""CD84 molecule """			9310491	Standard	NM_003874		Approved	SLAMF5, hCD84, mCD84	uc001fwh.4	Q9UIB8	OTTHUMG00000022788	ENST00000311224.4:c.576G>A	1.37:g.160523749C>T			B2R8T1|B7Z3R8|O15430|O95266|O95660|Q5H9R1|Q6FHA8|Q8WLP1|Q8WWI8|Q9UF04|Q9UIB6|Q9UIB7|Q9UIT7	Silent	SNP	ENST00000311224.4	37	CCDS53396.1																																																																																				0.507	CD84-003	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059092.1		NM_003874	
CLIP1	6249	hgsc.bcm.edu	37	12	122845659	122845660	+	Frame_Shift_Ins	INS	-	-	G			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr12:122845659_122845660insG	ENST00000540338.1	-	4	892_893	c.851_852insC	c.(850-852)cctfs	p.P284fs	CLIP1_ENST00000358808.2_Frame_Shift_Ins_p.P284fs|CLIP1_ENST00000361654.4_Frame_Shift_Ins_p.P284fs|CLIP1_ENST00000537178.1_Frame_Shift_Ins_p.P284fs|CLIP1_ENST00000302528.7_Frame_Shift_Ins_p.P284fs|CLIP1_ENST00000545889.1_5'UTR			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	284					microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|positive regulation of microtubule polymerization (GO:0031116)|transport (GO:0006810)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|intermediate filament (GO:0005882)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		GTGTAGTGGAAGGGAAGCCAAT	0.5																																																	0																																										SO:0001589	frameshift_variant	6249				CCDS9232.1, CCDS9233.1, CCDS58285.1	12q24.3	2013-01-17	2007-01-05	2007-01-05	ENSG00000130779	ENSG00000130779			10461	protein-coding gene	gene with protein product	"""restin"""	179838	"""restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)"""	RSN		8222754	Standard	NM_001247997		Approved	CYLN1, CLIP170, CLIP, CLIP-170	uc001ucg.2	P30622	OTTHUMG00000168922	ENST00000540338.1:c.852dupC	12.37:g.122845662_122845662dupG	ENSP00000439093:p.Pro284fs		A0AVD3|Q17RS4|Q29RG0	Frame_Shift_Ins	INS	ENST00000540338.1	37	CCDS58285.1																																																																																				0.500	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1		NM_002956	
CLPTM1L	81037	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	1330417	1330417	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr5:1330417G>A	ENST00000320895.5	-	9	1315	c.1058C>T	c.(1057-1059)gCg>gTg	p.A353V	CLPTM1L_ENST00000320927.6_Intron|CLPTM1L_ENST00000507807.1_Intron	NM_030782.3	NP_110409.2	Q96KA5	CLP1L_HUMAN	CLPTM1-like	353					apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.A353V(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24	Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09)		Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181)	KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208)		TCCAACACCCGCCGGGACCAG	0.627																																																	1	Substitution - Missense(1)	kidney(1)											75.0	70.0	72.0					5																	1330417		2202	4294	6496	SO:0001583	missense	81037			AK027306	CCDS3862.1	5p15.33	2008-02-05			ENSG00000049656	ENSG00000049656			24308	protein-coding gene	gene with protein product	"""cisplatin resistance related protein"""	612585				11162647	Standard	NM_030782		Approved	FLJ14400, CRR9	uc003jch.3	Q96KA5	OTTHUMG00000131015	ENST00000320895.5:c.1058C>T	5.37:g.1330417G>A	ENSP00000313854:p.Ala353Val		D3DTC1|Q658W6|Q7LG29|Q96AZ0|Q9H3N4	Missense_Mutation	SNP	ENST00000320895.5	37	CCDS3862.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.245658	0.59103	.	.	ENSG00000049656	ENST00000320895	T	0.41400	1.0	4.84	4.84	0.62591	.	0.051372	0.85682	D	0.000000	T	0.26304	0.0642	N	0.21194	0.64	0.80722	D	1	P	0.47034	0.889	B	0.39503	0.301	T	0.13980	-1.0489	10	0.02654	T	1	-30.2174	16.7303	0.85433	0.0:0.0:1.0:0.0	.	353	Q96KA5	CLP1L_HUMAN	V	353	ENSP00000313854:A353V	ENSP00000313854:A353V	A	-	2	0	CLPTM1L	1383417	1.000000	0.71417	0.041000	0.18516	0.050000	0.14768	9.124000	0.94394	2.213000	0.71641	0.655000	0.94253	GCG		0.627	CLPTM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253649.2		NM_030782	
CNGA1	1259	broad.mit.edu;hgsc.bcm.edu	37	4	47939840	47939840	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr4:47939840A>C	ENST00000514170.1	-	11	990	c.671T>G	c.(670-672)cTa>cGa	p.L224R	CNGA1_ENST00000358519.4_Missense_Mutation_p.L224R|CNGA1_ENST00000420489.2_Missense_Mutation_p.L224R|CNGA1_ENST00000544810.1_Missense_Mutation_p.L224R|CNGA1_ENST00000402813.3_Missense_Mutation_p.L293R			P29973	CNGA1_HUMAN	cyclic nucleotide gated channel alpha 1	224					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.L224R(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|urinary_tract(1)	28						TCCTTGTTCTAGGTAACCTAA	0.299																																																	1	Substitution - Missense(1)	kidney(1)											49.0	52.0	51.0					4																	47939840		1799	4059	5858	SO:0001583	missense	1259			M84741	CCDS43226.1, CCDS47050.1	4p12	2013-02-14				ENSG00000198515		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2148	protein-coding gene	gene with protein product		123825		CNCG1, CNCG		7683629, 16382102	Standard	NM_000087		Approved	RCNC1, RCNCa, CNG1, RP49	uc003gxu.3	P29973		ENST00000514170.1:c.671T>G	4.37:g.47939840A>C	ENSP00000426862:p.Leu224Arg		A8K7K6|J3KPZ2|Q16279|Q16485|Q4W5E3	Missense_Mutation	SNP	ENST00000514170.1	37	CCDS43226.1	.	.	.	.	.	.	.	.	.	.	A	17.86	3.493572	0.64186	.	.	ENSG00000198515	ENST00000402813;ENST00000514170;ENST00000544810;ENST00000358519;ENST00000420489	D;D;D;D;D	0.98362	-4.89;-4.89;-4.89;-4.89;-4.89	5.53	5.53	0.82687	Ion transport (1);	0.149549	0.46145	D	0.000314	D	0.98302	0.9437	M	0.93062	3.375	0.53688	D	0.999973	B;B	0.34255	0.445;0.445	B;B	0.37015	0.239;0.239	D	0.99320	1.0906	10	0.87932	D	0	.	15.7336	0.77825	1.0:0.0:0.0:0.0	.	224;224	Q4W5E3;P29973	.;CNGA1_HUMAN	R	293;224;224;224;224	ENSP00000384264:L293R;ENSP00000426862:L224R;ENSP00000443401:L224R;ENSP00000351320:L224R;ENSP00000389881:L224R	ENSP00000351320:L224R	L	-	2	0	CNGA1	47634597	1.000000	0.71417	0.998000	0.56505	0.949000	0.60115	8.962000	0.93254	2.113000	0.64589	0.529000	0.55759	CTA		0.299	CNGA1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372070.2		NM_000087	
COG1	9382	hgsc.bcm.edu;ucsc.edu	37	17	71197678	71197678	+	Frame_Shift_Del	DEL	G	G	-	rs141750466	byFrequency	TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr17:71197678delG	ENST00000299886.4	+	7	1792	c.1712delG	c.(1711-1713)cggfs	p.R571fs		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	571					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			GAGATGCTGCGGACTCAGTCC	0.567																																																	0													94.0	78.0	84.0					17																	71197678		2203	4300	6503	SO:0001589	frameshift_variant	9382				CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"""Components of oligomeric golgi complex"""	6545	protein-coding gene	gene with protein product		606973	"""low density lipoprotein receptor defect B complementing"""	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.1712delG	17.37:g.71197678delG	ENSP00000299886:p.Arg571fs		Q9NPV9|Q9P2G6	Frame_Shift_Del	DEL	ENST00000299886.4	37	CCDS11692.1																																																																																				0.567	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1			
DNMT3A	1788	hgsc.bcm.edu;ucsc.edu	37	2	25467027	25467027	+	Frame_Shift_Del	DEL	T	T	-			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr2:25467027delT	ENST00000264709.3	-	15	2185	c.1848delA	c.(1846-1848)gaafs	p.E616fs	DNMT3A_ENST00000380746.4_Frame_Shift_Del_p.E427fs|DNMT3A_ENST00000402667.1_Frame_Shift_Del_p.E393fs|DNMT3A_ENST00000321117.5_Frame_Shift_Del_p.E616fs|DNMT3A_ENST00000474887.1_5'UTR	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	616					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACTCACAAATTCCTGGTCGT	0.642			"""Mis, F, N, S"""		AML																																			Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	0													32.0	37.0	36.0					2																	25467027		2203	4300	6503	SO:0001589	frameshift_variant	1788				CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1848delA	2.37:g.25467027delT	ENSP00000264709:p.Glu616fs		E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Frame_Shift_Del	DEL	ENST00000264709.3	37	CCDS33157.1																																																																																				0.642	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1		NM_022552	
EIF4G2	1982	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	10825853	10825853	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr11:10825853G>C	ENST00000526148.1	-	6	974	c.464C>G	c.(463-465)cCa>cGa	p.P155R	SNORD97_ENST00000459187.1_RNA|RP11-685M7.5_ENST00000532365.1_RNA|EIF4G2_ENST00000339995.5_Missense_Mutation_p.P155R|EIF4G2_ENST00000396525.2_Missense_Mutation_p.P155R|EIF4G2_ENST00000525681.1_Missense_Mutation_p.P155R|EIF4G2_ENST00000525995.1_5'Flank	NM_001172705.1	NP_001166176			eukaryotic translation initiation factor 4 gamma, 2									p.P155R(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	43				all cancers(16;2.8e-07)|Epithelial(150;4.18e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		CTTCTGTCCTGGTTGACCCTC	0.428																																																	1	Substitution - Missense(1)	kidney(1)											151.0	139.0	143.0					11																	10825853		2201	4294	6495	SO:0001583	missense	1982			U73824	CCDS31428.1, CCDS41618.1	11p15	2005-09-29			ENSG00000110321	ENSG00000110321			3297	protein-coding gene	gene with protein product		602325				9030685, 9032289	Standard	NM_001042559		Approved	DAP5, NAT1, p97	uc001mjc.3	P78344	OTTHUMG00000165823	ENST00000526148.1:c.464C>G	11.37:g.10825853G>C	ENSP00000433664:p.Pro155Arg			Missense_Mutation	SNP	ENST00000526148.1	37	CCDS31428.1	.	.	.	.	.	.	.	.	.	.	G	17.58	3.425881	0.62733	.	.	ENSG00000110321	ENST00000526148;ENST00000525681;ENST00000339995;ENST00000396525;ENST00000429377;ENST00000531416;ENST00000532082;ENST00000524932;ENST00000527419	T;T;T;T;T;T;T;T	0.41400	2.13;2.13;2.13;2.13;1.83;1.89;1.87;1.0	5.67	5.67	0.87782	MIF4G-like, type 3 (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.150571	0.64402	D	0.000010	T	0.43743	0.1261	L	0.61036	1.89	0.40073	D	0.976040	P;P	0.38677	0.491;0.642	B;B	0.36378	0.124;0.223	T	0.38373	-0.9664	9	0.22706	T	0.39	-1.5291	20.1358	0.98028	0.0:0.0:1.0:0.0	.	155;228	P78344;B4DZF2	IF4G2_HUMAN;.	R	155;155;155;155;228;155;155;155;86	ENSP00000433664:P155R;ENSP00000433371:P155R;ENSP00000340281:P155R;ENSP00000379778:P155R;ENSP00000431583:P155R;ENSP00000433121:P155R;ENSP00000435523:P155R;ENSP00000434940:P86R	ENSP00000340281:P155R	P	-	2	0	EIF4G2	10782429	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.709000	0.74665	2.833000	0.97629	0.585000	0.79938	CCA		0.428	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1		NM_001418	
