#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_AAChange	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_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	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_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_NTotCov_SOL	i_NVarCov_SOL	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_TTotCov_SOL	i_TVarCov_SOL	i_Transcript_Id	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_dbSNPPopFreq	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_refseq_mrna_id	i_secondary_variant_classification
SETD2	29072	hgsc.bcm.edu	37	3	47125234	47125235	+	Frame_Shift_Ins	INS	-	-	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr3:47125234_47125235insA	ENST00000409792.3	-	12	6077_6078	c.6035_6036insT	c.(6034-6036)ctcfs	p.L2012fs	SETD2_ENST00000492397.1_5'UTR	NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2012					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.L2012R(1)|p.L1509R(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		AACTGTCCAGGAGTTTGGTGGC	0.411			"""N, F, S, Mis"""		clear cell renal carcinoma																																p.L2012fs		.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.6036_6037insT						.																																			SO:0001589	frameshift_variant	29072	exon12			GTCCAGGAGTTTG	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.6036dupT	3.37:g.47125235_47125235dupA	ENSP00000386759:p.Leu2012fs	Somatic	106	0		WXS	Illumina HiSeq	.	55	29	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Ins	INS	ENST00000409792.3	37	CCDS2749.2																																																																																			.		0.411	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
SLC30A1	7779	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	211749440	211749445	+	In_Frame_Del	DEL	AAAAGT	AAAAGT	-			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	AAAAGT	AAAAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr1:211749440_211749445delAAAAGT	ENST00000367001.4	-	2	938_943	c.809_814delACTTTT	c.(808-816)tacttttct>tct	p.YF270del		NM_021194.2	NP_067017.2	Q9Y6M5	ZNT1_HUMAN	solute carrier family 30 (zinc transporter), member 1	270					cadmium ion transmembrane transport (GO:0070574)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|cellular zinc ion homeostasis (GO:0006882)|detoxification of cadmium ion (GO:0071585)|in utero embryonic development (GO:0001701)|negative regulation of calcium ion import (GO:0090281)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of zinc ion transmembrane import (GO:0071584)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	calcium channel inhibitor activity (GO:0019855)|zinc ion transmembrane transporter activity (GO:0005385)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(3)|prostate(1)	11				OV - Ovarian serous cystadenocarcinoma(81;0.00535)|GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.0604)|Epithelial(68;0.0978)		CCTTTCCAAGAAAAGTAAAAGACTAA	0.403																																					p.270_272del		.											SLC30A1,NS,carcinoma,0,1	SLC30A1	0	0			c.810_815del						.																																			SO:0001651	inframe_deletion	7779	exon2			TCCAAGAAAAGTA	AF323590	CCDS1499.1	1q32.3	2013-05-22			ENSG00000170385	ENSG00000170385		"""Solute carriers"""	11012	protein-coding gene	gene with protein product		609521		ZNT1			Standard	NM_021194		Approved	ZRC1	uc001hio.1	Q9Y6M5	OTTHUMG00000036995	ENST00000367001.4:c.809_814delACTTTT	1.37:g.211749440_211749445delAAAAGT	ENSP00000355968:p.Tyr270_Phe271del	Somatic	62	0		WXS	Illumina HiSeq	.	74	26	NM_021194	Q0VAK9|Q9BZF6	In_Frame_Del	DEL	ENST00000367001.4	37	CCDS1499.1																																																																																			.		0.403	SLC30A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104738.2		
ZNF407	55628	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	18	72776395	72776396	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr18:72776395_72776396delAG	ENST00000299687.5	+	8	6718_6719	c.6718_6719delAG	c.(6718-6720)agafs	p.R2240fs		NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	2240					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		TCAGAGCCAAAGAGAAAGCAGC	0.649																																					p.2239_2240del		.											.	.	.	0			c.6717_6718del						.																																			SO:0001589	frameshift_variant	55628	exon8			AGCCAAAGAGAAA	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.6718_6719delAG	18.37:g.72776397_72776398delAG	ENSP00000299687:p.Arg2240fs	Somatic	66	0		WXS	Illumina HiSeq	.	53	15	NM_017757	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Frame_Shift_Del	DEL	ENST00000299687.5	37	CCDS45885.1																																																																																			.		0.649	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