ESYT2	57488	hgsc.bcm.edu;ucsc.edu	37	7	158557475	158557475	+	Frame_Shift_Del	DEL	C	C	-			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr7:158557475delC	ENST00000251527.5	-	9	1203	c.1138delG	c.(1138-1140)gtcfs	p.V380fs		NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	408	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				endocytosis (GO:0006897)|lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						TTTCCCTTGACAAGTCCCTTA	0.418																																																	0													140.0	130.0	133.0					7																	158557475		2203	4300	6503	SO:0001589	frameshift_variant	57488			AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"""Synaptotagmins"""	22211	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member B"""	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.1138delG	7.37:g.158557475delC	ENSP00000251527:p.Val380fs		A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Frame_Shift_Del	DEL	ENST00000251527.5	37	CCDS34791.1																																																																																				0.418	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1		NM_020728	
GPNMB	10457	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	23307604	23307604	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr7:23307604G>A	ENST00000381990.2	+	8	1414	c.1253G>A	c.(1252-1254)gGg>gAg	p.G418E	GPNMB_ENST00000453162.2_Missense_Mutation_p.G360E|GPNMB_ENST00000258733.4_Missense_Mutation_p.G406E|GPNMB_ENST00000539136.1_Missense_Mutation_p.G307E	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	418					bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)	p.G418E(1)		breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			ACCTGCCAAGGGAGGTGAGTA	0.493																																																	1	Substitution - Missense(1)	kidney(1)											118.0	114.0	116.0					7																	23307604		2203	4300	6503	SO:0001583	missense	10457			X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"""transmembrane glycoprotein"", ""glycoprotein NMB"", ""glycoprotein nmb-like protein"", ""osteoactivin"""	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.1253G>A	7.37:g.23307604G>A	ENSP00000371420:p.Gly418Glu		A4D155|Q6UVX1|Q8N1A1	Missense_Mutation	SNP	ENST00000381990.2	37	CCDS34610.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.075668	0.76415	.	.	ENSG00000136235	ENST00000258733;ENST00000435486;ENST00000381990;ENST00000425903;ENST00000539136;ENST00000453162	T;T;T;T	0.64438	0.07;-0.03;0.15;-0.1	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	D	0.83059	0.5172	M	0.87180	2.865	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.85343	0.1097	10	0.87932	D	0	-20.3965	19.7831	0.96426	0.0:0.0:1.0:0.0	.	307;360;418;406	F6SKP1;F5GY20;Q14956;Q14956-2	.;.;GPNMB_HUMAN;.	E	406;453;418;301;307;360	ENSP00000258733:G406E;ENSP00000371420:G418E;ENSP00000445266:G307E;ENSP00000405586:G360E	ENSP00000258733:G406E	G	+	2	0	GPNMB	23274129	1.000000	0.71417	0.897000	0.35233	0.346000	0.29079	7.443000	0.80521	2.687000	0.91594	0.561000	0.74099	GGG		0.493	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1		NM_001005340	
HHEX	3087	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	94454334	94454334	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr10:94454334C>G	ENST00000282728.5	+	4	2421	c.622C>G	c.(622-624)Ctg>Gtg	p.L208V	HHEX_ENST00000472590.2_Missense_Mutation_p.L36V|HHEX_ENST00000492654.2_Missense_Mutation_p.L36V	NM_002729.4	NP_002720.1	Q03014	HHEX_HUMAN	hematopoietically expressed homeobox	208					anterior/posterior pattern specification (GO:0009952)|B cell differentiation (GO:0030183)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|DNA conformation change (GO:0071103)|embryonic heart tube development (GO:0035050)|endoderm development (GO:0007492)|forebrain morphogenesis (GO:0048853)|gall bladder development (GO:0061010)|hepatic duct development (GO:0061011)|hepatoblast differentiation (GO:0061017)|hepatocyte differentiation (GO:0070365)|in utero embryonic development (GO:0001701)|interkinetic nuclear migration (GO:0022027)|mRNA export from nucleus (GO:0006406)|multicellular organism growth (GO:0035264)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription by transcription factor localization (GO:0010621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|pancreas development (GO:0031016)|poly(A)+ mRNA export from nucleus (GO:0016973)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|primary lung bud formation (GO:0060431)|primitive streak formation (GO:0090009)|protein localization to nucleus (GO:0034504)|regulation of cell proliferation (GO:0042127)|response to peptide hormone (GO:0043434)|response to wounding (GO:0009611)|thyroid gland development (GO:0030878)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|eukaryotic initiation factor 4E binding (GO:0008190)|protein homodimerization activity (GO:0042803)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.L208V(1)		kidney(2)|large_intestine(2)|lung(5)|ovary(1)	10						AAAAGAAGAACTGGAAAGTTT	0.403																																																	1	Substitution - Missense(1)	kidney(1)											77.0	80.0	79.0					10																	94454334		2203	4300	6503	SO:0001583	missense	3087			Z21533	CCDS7423.1	10q23.33	2011-06-20	2007-02-15		ENSG00000152804	ENSG00000152804		"""Homeoboxes / ANTP class : NKL subclass"""	4901	protein-coding gene	gene with protein product		604420		PRHX		8096636, 8103988	Standard	NM_002729		Approved	HEX, HOX11L-PEN	uc001kid.3	Q03014	OTTHUMG00000018762	ENST00000282728.5:c.622C>G	10.37:g.94454334C>G	ENSP00000282728:p.Leu208Val		B1AQ17|Q96CE9	Missense_Mutation	SNP	ENST00000282728.5	37	CCDS7423.1	.	.	.	.	.	.	.	.	.	.	C	11.74	1.727497	0.30593	.	.	ENSG00000152804	ENST00000282728;ENST00000472590;ENST00000492654	D;D;D	0.91011	-2.77;-1.67;-1.67	5.34	3.33	0.38152	.	0.636443	0.14858	N	0.294221	T	0.78799	0.4340	N	0.19112	0.55	0.25072	N	0.990985	B	0.10296	0.003	B	0.09377	0.004	T	0.62348	-0.6873	10	0.30078	T	0.28	-6.1972	0.7976	0.01069	0.1684:0.3846:0.1895:0.2575	.	208	Q03014	HHEX_HUMAN	V	208;36;36	ENSP00000282728:L208V;ENSP00000450017:L36V;ENSP00000447953:L36V	ENSP00000282728:L208V	L	+	1	2	HHEX	94444314	0.988000	0.35896	1.000000	0.80357	0.985000	0.73830	0.698000	0.25571	1.467000	0.48044	0.655000	0.94253	CTG		0.403	HHEX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049402.2			
HHIPL2	79802	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	222721137	222721137	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr1:222721137C>G	ENST00000343410.6	-	1	308	c.250G>C	c.(250-252)Gac>Cac	p.D84H		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	84					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)	p.D84H(1)		NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		TCCATGATGTCCCAGTACCGG	0.522																																																	1	Substitution - Missense(1)	kidney(1)											66.0	67.0	67.0					1																	222721137		1978	4150	6128	SO:0001583	missense	79802			BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"""KIAA1822-like"""	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.250G>C	1.37:g.222721137C>G	ENSP00000342118:p.Asp84His		Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Missense_Mutation	SNP	ENST00000343410.6	37	CCDS1530.2	.	.	.	.	.	.	.	.	.	.	C	6.377	0.437623	0.12104	.	.	ENSG00000143512	ENST00000343410	T	0.41758	0.99	4.93	4.93	0.64822	Folate receptor-like (1);	0.391477	0.27126	N	0.020809	T	0.42539	0.1207	M	0.61703	1.905	0.36699	D	0.879994	B	0.15141	0.012	B	0.21546	0.035	T	0.48917	-0.8992	10	0.45353	T	0.12	-30.4453	13.1658	0.59571	0.1597:0.8403:0.0:0.0	.	84	Q6UWX4	HIPL2_HUMAN	H	84	ENSP00000342118:D84H	ENSP00000342118:D84H	D	-	1	0	HHIPL2	220787760	0.279000	0.24239	0.993000	0.49108	0.063000	0.16089	0.685000	0.25378	2.250000	0.74265	0.655000	0.94253	GAC		0.522	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2		NM_024746	
HLA-DPA1	3113	broad.mit.edu;hgsc.bcm.edu	37	6	33036464	33036464	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr6:33036464C>T	ENST00000419277.1	-	5	875	c.746G>A	c.(745-747)cGt>cAt	p.R249H	HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.R249H|HLA-DPA1_ENST00000463066.1_5'Flank	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	249					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)	p.R249H(1)		kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						ATGGCCAGAACGCAGAGACTT	0.567																																																	1	Substitution - Missense(1)	kidney(1)											92.0	118.0	109.0					6																	33036464		1511	2709	4220	SO:0001583	missense	3113			X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.746G>A	6.37:g.33036464C>T	ENSP00000393566:p.Arg249His		A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	.	.	.	.	.	.	.	.	.	.	C	7.584	0.669437	0.14776	.	.	ENSG00000231389	ENST00000419277;ENST00000428995	T;T	0.02032	4.49;4.49	3.4	0.452	0.16634	.	0.689522	0.12134	N	0.496516	T	0.00967	0.0032	L	0.56769	1.78	0.09310	N	0.999991	B	0.09022	0.002	B	0.10450	0.005	T	0.42882	-0.9425	10	0.59425	D	0.04	.	5.7911	0.18361	0.0:0.5859:0.0:0.4141	.	249	P20036	DPA1_HUMAN	H	249	ENSP00000393566:R249H;ENSP00000402872:R249H	ENSP00000393566:R249H	R	-	2	0	HLA-DPA1	33144442	0.000000	0.05858	0.032000	0.17829	0.349000	0.29174	-1.173000	0.03108	-0.066000	0.12998	-0.148000	0.13756	CGT		0.567	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3		NM_033554	
INPPL1	3636	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	71948448	71948448	+	Missense_Mutation	SNP	C	C	G	rs374103936		TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr11:71948448C>G	ENST00000298229.2	+	26	3364	c.3160C>G	c.(3160-3162)Cca>Gca	p.P1054A	INPPL1_ENST00000541756.1_Missense_Mutation_p.P812A|INPPL1_ENST00000538751.1_Missense_Mutation_p.P812A|PHOX2A_ENST00000544057.1_5'Flank	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	1054	Pro-rich.				actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|endochondral ossification (GO:0001958)|endocytosis (GO:0006897)|glucose metabolic process (GO:0006006)|immune system process (GO:0002376)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|post-embryonic development (GO:0009791)|response to insulin (GO:0032868)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|SH2 domain binding (GO:0042169)	p.P1054A(1)		breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						TCCAGACTTTCCACCTCCACC	0.662													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17184	0.0		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)						C	ALA/PRO	1,4399	2.1+/-5.4	0,1,2199	56.0	57.0	56.0		3160	4.8	1.0	11		56	0,8586		0,0,4293	no	missense	INPPL1	NM_001567.3	27	0,1,6492	GG,GC,CC		0.0,0.0227,0.0077	possibly-damaging	1054/1259	71948448	1,12985	2200	4293	6493	SO:0001583	missense	3636			Y14385	CCDS8213.1	11q23	2013-02-14			ENSG00000165458	ENSG00000165458		"""Sterile alpha motif (SAM) domain containing"", ""SH2 domain containing"""	6080	protein-coding gene	gene with protein product	"""51C protein"""	600829				8530088	Standard	NM_001567		Approved	SHIP2	uc001osf.3	O15357	OTTHUMG00000167879	ENST00000298229.2:c.3160C>G	11.37:g.71948448C>G	ENSP00000298229:p.Pro1054Ala		B2RTX5|Q13577|Q13578	Missense_Mutation	SNP	ENST00000298229.2	37	CCDS8213.1	.	.	.	.	.	.	.	.	.	.	c	13.55	2.272065	0.40194	2.27E-4	0.0	ENSG00000165458	ENST00000298229;ENST00000541756;ENST00000538751;ENST00000541752	D;D;D;T	0.96967	-3.05;-4.19;-4.19;-0.06	4.85	4.85	0.62838	.	0.070851	0.56097	D	0.000028	D	0.91513	0.7320	N	0.24115	0.695	0.51012	D	0.999906	P	0.46987	0.888	B	0.41374	0.355	D	0.90289	0.4321	10	0.10636	T	0.68	.	15.505	0.75731	0.0:1.0:0.0:0.0	.	1054	O15357	SHIP2_HUMAN	A	1054;812;812;67	ENSP00000298229:P1054A;ENSP00000446360:P812A;ENSP00000444619:P812A;ENSP00000441094:P67A	ENSP00000298229:P1054A	P	+	1	0	INPPL1	71626096	1.000000	0.71417	0.997000	0.53966	0.956000	0.61745	4.834000	0.62774	2.513000	0.84729	0.563000	0.77884	CCA		0.662	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1		NM_001567	
KRT24	192666	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	38859430	38859430	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr17:38859430G>C	ENST00000264651.2	-	1	572	c.516C>G	c.(514-516)atC>atG	p.I172M		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	172	Coil 1A.|Rod.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	structural molecule activity (GO:0005198)	p.I172M(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00526)				ACCACTCCTTGATTTTGTTCT	0.463																																					GBM(61;380 1051 14702 23642 31441)												1	Substitution - Missense(1)	kidney(1)											191.0	188.0	189.0					17																	38859430		2203	4300	6503	SO:0001583	missense	192666				CCDS11372.1	17q21.2	2013-06-25			ENSG00000167916	ENSG00000167916		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	18527	protein-coding gene	gene with protein product		607742				16831889	Standard	NM_019016		Approved	FLJ20261, MGC138169, MGC138173	uc002hvd.3	Q2M2I5	OTTHUMG00000133372	ENST00000264651.2:c.516C>G	17.37:g.38859430G>C	ENSP00000264651:p.Ile172Met		Q9NXG7	Missense_Mutation	SNP	ENST00000264651.2	37	CCDS11372.1	.	.	.	.	.	.	.	.	.	.	G	19.58	3.854315	0.71719	.	.	ENSG00000167916	ENST00000264651	D	0.90197	-2.63	5.6	3.63	0.41609	Filament (1);	.	.	.	.	D	0.96873	0.8979	H	0.98849	4.35	0.45515	D	0.998478	D	0.89917	1.0	D	0.97110	1.0	D	0.95785	0.8820	9	0.87932	D	0	.	8.8096	0.34959	0.2279:0.0:0.7721:0.0	.	172	Q2M2I5	K1C24_HUMAN	M	172	ENSP00000264651:I172M	ENSP00000264651:I172M	I	-	3	3	KRT24	36112956	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.082000	0.57635	0.847000	0.35167	0.655000	0.94253	ATC		0.463	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1		NM_019016	
MAGEA4	4103	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	151092616	151092616	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chrX:151092616G>T	ENST00000360243.2	+	3	747	c.480G>T	c.(478-480)aaG>aaT	p.K160N	MAGEA4_ENST00000276344.2_Missense_Mutation_p.K160N|MAGEA4_ENST00000370335.1_Missense_Mutation_p.K160N|MAGEA4_ENST00000370340.3_Missense_Mutation_p.K160N|MAGEA4_ENST00000393920.1_Missense_Mutation_p.K160N|MAGEA4_ENST00000393921.1_Missense_Mutation_p.K160N|MAGEA4_ENST00000370337.4_Missense_Mutation_p.K160N	NM_001011550.1	NP_001011550.1	P43358	MAGA4_HUMAN	melanoma antigen family A, 4	160	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.K160N(1)		breast(2)|central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)	27	Acute lymphoblastic leukemia(192;6.56e-05)					AGTCCCTGAAGATGATCTTTG	0.522																																																	1	Substitution - Missense(1)	kidney(1)											107.0	105.0	106.0					X																	151092616		2203	4300	6503	SO:0001583	missense	4103				CCDS14702.1	Xq28	2009-03-13			ENSG00000147381	ENSG00000147381			6802	protein-coding gene	gene with protein product	"""melanoma-associated antigen 4"", ""cancer/testis antigen family 1, member 4"""	300175		MAGE4		8575766	Standard	XM_005274677		Approved	MAGE4A, MAGE4B, MAGE-41, MAGE-X2, MGC21336, CT1.4	uc004ffa.3	P43358	OTTHUMG00000024174	ENST00000360243.2:c.480G>T	X.37:g.151092616G>T	ENSP00000353379:p.Lys160Asn		Q14798	Missense_Mutation	SNP	ENST00000360243.2	37	CCDS14702.1	.	.	.	.	.	.	.	.	.	.	G	13.99	2.403286	0.42613	.	.	ENSG00000147381	ENST00000431963;ENST00000276344;ENST00000448295;ENST00000393921;ENST00000430273;ENST00000370337;ENST00000441865;ENST00000393920;ENST00000370340;ENST00000416020;ENST00000425182;ENST00000457310;ENST00000370335;ENST00000360243;ENST00000431971	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.05199	3.48;3.48;3.48;3.48;3.48;3.48;3.48;3.48;3.48;3.48;3.48;3.48;3.48;3.48;3.48	2.37	0.494	0.16884	.	0.614911	0.17092	N	0.187337	T	0.06645	0.0170	L	0.46157	1.445	0.09310	N	1	P	0.42161	0.772	B	0.43838	0.433	T	0.25187	-1.0139	10	0.66056	D	0.02	.	2.6101	0.04889	0.1745:0.0:0.5433:0.2822	.	160	P43358	MAGA4_HUMAN	N	160	ENSP00000387777:K160N;ENSP00000276344:K160N;ENSP00000391904:K160N;ENSP00000377498:K160N;ENSP00000394149:K160N;ENSP00000359362:K160N;ENSP00000402624:K160N;ENSP00000377497:K160N;ENSP00000359365:K160N;ENSP00000394073:K160N;ENSP00000400900:K160N;ENSP00000402186:K160N;ENSP00000359360:K160N;ENSP00000353379:K160N;ENSP00000390096:K160N	ENSP00000276344:K160N	K	+	3	2	MAGEA4	150843272	0.000000	0.05858	0.000000	0.03702	0.453000	0.32348	0.123000	0.15708	0.018000	0.15052	0.292000	0.19580	AAG		0.522	MAGEA4-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060898.1		NM_002362	
MCC	4163	hgsc.bcm.edu	37	5	112399691	112399692	+	Frame_Shift_Ins	INS	-	-	G	rs143092740		TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr5:112399691_112399692insG	ENST00000302475.4	-	12	2195_2196	c.1632_1633insC	c.(1630-1635)aacagcfs	p.S545fs	MCC_ENST00000408903.3_Frame_Shift_Ins_p.S735fs|MCC_ENST00000514701.3_5'UTR|MCC_ENST00000515367.2_Frame_Shift_Ins_p.S482fs	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	545					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		CTGGTGTGGCTGTTGGAGGAAA	0.629																																																	0																																										SO:0001589	frameshift_variant	4163				CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"""EF-hand domain containing"""	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000302475.4:c.1633dupC	5.37:g.112399692_112399692dupG	ENSP00000305617:p.Ser545fs		D3DT05|Q6ZR04	Frame_Shift_Ins	INS	ENST00000302475.4	37	CCDS4111.1																																																																																				0.629	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3		NM_001085377	
MICALL2	79778	broad.mit.edu;ucsc.edu	37	7	1474748	1474748	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr7:1474748A>G	ENST00000297508.7	-	16	2802	c.2627T>C	c.(2626-2628)aTt>aCt	p.I876T	MICALL2_ENST00000471899.1_Intron|MICALL2_ENST00000405088.4_Missense_Mutation_p.I664T	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	876	Mediates interaction with RAB13 and is required for transition from the closed to the opened conformation. {ECO:0000250}.				actin cytoskeleton reorganization (GO:0031532)|actin filament polymerization (GO:0030041)|endocytic recycling (GO:0032456)|neuron projection development (GO:0031175)|substrate adhesion-dependent cell spreading (GO:0034446)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin filament binding (GO:0051015)|filamin binding (GO:0031005)|zinc ion binding (GO:0008270)	p.I876T(1)		breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(8)|ovary(2)|skin(2)	19		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		CAGCTTCTCAATCATGTCCCG	0.657																																																	1	Substitution - Missense(1)	kidney(1)											105.0	98.0	100.0					7																	1474748		2202	4299	6501	SO:0001583	missense	79778			BC037988	CCDS5324.1	7p22.3	2006-11-24			ENSG00000164877	ENSG00000164877			29672	protein-coding gene	gene with protein product	"""junctional Rab13-binding protein"""					12110185, 16525024	Standard	NM_182924		Approved	MGC46023, FLJ23471, MICAL-L2, JRAB	uc003skj.4	Q8IY33	OTTHUMG00000119021	ENST00000297508.7:c.2627T>C	7.37:g.1474748A>G	ENSP00000297508:p.Ile876Thr		D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Missense_Mutation	SNP	ENST00000297508.7	37	CCDS5324.1	.	.	.	.	.	.	.	.	.	.	A	5.697	0.313055	0.10789	.	.	ENSG00000164877	ENST00000405088;ENST00000297508	T;T	0.73469	2.11;-0.75	3.91	3.91	0.45181	.	0.204244	0.24260	N	0.040082	T	0.73705	0.3621	N	0.20986	0.625	0.34595	D	0.715937	D;B	0.69078	0.997;0.009	P;B	0.60682	0.878;0.005	T	0.81887	-0.0726	10	0.87932	D	0	.	11.772	0.51965	1.0:0.0:0.0:0.0	.	876;664	Q8IY33;D3YTD2	MILK2_HUMAN;.	T	664;876	ENSP00000385928:I664T;ENSP00000297508:I876T	ENSP00000297508:I876T	I	-	2	0	MICALL2	1441274	1.000000	0.71417	0.996000	0.52242	0.025000	0.11179	2.921000	0.48852	1.644000	0.50603	0.449000	0.29647	ATT		0.657	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2		NM_182924	
MUC16	94025	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	9070296	9070296	+	Missense_Mutation	SNP	T	T	G			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr19:9070296T>G	ENST00000397910.4	-	3	17353	c.17150A>C	c.(17149-17151)aAc>aCc	p.N5717T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5719	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.N5717T(2)|p.N1350T(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CACTGCAGTGTTTGTATGCAT	0.498																																																	3	Substitution - Missense(3)	kidney(3)											160.0	156.0	157.0					19																	9070296		2099	4224	6323	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.17150A>C	19.37:g.9070296T>G	ENSP00000381008:p.Asn5717Thr		Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	3.328	-0.137256	0.06711	.	.	ENSG00000181143	ENST00000397910	T	0.26067	1.76	1.54	1.54	0.23209	.	.	.	.	.	T	0.15262	0.0368	L	0.39898	1.24	.	.	.	P	0.50710	0.938	B	0.34931	0.192	T	0.23691	-1.0181	8	0.87932	D	0	.	5.1848	0.15178	0.0:0.0:0.0:1.0	.	5717	B5ME49	.	T	5717	ENSP00000381008:N5717T	ENSP00000381008:N5717T	N	-	2	0	MUC16	8931296	0.017000	0.18338	0.001000	0.08648	0.002000	0.02628	-0.820000	0.04457	0.983000	0.38602	0.379000	0.24179	AAC		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1		NM_024690	
MYH9	4627	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	36693020	36693020	+	Silent	SNP	C	C	T			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr22:36693020C>T	ENST00000216181.5	-	25	3371	c.3141G>A	c.(3139-3141)gaG>gaA	p.E1047E		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1047					actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)	p.E1047E(1)		NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						GGCGGGTCTTCTCCAGCTCCT	0.632			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated																															Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	1	Substitution - coding silent(1)	kidney(1)											54.0	53.0	53.0					22																	36693020		2203	4300	6503	SO:0001819	synonymous_variant	4627	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"""Myosins / Myosin superfamily : Class II"""	7579	protein-coding gene	gene with protein product	"""nonmuscle myosin heavy chain II-A"""	160775	"""myosin, heavy polypeptide 9, non-muscle"""	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.3141G>A	22.37:g.36693020C>T			A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	37	CCDS13927.1																																																																																				0.632	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3		NM_002473	
MYO6	4646	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	76591436	76591436	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr6:76591436G>A	ENST00000369977.3	+	23	2456	c.2317G>A	c.(2317-2319)Gac>Aac	p.D773N	MYO6_ENST00000369985.4_Missense_Mutation_p.D773N|MYO6_ENST00000462633.1_3'UTR|MYO6_ENST00000369981.3_Missense_Mutation_p.D773N|MYO6_ENST00000369975.1_Missense_Mutation_p.D773N	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	773					actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)	p.D773N(1)		breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		CATGAAGTCTGACCCTGACCA	0.373																																																	1	Substitution - Missense(1)	kidney(1)											119.0	113.0	115.0					6																	76591436		2203	4300	6503	SO:0001583	missense	4646			U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"""Myosins / Myosin superfamily : Class VI"""	7605	protein-coding gene	gene with protein product		600970	"""deafness, autosomal recessive 37"""	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.2317G>A	6.37:g.76591436G>A	ENSP00000358994:p.Asp773Asn		A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	37	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	G	36	5.634745	0.96682	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.84083	0.5394	M	0.83692	2.655	0.80722	D	1	D;D	0.89917	1.0;0.992	D;D	0.91635	0.999;0.987	D	0.85316	0.1081	10	0.62326	D	0.03	.	19.4895	0.95044	0.0:0.0:1.0:0.0	.	773;773	Q9UM54-2;Q9UM54-1	.;.	N	773	ENSP00000358998:D773N;ENSP00000359002:D773N;ENSP00000358994:D773N;ENSP00000358992:D773N	ENSP00000358992:D773N	D	+	1	0	MYO6	76648156	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.447000	0.97595	2.596000	0.87737	0.655000	0.94253	GAC		0.373	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2		NM_004999	
MZF1	7593	broad.mit.edu	37	19	59073897	59073897	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr19:59073897T>C	ENST00000215057.2	-	6	2307	c.1747A>G	c.(1747-1749)Acg>Gcg	p.T583A	MZF1_ENST00000599369.1_Missense_Mutation_p.T583A|MZF1_ENST00000594234.1_3'UTR|AC016629.8_ENST00000600726.1_RNA|AC016629.8_ENST00000600534.1_RNA|AC016629.8_ENST00000593642.1_RNA	NM_001267033.1|NM_198055.1	NP_001253962.1|NP_932172.1	P28698	MZF1_HUMAN	myeloid zinc finger 1	583					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.T583A(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0443)|all cancers(4;7.92e-14)|Epithelial(4;5.57e-11)|OV - Ovarian serous cystadenocarcinoma(4;1.13e-09)|GBM - Glioblastoma multiforme(193;0.0108)|Lung(386;0.182)		TGCGTGAGCGTAGGCCGCTGG	0.687																																																	1	Substitution - Missense(1)	kidney(1)											20.0	19.0	19.0					19																	59073897		2202	4298	6500	SO:0001583	missense	7593			M58297	CCDS12988.1, CCDS59427.1	19q13.43	2014-08-22	2006-06-15	2006-06-15	ENSG00000099326	ENSG00000099326		"""-"", ""Zinc fingers, C2H2-type"""	13108	protein-coding gene	gene with protein product		194550	"""zinc finger protein 42 (myeloid-specific retinoic acid-responsive)"""	ZNF42		1860835	Standard	NM_198055		Approved	ZSCAN6, MZF1B, MZF-1, Zfp98	uc002qtn.3	P28698	OTTHUMG00000183550	ENST00000215057.2:c.1747A>G	19.37:g.59073897T>C	ENSP00000215057:p.Thr583Ala		M0QXU0|Q7Z729|Q96I71|Q9NRY0|Q9UBW2	Missense_Mutation	SNP	ENST00000215057.2	37	CCDS12988.1	.	.	.	.	.	.	.	.	.	.	T	13.14	2.148775	0.37923	.	.	ENSG00000099326	ENST00000215057	T	0.06849	3.25	3.45	2.43	0.29744	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.190605	0.25909	N	0.027505	T	0.02571	0.0078	N	0.01202	-0.96	0.19775	N	0.99995	B	0.12013	0.005	B	0.12156	0.007	T	0.44003	-0.9356	10	0.27785	T	0.31	-6.6904	7.137	0.25533	0.0:0.1144:0.0:0.8856	.	583	P28698	MZF1_HUMAN	A	583	ENSP00000215057:T583A	ENSP00000215057:T583A	T	-	1	0	MZF1	63765709	0.000000	0.05858	0.999000	0.59377	0.965000	0.64279	-0.250000	0.08830	0.690000	0.31570	0.379000	0.24179	ACG		0.687	MZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467112.1		NM_198055	
NSUN2	54888	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	6600260	6600260	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr5:6600260G>C	ENST00000264670.6	-	19	2394	c.2083C>G	c.(2083-2085)Cgg>Ggg	p.R695G	NSUN2_ENST00000539938.1_Missense_Mutation_p.R459G|NSUN2_ENST00000506139.1_Missense_Mutation_p.R660G	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	695					mitotic nuclear division (GO:0007067)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|tRNA (cytosine-5-)-methyltransferase activity (GO:0016428)|tRNA binding (GO:0000049)	p.R695G(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						TAATGAAGCCGTTCATTCTTG	0.517																																																	1	Substitution - Missense(1)	kidney(1)											86.0	87.0	87.0					5																	6600260		2203	4300	6503	SO:0001583	missense	54888			AK000310	CCDS3869.1, CCDS54832.1	5p15.32	2014-01-31	2012-06-12		ENSG00000037474	ENSG00000037474		"""NOP2/Sun domain containing"""	25994	protein-coding gene	gene with protein product	"""tRNA methyltransferase 4 homolog (S. cerevisiae)"", ""Myc-induced SUN-domain-containing protein"""	610916	"""NOL1/NOP2/Sun domain family, member 2"", ""NOP2/Sun domain family, member 2"", ""mental retardation, non-syndromic, autosomal recessive, 5"""	MRT5		17071714, 22541559	Standard	NM_017755		Approved	FLJ20303, TRM4, Misu	uc003jdu.3	Q08J23	OTTHUMG00000090455	ENST00000264670.6:c.2083C>G	5.37:g.6600260G>C	ENSP00000264670:p.Arg695Gly		A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Missense_Mutation	SNP	ENST00000264670.6	37	CCDS3869.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.122018	0.77436	.	.	ENSG00000037474	ENST00000264670;ENST00000539938;ENST00000506139	T;T;T	0.66099	-0.19;-0.19;-0.19	5.43	4.51	0.55191	.	0.047371	0.85682	D	0.000000	T	0.77665	0.4164	M	0.82823	2.61	0.52501	D	0.999959	D;D;D	0.89917	1.0;0.959;0.98	D;P;P	0.75484	0.986;0.867;0.9	T	0.76686	-0.2868	10	0.33940	T	0.23	-35.7651	11.5708	0.50832	0.0:0.0:0.6463:0.3537	.	660;695;695	B4DQW2;Q08J23;A8K529	.;NSUN2_HUMAN;.	G	695;459;660	ENSP00000264670:R695G;ENSP00000444338:R459G;ENSP00000420957:R660G	ENSP00000264670:R695G	R	-	1	2	NSUN2	6653260	1.000000	0.71417	0.986000	0.45419	0.968000	0.65278	1.914000	0.39966	2.532000	0.85374	0.563000	0.77884	CGG		0.517	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1		NM_017755	
OR10G3	26533	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	22038804	22038804	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr14:22038804C>A	ENST00000303532.1	-	1	71	c.72G>T	c.(70-72)agG>agT	p.R24S		NM_001005465.1	NP_001005465.1	Q8NGC4	O10G3_HUMAN	olfactory receptor, family 10, subfamily G, member 3	24						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R24S(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)	15	all_cancers(95;0.000987)			GBM - Glioblastoma multiforme(265;0.0139)		AAAAGAGTGTCCTTAGCCTGA	0.443																																																	1	Substitution - Missense(1)	kidney(1)											80.0	79.0	80.0					14																	22038804		2203	4300	6503	SO:0001583	missense	26533				CCDS32046.1	14q11.2	2013-09-24			ENSG00000169208	ENSG00000169208		"""GPCR / Class A : Olfactory receptors"""	8171	protein-coding gene	gene with protein product						8188290	Standard	NM_001005465		Approved		uc010tmb.2	Q8NGC4	OTTHUMG00000168886	ENST00000303532.1:c.72G>T	14.37:g.22038804C>A	ENSP00000302437:p.Arg24Ser		Q6IET7|Q96R77	Missense_Mutation	SNP	ENST00000303532.1	37	CCDS32046.1	.	.	.	.	.	.	.	.	.	.	C	2.858	-0.236705	0.05944	.	.	ENSG00000169208	ENST00000303532	T	0.02737	4.18	4.33	-1.65	0.08291	.	0.000000	0.52532	D	0.000079	T	0.02929	0.0087	L	0.46157	1.445	0.09310	N	0.999998	B	0.12630	0.006	B	0.12156	0.007	T	0.36768	-0.9734	10	0.48119	T	0.1	-10.9123	9.1233	0.36799	0.0:0.3889:0.0:0.6111	.	24	Q8NGC4	O10G3_HUMAN	S	24	ENSP00000302437:R24S	ENSP00000302437:R24S	R	-	3	2	OR10G3	21108644	0.000000	0.05858	0.166000	0.22797	0.091000	0.18340	-0.907000	0.04067	-0.294000	0.08973	-0.237000	0.12165	AGG		0.443	OR10G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401521.1			
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52663035	52663035	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr3:52663035G>A	ENST00000296302.7	-	12	1319	c.1318C>T	c.(1318-1320)Caa>Taa	p.Q440*	PBRM1_ENST00000409767.1_Nonsense_Mutation_p.Q440*|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.Q440*|PBRM1_ENST00000337303.4_Nonsense_Mutation_p.Q440*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.Q440*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.Q440*|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.Q408*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.Q440*			Q86U86	PB1_HUMAN	polybromo 1	440	Bromo 3. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.Q440*(3)|p.Q408*(1)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TCATATTCTTGATTCTTCAGT	0.328			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	4	Substitution - Nonsense(4)	kidney(4)											65.0	60.0	62.0					3																	52663035		2203	4300	6503	SO:0001587	stop_gained	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.1318C>T	3.37:g.52663035G>A	ENSP00000296302:p.Gln440*		A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	G	36	5.669622	0.96754	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	.	.	.	5.38	5.38	0.77491	.	0.173757	0.52532	D	0.000078	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	-18.944	14.8112	0.69996	0.0:0.0:0.8554:0.1446	.	.	.	.	X	408;440;440;440;440;440;440;440;440;384	.	ENSP00000296302:Q440X	Q	-	1	0	PBRM1	52638075	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	3.054000	0.49908	2.532000	0.85374	0.467000	0.42956	CAA		0.328	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PDE4DIP	9659	broad.mit.edu;hgsc.bcm.edu	37	1	144931029	144931029	+	Intron	SNP	G	G	A			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr1:144931029G>A	ENST00000369354.3	-	6	826				PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000479408.2_Intron|PDE4DIP_ENST00000369351.3_Intron|PDE4DIP_ENST00000369349.3_Intron|PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000313431.9_Missense_Mutation_p.P227L|PDE4DIP_ENST00000529945.1_Missense_Mutation_p.P227L|PDE4DIP_ENST00000313382.9_Intron|PDE4DIP_ENST00000530740.1_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein						cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)	p.P227L(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TCCATCTGGGGGTACCTTTGT	0.552			T	PDGFRB	MPD																																			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	1	Substitution - Missense(1)	kidney(1)											97.0	99.0	99.0					1																	144931029		2203	4300	6503	SO:0001627	intron_variant	9659			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.637-7208C>T	1.37:g.144931029G>A			A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	G	13.90	2.375941	0.42105	.	.	ENSG00000178104	ENST00000369353;ENST00000313431;ENST00000529945	T;T	0.12569	2.67;2.67	5.28	4.32	0.51571	.	.	.	.	.	T	0.07548	0.0190	L	0.47716	1.5	0.51767	D	0.999939	B	0.15930	0.015	B	0.18871	0.023	T	0.04255	-1.0965	9	0.66056	D	0.02	.	13.0409	0.58899	0.0:0.0:0.8388:0.1612	.	227	Q5VU43-2	.	L	227	ENSP00000316434:P227L;ENSP00000433392:P227L	ENSP00000316434:P227L	P	-	2	0	PDE4DIP	143642386	0.004000	0.15560	0.939000	0.37840	0.994000	0.84299	1.455000	0.35190	2.470000	0.83445	0.491000	0.48974	CCC		0.552	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2		NM_022359	
PDS5B	23047	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	33222938	33222938	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr13:33222938A>C	ENST00000315596.10	+	2	215	c.29A>C	c.(28-30)gAt>gCt	p.D10A		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	10					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)	p.D10A(1)		NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		AGGACCAATGATGGAAAAATT	0.328																																																	1	Substitution - Missense(1)	kidney(1)											119.0	118.0	118.0					13																	33222938		1828	4068	5896	SO:0001583	missense	23047			AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"""androgen-induced proliferation inhibitor"""	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.29A>C	13.37:g.33222938A>C	ENSP00000313851:p.Asp10Ala		Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Missense_Mutation	SNP	ENST00000315596.10	37	CCDS41878.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.722486	0.89298	.	.	ENSG00000083642	ENST00000315596;ENST00000421084	.	.	.	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.67487	0.2898	L	0.51422	1.61	0.80722	D	1	D;D;P	0.63880	0.993;0.971;0.951	D;P;P	0.62955	0.909;0.641;0.702	T	0.63616	-0.6597	9	0.23891	T	0.37	-3.5545	15.508	0.75757	1.0:0.0:0.0:0.0	.	10;10;10	Q9NTI5;Q9NTI5-3;Q9NTI5-4	PDS5B_HUMAN;.;.	A	10	.	ENSP00000313851:D10A	D	+	2	0	PDS5B	32120938	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.134000	0.94467	2.060000	0.61445	0.482000	0.46254	GAT		0.328	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3		NM_015032	
PDS5B	23047	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	33316758	33316758	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr13:33316758G>A	ENST00000315596.10	+	23	2691	c.2505G>A	c.(2503-2505)tgG>tgA	p.W835*		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	835					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)	p.W835*(1)		NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		TGGTTCGATGGCTACTTGGAA	0.328																																																	1	Substitution - Nonsense(1)	kidney(1)											122.0	112.0	115.0					13																	33316758		1842	4094	5936	SO:0001587	stop_gained	23047			AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"""androgen-induced proliferation inhibitor"""	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.2505G>A	13.37:g.33316758G>A	ENSP00000313851:p.Trp835*		Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Nonsense_Mutation	SNP	ENST00000315596.10	37	CCDS41878.1	.	.	.	.	.	.	.	.	.	.	G	40	8.437184	0.98810	.	.	ENSG00000083642	ENST00000315596;ENST00000421084	.	.	.	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	-14.1014	20.3495	0.98807	0.0:0.0:1.0:0.0	.	.	.	.	X	835	.	ENSP00000313851:W835X	W	+	3	0	PDS5B	32214758	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.756000	0.98918	2.814000	0.96858	0.591000	0.81541	TGG		0.328	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3		NM_015032	
PDXDC2P	283970	broad.mit.edu	37	16	70012183	70012183	+	RNA	SNP	T	T	G			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr16:70012183T>G	ENST00000531894.1	-	0	2519				RP11-419C5.2_ENST00000525562.1_RNA	NR_003610.1		Q6P474	PDXD2_HUMAN	pyridoxal-dependent decarboxylase domain containing 2, pseudogene						carboxylic acid metabolic process (GO:0019752)		carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)	p.K183T(2)|p.K151T(1)									TTGAAACATTTTCCTATGGAT	0.443																																																	3	Substitution - Missense(3)	kidney(3)																																										0					16q22.1	2014-03-20	2010-09-02	2010-09-02	ENSG00000196696	ENSG00000196696			27559	pseudogene	pseudogene			"""pyridoxal-dependent decarboxylase domain containing 2"""	PDXDC2			Standard	NR_003610		Approved	DKFZp761H1120	uc010vlq.1	Q6P474	OTTHUMG00000167595		16.37:g.70012183T>G			A8K9Z5	Missense_Mutation	SNP	ENST00000531894.1	37		.	.	.	.	.	.	.	.	.	.	.	11.62	1.693838	0.30052	.	.	ENSG00000226232	ENST00000532298;ENST00000325845	T;T	0.50813	0.73;0.73	0.659	0.659	0.17861	.	.	.	.	.	T	0.59032	0.2164	.	.	.	.	.	.	P	0.52316	0.952	P	0.60012	0.867	T	0.68349	-0.5432	6	0.56958	D	0.05	.	.	.	.	.	183	A8MZ50	NPIL4_HUMAN	T	183;151	ENSP00000448651:K183T;ENSP00000449128:K151T	ENSP00000449128:K151T	K	-	2	0	RP11-419C5.2	68569684	0.042000	0.20092	0.004000	0.12327	0.003000	0.03518	0.972000	0.29409	0.571000	0.29365	0.310000	0.20435	AAA		0.443	PDXDC2P-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000395258.1			
PRDM12	59335	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	133543580	133543580	+	Silent	SNP	C	C	A			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr9:133543580C>A	ENST00000253008.2	+	3	510	c.450C>A	c.(448-450)atC>atA	p.I150I		NM_021619.2	NP_067632.2	Q9H4Q4	PRD12_HUMAN	PR domain containing 12	150	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				neurogenesis (GO:0022008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)	p.I150I(1)		kidney(2)|large_intestine(3)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	11		all_hematologic(13;0.0433)|Acute lymphoblastic leukemia(5;0.0534)		OV - Ovarian serous cystadenocarcinoma(145;0.000344)		GCTACTTCATCGATGCCAGCC	0.567																																																	1	Substitution - coding silent(1)	kidney(1)											176.0	130.0	146.0					9																	133543580		2203	4300	6503	SO:0001819	synonymous_variant	59335			AY004252	CCDS6934.1	9q33-q34	2013-01-08			ENSG00000130711	ENSG00000130711		"""Zinc fingers, C2H2-type"""	13997	protein-coding gene	gene with protein product	"""PR-domain containing protein 12"", ""PR-domain zinc finger protein 12"""					14523459	Standard	NM_021619		Approved		uc004bzt.1	Q9H4Q4	OTTHUMG00000020808	ENST00000253008.2:c.450C>A	9.37:g.133543580C>A			A3KFK9	Silent	SNP	ENST00000253008.2	37	CCDS6934.1																																																																																				0.567	PRDM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054664.1		NM_021619	
PYGB	5834	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	25249816	25249816	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr20:25249816G>T	ENST00000216962.4	+	3	507	c.397G>T	c.(397-399)Ggg>Tgg	p.G133W		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	133					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glycogen phosphorylase activity (GO:0008184)|pyridoxal phosphate binding (GO:0030170)	p.G133W(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	31						TGCTGGCCTTGGGAATGGAGG	0.542																																																	1	Substitution - Missense(1)	kidney(1)											84.0	91.0	88.0					20																	25249816		2203	4300	6503	SO:0001583	missense	5834				CCDS13171.1	20p11.21	2013-03-01			ENSG00000100994	ENSG00000100994	2.4.1.1	"""Glycogen phosphorylases"""	9723	protein-coding gene	gene with protein product	"""glycogen phosphorylase, brain form"""	138550					Standard	NM_002862		Approved		uc002wup.3	P11216	OTTHUMG00000032117	ENST00000216962.4:c.397G>T	20.37:g.25249816G>T	ENSP00000216962:p.Gly133Trp		Q96AK1|Q9NPX8	Missense_Mutation	SNP	ENST00000216962.4	37	CCDS13171.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.477873	0.84747	.	.	ENSG00000100994	ENST00000216962	D	0.97303	-4.33	4.18	4.18	0.49190	.	0.000000	0.85682	D	0.000000	D	0.99155	0.9708	H	0.98802	4.335	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98669	1.0687	10	0.87932	D	0	-30.3435	16.6438	0.85155	0.0:0.0:1.0:0.0	.	133	P11216	PYGB_HUMAN	W	133	ENSP00000216962:G133W	ENSP00000216962:G133W	G	+	1	0	PYGB	25197816	1.000000	0.71417	0.859000	0.33776	0.988000	0.76386	9.486000	0.97944	2.314000	0.78098	0.484000	0.47621	GGG		0.542	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2		NM_002862	
RAB21	23011	hgsc.bcm.edu;ucsc.edu	37	12	72164429	72164431	+	In_Frame_Del	DEL	AAT	AAT	-			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr12:72164429_72164431delAAT	ENST00000261263.3	+	3	533_535	c.277_279delAAT	c.(277-279)aatdel	p.N93del		NM_014999.2	NP_055814.1	Q9UL25	RAB21_HUMAN	RAB21, member RAS oncogene family	93					GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(1)|lung(4)|prostate(1)	6						CAGAGATTCAAATGGAGCGATTT	0.335																																																	0																																										SO:0001651	inframe_deletion	23011			AF091035	CCDS9003.1	12q21.1	2014-09-04			ENSG00000080371	ENSG00000080371		"""RAB, member RAS oncogene"""	18263	protein-coding gene	gene with protein product		612398				10887961, 11697911, 16754960	Standard	NM_014999		Approved	KIAA0118	uc001swt.3	Q9UL25	OTTHUMG00000169572	ENST00000261263.3:c.277_279delAAT	12.37:g.72164429_72164431delAAT	ENSP00000261263:p.Asn93del		Q14466|Q569H3	In_Frame_Del	DEL	ENST00000261263.3	37	CCDS9003.1																																																																																				0.335	RAB21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404855.1			
RCC2	55920	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	17747210	17747210	+	Splice_Site	SNP	C	C	G			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr1:17747210C>G	ENST00000375436.4	-	7	1046	c.859G>C	c.(859-861)Gga>Cga	p.G287R	RCC2_ENST00000375433.3_Splice_Site_p.G287R	NM_018715.3	NP_061185.1	Q9P258	RCC2_HUMAN	regulator of chromosome condensation 2	287					chromosome passenger complex localization to kinetochore (GO:0072356)|endosome organization (GO:0007032)|focal adhesion assembly (GO:0048041)|integrin-mediated signaling pathway (GO:0007229)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of GTPase activity (GO:0034260)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|regulation of cell migration (GO:0030334)	chromosome, centromeric core domain (GO:0034506)|cytosol (GO:0005829)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|Rac GTPase binding (GO:0048365)	p.G287R(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(7)|lung(4)	17		Colorectal(325;0.000147)|Breast(348;0.00122)|Renal(390;0.00145)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00492)|BRCA - Breast invasive adenocarcinoma(304;7.69e-06)|COAD - Colon adenocarcinoma(227;1.19e-05)|Kidney(64;0.000189)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.0135)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19)		ACTTCCATACCCAGCTGACCA	0.423																																																	1	Substitution - Missense(1)	kidney(1)											64.0	65.0	65.0					1																	17747210		2203	4300	6503	SO:0001630	splice_region_variant	55920				CCDS181.1	1p36.13	2010-05-05			ENSG00000179051	ENSG00000179051			30297	protein-coding gene	gene with protein product		609587				10819331, 12919680	Standard	NM_018715		Approved	TD-60	uc001bal.3	Q9P258	OTTHUMG00000002513	ENST00000375436.4:c.859+1G>C	1.37:g.17747210C>G			Q8IVL9|Q9BSN6|Q9NPV8	Missense_Mutation	SNP	ENST00000375436.4	37	CCDS181.1	.	.	.	.	.	.	.	.	.	.	C	34	5.297057	0.95574	.	.	ENSG00000179051	ENST00000375436;ENST00000375433	D;D	0.98747	-5.11;-5.11	5.45	5.45	0.79879	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.99504	0.9823	H	0.97732	4.065	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98171	1.0452	9	.	.	.	-19.3109	18.2081	0.89861	0.0:1.0:0.0:0.0	.	287	Q9P258	RCC2_HUMAN	R	287	ENSP00000364585:G287R;ENSP00000364582:G287R	.	G	-	1	0	RCC2	17619797	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.717000	0.84732	2.720000	0.93068	0.655000	0.94253	GGA		0.423	RCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007144.1		NM_018715	Missense_Mutation
RDH11	51109	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	68151872	68151872	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr14:68151872T>A	ENST00000381346.4	-	6	824	c.714A>T	c.(712-714)gaA>gaT	p.E238D	RP11-1012A1.4_ENST00000554493.1_5'UTR|RP11-1012A1.4_ENST00000553306.1_Missense_Mutation_p.N69I|RDH11_ENST00000553384.1_Missense_Mutation_p.E225D|RDH11_ENST00000428130.2_Missense_Mutation_p.E168D	NM_001252650.1|NM_016026.3	NP_001239579.1|NP_057110.3	Q8TC12	RDH11_HUMAN	retinol dehydrogenase 11 (all-trans/9-cis/11-cis)	238					adaptation of rhodopsin mediated signaling (GO:0016062)|phototransduction, visible light (GO:0007603)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|photoreceptor inner segment (GO:0001917)	NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)	p.E238D(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(3)|ovary(1)	12				all cancers(60;0.00047)|OV - Ovarian serous cystadenocarcinoma(108;0.00206)|BRCA - Breast invasive adenocarcinoma(234;0.00924)	Vitamin A(DB00162)	GCCGAACCAGTTCAGATTGGA	0.522																																																	1	Substitution - Missense(1)	kidney(1)											94.0	78.0	84.0					14																	68151872		2203	4300	6503	SO:0001583	missense	51109			AF151840	CCDS32104.1, CCDS58326.1	14q24.1	2013-10-15	2006-05-09		ENSG00000072042	ENSG00000072042	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	17964	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 7C, member 1"", ""androgen-regulated short-chain dehydrogenase/reductase 1"""	607849	"""retinol dehydrogenase 11 (all-trans and 9-cis)"""			12226107, 8018917, 19027726	Standard	NM_016026		Approved	MDT1, SDR7C1, ARSDR1	uc001xjv.4	Q8TC12	OTTHUMG00000171196	ENST00000381346.4:c.714A>T	14.37:g.68151872T>A	ENSP00000370750:p.Glu238Asp		A6NDK3|A8K062|B2RB26|B4DDW0|Q0QD40|Q6IAH5|Q9NRW0|Q9Y391	Missense_Mutation	SNP	ENST00000381346.4	37	CCDS32104.1	.	.	.	.	.	.	.	.	.	.	T	17.23	3.336356	0.60963	.	.	ENSG00000072042	ENST00000381346;ENST00000553384;ENST00000428130;ENST00000554035;ENST00000557273;ENST00000557726	D;D;D;D;D;T	0.89415	-2.51;-2.51;-2.51;-2.51;-2.26;1.99	5.07	1.12	0.20585	NAD(P)-binding domain (1);	0.099482	0.64402	D	0.000002	T	0.77054	0.4074	N	0.25890	0.77	0.18873	N	0.999986	B;B;B	0.14805	0.011;0.008;0.004	B;B;B	0.15870	0.012;0.014;0.006	T	0.61855	-0.6977	10	0.33940	T	0.23	.	3.7489	0.08559	0.2361:0.2277:0.0:0.5362	.	168;225;238	B4DDW0;Q8TC12-2;Q8TC12	.;.;RDH11_HUMAN	D	238;225;168;124;151;186	ENSP00000370750:E238D;ENSP00000452079:E225D;ENSP00000416395:E168D;ENSP00000450802:E124D;ENSP00000450651:E151D;ENSP00000450435:E186D	ENSP00000370750:E238D	E	-	3	2	RDH11	67221625	0.274000	0.24191	0.054000	0.19295	0.887000	0.51463	-0.331000	0.07914	0.381000	0.24851	0.482000	0.46254	GAA		0.522	RDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412257.3			
RELL2	285613	hgsc.bcm.edu;ucsc.edu	37	5	141019628	141019628	+	Silent	SNP	G	G	A			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr5:141019628G>A	ENST00000297164.3	+	5	1845	c.645G>A	c.(643-645)ggG>ggA	p.G215G	RELL2_ENST00000518025.1_3'UTR|RELL2_ENST00000518856.1_Silent_p.G149G|FCHSD1_ENST00000523856.1_5'UTR|FCHSD1_ENST00000435817.2_3'UTR|RELL2_ENST00000521367.1_Silent_p.G149G|RELL2_ENST00000444782.1_Silent_p.G215G	NM_173828.4	NP_776189.3	Q8NC24	RELL2_HUMAN	RELT-like 2	215					positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCAAGGCAGGGATGCCTGCCA	0.677																																																	0													27.0	30.0	29.0					5																	141019628		2203	4299	6502	SO:0001819	synonymous_variant	285613			AK054889	CCDS4265.1	5q31.3	2011-10-11	2007-06-15	2007-06-15	ENSG00000164620	ENSG00000164620			26902	protein-coding gene	gene with protein product		611213	"""chromosome 5 open reading frame 16"""	C5orf16		12975309, 16389068	Standard	NM_173828		Approved	FLJ90583	uc003lli.3	Q8NC24	OTTHUMG00000129612	ENST00000297164.3:c.645G>A	5.37:g.141019628G>A			D3DQE2|Q6P4E7|Q6UXY2	Silent	SNP	ENST00000297164.3	37	CCDS4265.1																																																																																				0.677	RELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251807.2		NM_173828	
RFX7	64864	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	56390306	56390306	+	Silent	SNP	A	A	G			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr15:56390306A>G	ENST00000559447.2	-	8	1060	c.789T>C	c.(787-789)gtT>gtC	p.V263V	RFX7_ENST00000317318.6_Silent_p.V360V|RFX7_ENST00000423270.1_Silent_p.V360V|RFX7_ENST00000422057.1_Silent_p.V263V			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	263					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.V360V(1)|p.V263V(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						CAGCTGCCACAACGATACCAA	0.398																																																	2	Substitution - coding silent(2)	kidney(2)											91.0	87.0	88.0					15																	56390306		1864	4094	5958	SO:0001819	synonymous_variant	64864					15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"""regulatory factor X domain containing 2"""	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.789T>C	15.37:g.56390306A>G			Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Silent	SNP	ENST00000559447.2	37																																																																																					0.398	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3		NM_022841	
RP1	6101	hgsc.bcm.edu;ucsc.edu	37	8	55539690	55539695	+	In_Frame_Del	DEL	TACCAG	TACCAG	-			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	TACCAG	TACCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr8:55539690_55539695delTACCAG	ENST00000220676.1	+	4	3396_3401	c.3248_3253delTACCAG	c.(3247-3255)ttaccagtc>ttc	p.1083_1085LPV>F		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1083					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			AAAGACCTCTTACCAGTCCTGATGCT	0.422																																					Colon(91;1014 1389 7634 14542 40420)												0																																										SO:0001651	inframe_deletion	6101			AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.3248_3253delTACCAG	8.37:g.55539690_55539695delTACCAG	ENSP00000220676:p.Leu1083_Val1085delinsPhe			In_Frame_Del	DEL	ENST00000220676.1	37	CCDS6160.1																																																																																				0.422	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2		NM_006269	
RYR3	6263	broad.mit.edu	37	15	34119402	34119402	+	Frame_Shift_Del	DEL	T	T	-			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr15:34119402delT	ENST00000389232.4	+	85	11318	c.11248delT	c.(11248-11250)tttfs	p.F3750fs	RYR3_ENST00000415757.3_Frame_Shift_Del_p.F3745fs	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3750					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GCTCTCAGACTTTCAGAACTT	0.557																																																	0													49.0	53.0	52.0					15																	34119402		1983	3988	5971	SO:0001589	frameshift_variant	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.11248delT	15.37:g.34119402delT	ENSP00000373884:p.Phe3750fs		O15175|Q15412	Frame_Shift_Del	DEL	ENST00000389232.4	37	CCDS45210.1																																																																																				0.557	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			
SETD1A	9739	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	30977377	30977377	+	Silent	SNP	C	C	G			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr16:30977377C>G	ENST00000262519.8	+	8	2861	c.2175C>G	c.(2173-2175)gcC>gcG	p.A725A		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	725					histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.A725A(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						AGGAGGCAGCCTACGGCTTGC	0.677																																																	1	Substitution - coding silent(1)	kidney(1)											38.0	43.0	41.0					16																	30977377		2178	4271	6449	SO:0001819	synonymous_variant	9739			AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.2175C>G	16.37:g.30977377C>G			A6NP62|Q6PIF3|Q8TAJ6	Silent	SNP	ENST00000262519.8	37	CCDS32435.1																																																																																				0.677	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2		NM_014712	
SSX2IP	117178	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	85117618	85117618	+	Silent	SNP	G	G	T			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr1:85117618G>T	ENST00000342203.3	-	12	1715	c.1452C>A	c.(1450-1452)acC>acA	p.T484T	SSX2IP_ENST00000437941.2_Silent_p.T457T|SSX2IP_ENST00000370612.4_Silent_p.T484T|SSX2IP_ENST00000603677.1_Silent_p.T3T|SSX2IP_ENST00000605755.1_Silent_p.T457T	NM_001166293.1|NM_001166294.1|NM_014021.3	NP_001159765.1|NP_001159766.1|NP_054740.3	Q9Y2D8	ADIP_HUMAN	synovial sarcoma, X breakpoint 2 interacting protein	484					cell adhesion (GO:0007155)|centrosome organization (GO:0051297)|regulation of cell motility (GO:2000145)|regulation of Rac protein signal transduction (GO:0035020)	cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|centriolar satellite (GO:0034451)|nucleus (GO:0005634)|protein complex (GO:0043234)		p.T484T(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|urinary_tract(1)	19				all cancers(265;0.0053)|Epithelial(280;0.0214)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		GGTGGTCAAAGGTAGTCATAT	0.328																																																	1	Substitution - coding silent(1)	kidney(1)											137.0	130.0	132.0					1																	85117618		2203	4300	6503	SO:0001819	synonymous_variant	117178				CCDS699.1, CCDS53337.1	1p22.3	2008-02-05			ENSG00000117155	ENSG00000117155			16509	protein-coding gene	gene with protein product		608690					Standard	NM_014021		Approved		uc001dkj.3	Q9Y2D8	OTTHUMG00000009926	ENST00000342203.3:c.1452C>A	1.37:g.85117618G>T			A8K8W0|B4DFE3|D3DT13|J3KR02|Q6P2P8|Q6ULS1|Q7L168|Q9UIX0	Silent	SNP	ENST00000342203.3	37	CCDS699.1																																																																																				0.328	SSX2IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027469.1		NM_014021	
TALDO1	6888	broad.mit.edu	37	11	747520	747520	+	Silent	SNP	C	C	T			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr11:747520C>T	ENST00000319006.3	+	1	192	c.39C>T	c.(37-39)tcC>tcT	p.S13S	TALDO1_ENST00000528097.1_Silent_p.S13S			P37837	TALDO_HUMAN	transaldolase 1	13					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glyceraldehyde-3-phosphate metabolic process (GO:0019682)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|small molecule metabolic process (GO:0044281)|xylulose biosynthetic process (GO:0005999)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	monosaccharide binding (GO:0048029)|sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate glyceronetransferase activity (GO:0004801)	p.S13S(1)		breast(1)|kidney(2)|large_intestine(5)|lung(4)|prostate(2)	14		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)		all cancers(45;4.66e-26)|Epithelial(43;2.97e-25)|OV - Ovarian serous cystadenocarcinoma(40;1.48e-19)|BRCA - Breast invasive adenocarcinoma(625;4.41e-05)|Lung(200;0.0595)|LUSC - Lung squamous cell carcinoma(625;0.0712)		GGATGGAGTCCGCGCTGGACC	0.736																																																	1	Substitution - coding silent(1)	kidney(1)											22.0	20.0	20.0					11																	747520		2193	4289	6482	SO:0001819	synonymous_variant	6888				CCDS7712.1	11p15.5-p15.4	2009-12-02			ENSG00000177156	ENSG00000177156	2.2.1.2		11559	protein-coding gene	gene with protein product		602063				9339383	Standard	NM_006755		Approved		uc001lqz.3	P37837	OTTHUMG00000133318	ENST00000319006.3:c.39C>T	11.37:g.747520C>T			B2R8M2|O00751|Q8WV32|Q8WZ45	Silent	SNP	ENST00000319006.3	37	CCDS7712.1																																																																																				0.736	TALDO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257116.1		NM_006755	
TEKT2	27285	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	36552420	36552420	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr1:36552420A>G	ENST00000207457.3	+	5	731	c.604A>G	c.(604-606)Aag>Gag	p.K202E	ADPRHL2_ENST00000373178.4_5'Flank	NM_014466.2	NP_055281.2	Q9UIF3	TEKT2_HUMAN	tektin 2 (testicular)	202					cell projection organization (GO:0030030)|inner dynein arm assembly (GO:0036159)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)		p.K202E(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|pancreas(1)|skin(2)	13		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CATCTCGCTGAAGGTTGACCC	0.547																																																	1	Substitution - Missense(1)	kidney(1)											158.0	133.0	142.0					1																	36552420		2203	4300	6503	SO:0001583	missense	27285			AB033823	CCDS401.1	1p34.3	2008-02-05			ENSG00000092850	ENSG00000092850			11725	protein-coding gene	gene with protein product		608953				12029069, 11751288	Standard	NM_014466		Approved	TEKTB1	uc001bzr.3	Q9UIF3	OTTHUMG00000007629	ENST00000207457.3:c.604A>G	1.37:g.36552420A>G	ENSP00000207457:p.Lys202Glu		A6NIS6|O60638	Missense_Mutation	SNP	ENST00000207457.3	37	CCDS401.1	.	.	.	.	.	.	.	.	.	.	A	17.94	3.512128	0.64522	.	.	ENSG00000092850	ENST00000207457	T	0.02763	4.17	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.17066	0.0410	M	0.86953	2.85	0.80722	D	1	D	0.69078	0.997	D	0.68483	0.958	T	0.02398	-1.1165	10	0.32370	T	0.25	.	15.8542	0.78965	1.0:0.0:0.0:0.0	.	202	Q9UIF3	TEKT2_HUMAN	E	202	ENSP00000207457:K202E	ENSP00000207457:K202E	K	+	1	0	TEKT2	36325007	1.000000	0.71417	0.998000	0.56505	0.170000	0.22686	9.187000	0.94912	2.144000	0.66660	0.460000	0.39030	AAG		0.547	TEKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020200.1		NM_014466	
THY1	7070	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	119290972	119290972	+	Silent	SNP	C	C	G	rs199847788		TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr11:119290972C>G	ENST00000284240.5	-	3	1201	c.162G>C	c.(160-162)ctG>ctC	p.L54L	USP2-AS1_ENST00000498979.2_RNA|USP2-AS1_ENST00000500970.1_RNA|THY1_ENST00000528522.1_Silent_p.L54L|USP2-AS1_ENST00000578923.1_RNA|USP2-AS1_ENST00000530002.1_RNA|RP11-334E6.12_ENST00000578216.1_RNA|THY1_ENST00000580275.1_Silent_p.L37L|THY1_ENST00000527590.1_5'UTR	NM_006288.3	NP_006279.2	P04216	THY1_HUMAN	Thy-1 cell surface antigen	54	Ig-like V-type.			LT -> AP (in Ref. 5). {ECO:0000305}.	angiogenesis (GO:0001525)|cytoskeleton organization (GO:0007010)|focal adhesion assembly (GO:0048041)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of GTPase activity (GO:0043547)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of T cell activation (GO:0050870)|retinal cone cell development (GO:0046549)|single organismal cell-cell adhesion (GO:0016337)|T cell receptor signaling pathway (GO:0050852)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|integrin binding (GO:0005178)|Rho GTPase activator activity (GO:0005100)	p.L54L(1)		breast(1)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12		Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.83e-05)		TCTCACGGGTCAGGCTGAACT	0.562																																																	1	Substitution - coding silent(1)	kidney(1)											214.0	189.0	197.0					11																	119290972		2199	4295	6494	SO:0001819	synonymous_variant	7070			M11749	CCDS8424.1	11q23.3	2013-01-14				ENSG00000154096		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11801	protein-coding gene	gene with protein product		188230				2864690	Standard	NM_006288		Approved	CD90	uc001pwr.3	P04216		ENST00000284240.5:c.162G>C	11.37:g.119290972C>G			Q16008|Q9NSP1	Silent	SNP	ENST00000284240.5	37	CCDS8424.1	.	.	.	.	.	.	.	.	.	.	C	9.956	1.221554	0.22457	.	.	ENSG00000154096	ENST00000527590	.	.	.	4.98	4.98	0.66077	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.557	11.8965	0.52659	0.0:0.8091:0.1909:0.0	.	.	.	.	S	62	.	.	X	-	2	2	THY1	118796182	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.675000	0.37555	2.302000	0.77476	0.591000	0.81541	TGA		0.562	THY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388370.2		NM_006288	
TMBIM1	64114	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	219140333	219140333	+	Silent	SNP	G	G	A	rs377618088		TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr2:219140333G>A	ENST00000444881.1	-	13	1526	c.801C>T	c.(799-801)taC>taT	p.Y267Y	TMBIM1_ENST00000258412.3_Silent_p.Y267Y|PNKD_ENST00000472650.1_Intron|TMBIM1_ENST00000445635.1_Silent_p.Y93Y|PNKD_ENST00000273077.4_Intron|TMBIM1_ENST00000396809.2_Silent_p.Y267Y			Q969X1	LFG3_HUMAN	transmembrane BAX inhibitor motif containing 1	267					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of Fas signaling pathway (GO:1902045)|negative regulation of metalloenzyme activity (GO:0048553)|positive regulation of blood vessel remodeling (GO:2000504)	endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	death receptor binding (GO:0005123)	p.Y267Y(1)		NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(2)	9		Renal(207;0.0474)		Epithelial(149;8.56e-07)|all cancers(144;0.000154)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCTGTGTGTCGTAAGCCAGGA	0.527																																																	1	Substitution - coding silent(1)	kidney(1)						G	,	0,4406		0,0,2203	159.0	135.0	143.0		,801	-10.6	0.1	2		143	1,8599	1.2+/-3.3	0,1,4299	no	intron,coding-synonymous	PNKD,TMBIM1	NM_015488.4,NM_022152.4	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	,267/312	219140333	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	64114			BN000408	CCDS2412.1	2q35	2010-03-18			ENSG00000135926	ENSG00000135926			23410	protein-coding gene	gene with protein product		610364				12477932	Standard	NM_022152		Approved	PP1201, RECS1, LFG3	uc002vhp.1	Q969X1	OTTHUMG00000133105	ENST00000444881.1:c.801C>T	2.37:g.219140333G>A			B3KQY6|Q8N1R3|Q8TAM3|Q96K13	Silent	SNP	ENST00000444881.1	37	CCDS2412.1																																																																																				0.527	TMBIM1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338559.1		NM_022152	
TMEM59L	25789	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	18724826	18724826	+	Splice_Site	SNP	G	G	C			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr19:18724826G>C	ENST00000600490.1	+	3	501	c.316G>C	c.(316-318)Gcc>Ccc	p.A106P	TMEM59L_ENST00000262817.3_Splice_Site_p.A106P			Q9UK28	TM59L_HUMAN	transmembrane protein 59-like	106						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.A106P(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|skin(2)	13						GTGTGAAGCAGGTGAGGGCCC	0.667																																																	1	Substitution - Missense(1)	kidney(1)											35.0	39.0	38.0					19																	18724826		2203	4300	6503	SO:0001630	splice_region_variant	25789			AF186264	CCDS12383.1	19p12	2008-02-05	2007-03-14	2007-03-14		ENSG00000105696			13237	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 4"""	C19orf4		10527841	Standard	NM_012109		Approved	BSMAP	uc002njy.4	Q9UK28		ENST00000600490.1:c.316+1G>C	19.37:g.18724826G>C				Missense_Mutation	SNP	ENST00000600490.1	37	CCDS12383.1	.	.	.	.	.	.	.	.	.	.	G	32	5.111816	0.94339	.	.	ENSG00000105696	ENST00000262817	T	0.54071	0.59	4.48	4.48	0.54585	.	0.054327	0.64402	D	0.000001	T	0.70491	0.3230	M	0.69358	2.11	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.74870	-0.3517	10	0.72032	D	0.01	-25.4767	15.7214	0.77713	0.0:0.0:1.0:0.0	.	106	Q9UK28	TM59L_HUMAN	P	106	ENSP00000262817:A106P	ENSP00000262817:A106P	A	+	1	0	TMEM59L	18585826	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	4.055000	0.57441	2.020000	0.59435	0.561000	0.74099	GCC		0.667	TMEM59L-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465143.2			Missense_Mutation
TPR	7175	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	186324584	186324584	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr1:186324584T>C	ENST00000367478.4	-	17	2425	c.2129A>G	c.(2128-2130)cAa>cGa	p.Q710R	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	710					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)	p.Q711R(1)|p.Q710R(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TTTGGTATTTTGTGATCGCAA	0.274			T	NTRK1	papillary thyroid																																			Dom	yes		1	1q25	7175	translocated promoter region		E	2	Substitution - Missense(2)	kidney(2)											130.0	120.0	123.0					1																	186324584		1798	4065	5863	SO:0001583	missense	7175			U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.2129A>G	1.37:g.186324584T>C	ENSP00000356448:p.Gln710Arg		Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.018212	0.75275	.	.	ENSG00000047410	ENST00000367478	T	0.17054	2.3	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.22589	0.0545	M	0.63428	1.95	0.58432	D	0.999994	P	0.52842	0.956	B	0.41764	0.366	T	0.02766	-1.1113	10	0.62326	D	0.03	.	15.9669	0.79979	0.0:0.0:0.0:1.0	.	710	P12270	TPR_HUMAN	R	710	ENSP00000356448:Q710R	ENSP00000356448:Q710R	Q	-	2	0	TPR	184591207	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.612000	0.82975	2.236000	0.73375	0.533000	0.62120	CAA		0.274	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2		NM_003292	
CHEK2P2	646096	broad.mit.edu	37	15	20496765	20496765	+	RNA	SNP	G	G	T			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr15:20496765G>T	ENST00000555186.1	+	0	818					NR_038836.1				checkpoint kinase 2 pseudogene 2																		GTTTTTTATAGTGTGTATTTT	0.358																																																	0																																												0					15q11.1	2011-11-11			ENSG00000259156	ENSG00000259156			43578	pseudogene	pseudogene							Standard	NR_038836		Approved		uc001ytf.1		OTTHUMG00000171660		15.37:g.20496765G>T				RNA	SNP	ENST00000555186.1	37																																																																																					0.358	CHEK2P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000414654.1		NR_038836	
USP33	23032	hgsc.bcm.edu;ucsc.edu	37	1	78167136	78167136	+	Frame_Shift_Del	DEL	T	T	-			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr1:78167136delT	ENST00000370793.1	-	23	2866	c.2520delA	c.(2518-2520)aaafs	p.K840fs	USP33_ENST00000370794.3_Frame_Shift_Del_p.K809fs|USP33_ENST00000357428.1_Frame_Shift_Del_p.K840fs	NM_015017.4	NP_055832.3	Q8TEY7	UBP33_HUMAN	ubiquitin specific peptidase 33	840	DUSP 2. {ECO:0000255|PROSITE- ProRule:PRU00613}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|centrosome duplication (GO:0051298)|endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell body (GO:0044297)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|VCB complex (GO:0030891)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	44						GAGAGTCCTCTTTTTGGAACG	0.383																																					Melanoma(152;72 1870 11110 26780 42647)												0													106.0	114.0	111.0					1																	78167136		2203	4300	6503	SO:0001589	frameshift_variant	23032			AF383173	CCDS678.1, CCDS679.1, CCDS680.1	1p31	2008-02-05	2005-08-08		ENSG00000077254	ENSG00000077254		"""Ubiquitin-specific peptidases"""	20059	protein-coding gene	gene with protein product		615146	"""ubiquitin specific protease 33"""			12838346	Standard	NM_015017		Approved	KIAA1097, VDU1	uc001dht.4	Q8TEY7	OTTHUMG00000009651	ENST00000370793.1:c.2520delA	1.37:g.78167136delT	ENSP00000359829:p.Lys840fs		Q8TEY6|Q96AV6|Q9H9F0|Q9UPQ5	Frame_Shift_Del	DEL	ENST00000370793.1	37	CCDS678.1																																																																																				0.383	USP33-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026923.2		NM_015017	
VHL	7428	broad.mit.edu;hgsc.bcm.edu	37	3	10183763	10183763	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina Miseq;PacBio			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr3:10183763A>G	ENST00000256474.2	+	1	1072	c.232A>G	c.(232-234)Aat>Gat	p.N78D	snoU13_ENST00000458986.1_RNA|VHL_ENST00000345392.2_Missense_Mutation_p.N78D	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	78			N -> H (in VHLD; type I). {ECO:0000269|PubMed:8956040}.|N -> S (in VHLD; type I; common mutation; dbSNP:rs5030804). {ECO:0000269|PubMed:8956040}.|N -> T (in VHLD; type I). {ECO:0000269|PubMed:8956040}.		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.N78D(3)|p.F76fs*80(2)|p.F76fs*81(2)|p.N78Y(2)|p.N78H(2)|p.S72_V87>L(1)|p.C77_N78>Y(1)|p.R60fs*35(1)|p.V74fs*51(1)|p.C77fs*53(1)|p.V74fs*77(1)|p.N78fs*54(1)|p.C77_R79del(1)|p.N78fs*53(1)|p.C77*(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)		CATCTTCTGCAATCGCAGTCC	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"""	21	Deletion - Frameshift(8)|Substitution - Missense(7)|Complex - frameshift(2)|Complex - deletion inframe(2)|Deletion - In frame(1)|Insertion - Frameshift(1)	kidney(19)|soft_tissue(2)	GRCh37	CM941365	VHL	M							12.0	15.0	14.0					3																	10183763		2175	4240	6415	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.232A>G	3.37:g.10183763A>G	ENSP00000256474:p.Asn78Asp		B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	A	35	5.555516	0.96514	.	.	ENSG00000134086	ENST00000256474;ENST00000345392	D;D	0.99960	-9.15;-9.15	5.43	5.43	0.79202	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.043720	0.85682	D	0.000000	D	0.99951	0.9979	M	0.84773	2.715	0.42535	D	0.993053	D;D	0.65815	0.994;0.995	D;P	0.63703	0.917;0.866	D	0.94627	0.7818	10	0.87932	D	0	-4.0134	13.5016	0.61459	1.0:0.0:0.0:0.0	.	78;78	P40337-2;P40337	.;VHL_HUMAN	D	78	ENSP00000256474:N78D;ENSP00000344757:N78D	ENSP00000256474:N78D	N	+	1	0	VHL	10158763	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.728000	0.68531	2.069000	0.61940	0.450000	0.29827	AAT		0.721	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
ZC3H7A	29066	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	11873154	11873154	+	Silent	SNP	A	A	G			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr16:11873154A>G	ENST00000396516.2	-	3	371	c.174T>C	c.(172-174)gaT>gaC	p.D58D	ZC3H7A_ENST00000355758.4_Silent_p.D58D|ZC3H7A_ENST00000575170.1_5'UTR			Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	58						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.D58D(1)		breast(2)|endometrium(3)|kidney(5)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(2)	25						AGTTGTTCCAATCATGTTCCC	0.333																																																	1	Substitution - coding silent(1)	kidney(1)											137.0	143.0	141.0					16																	11873154		2196	4300	6496	SO:0001819	synonymous_variant	29066			AF161540	CCDS10550.1	16p13-p12	2013-01-11	2005-06-02	2005-06-08	ENSG00000122299	ENSG00000122299		"""Zinc fingers, CCCH-type domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	30959	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 7"", ""zinc finger CCCH-type containing 7"""	ZC3HDC7, ZC3H7		11042152	Standard	NM_014153		Approved	HSPC055, FLJ20318	uc002dbl.3	Q8IWR0	OTTHUMG00000129825	ENST00000396516.2:c.174T>C	16.37:g.11873154A>G			D3DUG5|Q9NPE9	Silent	SNP	ENST00000396516.2	37	CCDS10550.1																																																																																				0.333	ZC3H7A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437066.1		NM_014153	
ZFAND2B	130617	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	220073738	220073738	+	Silent	SNP	G	G	A			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr2:220073738G>A	ENST00000289528.5	+	8	891	c.696G>A	c.(694-696)ctG>ctA	p.L232L	ZFAND2B_ENST00000409097.1_3'UTR|ZFAND2B_ENST00000409336.1_Silent_p.L232L|ZFAND2B_ENST00000409594.1_3'UTR|ZFAND2B_ENST00000444522.2_3'UTR	NM_001270998.1|NM_001270999.1|NM_138802.2	NP_001257927.1|NP_001257928.1|NP_620157.1	Q8WV99	ZFN2B_HUMAN	zinc finger, AN1-type domain 2B	232						endoplasmic reticulum (GO:0005783)	zinc ion binding (GO:0008270)	p.L232L(1)		endometrium(2)|kidney(4)|lung(4)|upper_aerodigestive_tract(1)	11		Renal(207;0.0915)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CACAAGCACTGTCAGCCAGTG	0.488																																																	1	Substitution - coding silent(1)	kidney(1)											91.0	88.0	89.0					2																	220073738		2203	4300	6503	SO:0001819	synonymous_variant	130617			AK074571	CCDS2435.1, CCDS74656.1	2q35	2010-04-23	2005-08-22		ENSG00000158552	ENSG00000158552		"""Zinc fingers, AN1-type domain containing"""	25206	protein-coding gene	gene with protein product	"""arsenite inducible RNA associated protein-like"""	613474	"""zinc finger, AN1-type 2B"""			18467495	Standard	NM_138802		Approved	AIRAPL	uc002vka.4	Q8WV99	OTTHUMG00000133135	ENST00000289528.5:c.696G>A	2.37:g.220073738G>A			Q8NB98	Silent	SNP	ENST00000289528.5	37	CCDS2435.1																																																																																				0.488	ZFAND2B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256824.2		NM_138802	
ZFYVE19	84936	broad.mit.edu;hgsc.bcm.edu	37	15	41105065	41105065	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr15:41105065G>T	ENST00000355341.4	+	7	1496	c.995G>T	c.(994-996)cGa>cTa	p.R332L	ZFYVE19_ENST00000299173.10_Intron|ZFYVE19_ENST00000564258.1_Missense_Mutation_p.R157L|ZFYVE19_ENST00000570108.1_Missense_Mutation_p.R309L|ZFYVE19_ENST00000336455.5_Missense_Mutation_p.R322L	NM_001077268.1	NP_001070736.1	Q96K21	ANCHR_HUMAN	zinc finger, FYVE domain containing 19	332					abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis checkpoint (GO:0031565)|negative regulation of cytokinesis (GO:0032466)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|midbody (GO:0030496)	phosphatidylinositol-3-phosphate binding (GO:0032266)|zinc ion binding (GO:0008270)	p.R332L(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	9		all_cancers(109;3.31e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.76e-05)|COAD - Colon adenocarcinoma(120;0.151)|BRCA - Breast invasive adenocarcinoma(123;0.164)		CTGGCCAAGCGACTAGCCATG	0.627																																																	1	Substitution - Missense(1)	kidney(1)											54.0	64.0	61.0					15																	41105065		2057	4190	6247	SO:0001583	missense	84936			AK027746	CCDS42025.1, CCDS58353.1, CCDS58354.1, CCDS58355.1	15q14	2008-05-02				ENSG00000166140		"""Zinc fingers, FYVE domain containing"""	20758	protein-coding gene	gene with protein product							Standard	NM_001077268		Approved	FLJ14840	uc031qrk.1	Q96K21		ENST00000355341.4:c.995G>T	15.37:g.41105065G>T	ENSP00000347498:p.Arg332Leu		B3KVB2|C9JNF4|H3BUF9|Q86WC2|Q8WU96	Missense_Mutation	SNP	ENST00000355341.4	37	CCDS42025.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.013066	0.75161	.	.	ENSG00000166140	ENST00000355341;ENST00000336455	T;T	0.25579	1.79;1.79	5.41	4.49	0.54785	.	0.097794	0.64402	D	0.000002	T	0.49966	0.1588	M	0.78456	2.415	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.71656	0.951;0.974	T	0.52983	-0.8502	10	0.62326	D	0.03	-18.7505	13.4047	0.60906	0.0788:0.0:0.9212:0.0	.	322;332	Q96K21-2;Q96K21	.;ZFY19_HUMAN	L	332;322	ENSP00000347498:R332L;ENSP00000337824:R322L	ENSP00000337824:R322L	R	+	2	0	ZFYVE19	38892357	1.000000	0.71417	0.985000	0.45067	0.310000	0.27922	5.327000	0.65881	2.534000	0.85438	0.555000	0.69702	CGA		0.627	ZFYVE19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418996.1		NM_032850	
ZNF607	84775	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	38190552	38190552	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr19:38190552A>T	ENST00000355202.4	-	5	1075	c.480T>A	c.(478-480)caT>caA	p.H160Q	ZNF607_ENST00000395835.3_Missense_Mutation_p.H159Q|CTD-2528L19.4_ENST00000586606.2_Intron	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	160					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H160Q(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			TAATTTTCTGATGCTTTCTAA	0.388																																																	1	Substitution - Missense(1)	kidney(1)											127.0	119.0	122.0					19																	38190552		2203	4300	6503	SO:0001583	missense	84775			AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"""Zinc fingers, C2H2-type"", ""-"""	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.480T>A	19.37:g.38190552A>T	ENSP00000347338:p.His160Gln		F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Missense_Mutation	SNP	ENST00000355202.4	37	CCDS33006.1	.	.	.	.	.	.	.	.	.	.	A	17.20	3.327932	0.60743	.	.	ENSG00000198182	ENST00000355202;ENST00000395835	D;D	0.86865	-2.18;-2.18	2.07	2.07	0.26955	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.93462	0.7914	M	0.90595	3.13	0.24387	N	0.994761	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.84219	0.0460	9	0.62326	D	0.03	.	8.8596	0.35249	1.0:0.0:0.0:0.0	.	160;159	Q96SK3;F5H141	ZN607_HUMAN;.	Q	160;159	ENSP00000347338:H160Q;ENSP00000438015:H159Q	ENSP00000347338:H160Q	H	-	3	2	ZNF607	42882392	0.006000	0.16342	0.024000	0.17045	0.643000	0.38383	0.047000	0.14056	0.942000	0.37525	0.402000	0.26972	CAT		0.388	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2		NM_032689	
ZNF658	26149	broad.mit.edu	37	9	40772750	40772750	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4999-01A-01D-1462-08	TCGA-BP-4999-11A-01D-1462-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86ffb814-7c65-426b-b7b5-7250322c4d01	5f731fb4-2c74-4c8b-b498-7e5d036658a8	g.chr9:40772750C>T	ENST00000602553.1	-	5	2819	c.2525G>A	c.(2524-2526)tGt>tAt	p.C842Y	ZNF658_ENST00000441795.1_Intron|ZNF658_ENST00000377626.3_Missense_Mutation_p.C842Y			Q5TYW1	ZN658_HUMAN	zinc finger protein 658	842					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C842Y(1)		breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	46				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		CTGATGTGCACAGAGGTGTGT	0.428																																																	1	Substitution - Missense(1)	kidney(1)											21.0	20.0	20.0					9																	40772750		2200	4277	6477	SO:0001583	missense	26149			AA482262	CCDS75846.1	9p13.1	2013-01-08			ENSG00000196409	ENSG00000274349		"""Zinc fingers, C2H2-type"", ""-"""	25226	protein-coding gene	gene with protein product							Standard	NM_033160		Approved	MGC35232, DKFZp572C163, FLJ32813	uc004abs.2	Q5TYW1	OTTHUMG00000013392	ENST00000602553.1:c.2525G>A	9.37:g.40772750C>T	ENSP00000473484:p.Cys842Tyr		Q6PIP3|Q96M55|Q9H9S6|Q9UG02	Missense_Mutation	SNP	ENST00000602553.1	37	CCDS35023.1	.	.	.	.	.	.	.	.	.	.	c	7.958	0.746301	0.15710	.	.	ENSG00000196409	ENST00000377626	T	0.00986	5.47	1.97	-1.51	0.08664	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00412	0.0013	N	0.03050	-0.425	0.09310	N	1	P	0.36171	0.541	B	0.35688	0.208	T	0.35425	-0.9789	9	0.10111	T	0.7	.	0.9006	0.01273	0.3981:0.2619:0.1969:0.1431	.	842	Q5TYW1	ZN658_HUMAN	Y	842	ENSP00000366853:C842Y	ENSP00000366853:C842Y	C	-	2	0	ZNF658	40762750	0.000000	0.05858	0.001000	0.08648	0.990000	0.78478	-1.369000	0.02578	-0.364000	0.08088	0.518000	0.50308	TGT		0.428	ZNF658-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467800.1		NM_033160	