SLC25A33	84275	hgsc.bcm.edu	37	1	9640237	9640238	+	Frame_Shift_Ins	INS	-	-	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr1:9640237_9640238insA	ENST00000302692.6	+	6	918_919	c.708_709insA	c.(709-711)atgfs	p.M237fs		NM_032315.2	NP_115691.1	Q9BSK2	S2533_HUMAN	solute carrier family 25 (pyrimidine nucleotide carrier), member 33	237					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|kidney(1)|lung(4)|prostate(1)|skin(1)	9	all_lung(157;0.246)	all_epithelial(116;1.16e-18)|all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Breast(348;0.00191)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.44e-05)|Kidney(185;0.000262)|KIRC - Kidney renal clear cell carcinoma(229;0.000957)|BRCA - Breast invasive adenocarcinoma(304;0.0019)|STAD - Stomach adenocarcinoma(132;0.00355)|READ - Rectum adenocarcinoma(331;0.0419)		TTTTTGGACTTATGGCAGCTGC	0.416																																					p.L236fs		.											.	.	.	0			c.708_709insA						.																																			SO:0001589	frameshift_variant	84275	exon6			TGGACTTATGGCA	AF495714	CCDS103.1	1p36.22	2013-05-22	2012-03-29		ENSG00000171612	ENSG00000171612		"""Solute carriers"""	29681	protein-coding gene	gene with protein product		610816	"""solute carrier family 25, member 33"""			14715278, 16949250	Standard	XM_005263503		Approved	MGC4399, BMSC-MCP, PNC1	uc001apw.3	Q9BSK2	OTTHUMG00000001322	ENST00000302692.6:c.709dupA	1.37:g.9640238_9640238dupA	ENSP00000306328:p.Met237fs	Somatic	68	0		WXS	Illumina HiSeq	.	45	23	NM_032315		Frame_Shift_Ins	INS	ENST00000302692.6	37	CCDS103.1																																																																																			.		0.416	SLC25A33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003851.2	NM_032315	
BAP1	8314	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	3	52437221	52437221	+	Frame_Shift_Del	DEL	T	T	-			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr3:52437221delT	ENST00000460680.1	-	14	2294	c.1823delA	c.(1822-1824)gacfs	p.D608fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.D590fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CTCTCTGCTGTCCGTGGCTTC	0.597			"""N, Mis, F, S, O"""		"""uveal melanoma, breast, NSCLC, RCC"""	"""mesothelioma, uveal melanoma"""																															p.D608fs	GBM(101;493 1458 7992 21037 25532)	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	.	.	0			c.1824delC						.						117.0	110.0	113.0					3																	52437221		2203	4300	6503	SO:0001589	frameshift_variant	8314	exon14			CTGCTGTCCGTGG	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1823delA	3.37:g.52437221delT	ENSP00000417132:p.Asp608fs	Somatic	33	0		WXS	Illumina HiSeq	.	22	15	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Del	DEL	ENST00000460680.1	37	CCDS2853.1																																																																																			.		0.597	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1		
TYK2	7297	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	10468512	10468519	+	Frame_Shift_Del	DEL	CCACTTGT	CCACTTGT	-			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	CCACTTGT	CCACTTGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:10468512_10468519delCCACTTGT	ENST00000525621.1	-	17	2868_2875	c.2387_2394delACAAGTGG	c.(2386-2394)gacaagtggfs	p.DKW796fs	TYK2_ENST00000529370.1_Frame_Shift_Del_p.DKW796fs|TYK2_ENST00000264818.6_Frame_Shift_Del_p.DKW796fs|TYK2_ENST00000524462.1_Frame_Shift_Del_p.DKW611fs	NM_003331.4	NP_003322.3	P29597	TYK2_HUMAN	tyrosine kinase 2	796	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(11)|kidney(6)|large_intestine(3)|lung(19)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			CGCCAAACCCCCACTTGTCCATGGCGGT	0.654																																					p.796_799del		.											.	.	.	0			c.2388_2395del						.																																			SO:0001589	frameshift_variant	7297	exon17			AAACCCCCACTTG		CCDS12236.1	19p13.2	2014-09-17			ENSG00000105397	ENSG00000105397	2.7.10.1		12440	protein-coding gene	gene with protein product		176941				2156206	Standard	NM_003331		Approved	JTK1	uc002moc.4	P29597	OTTHUMG00000166373	ENST00000525621.1:c.2387_2394delACAAGTGG	19.37:g.10468512_10468519delCCACTTGT	ENSP00000431885:p.Asp796fs	Somatic	100	0		WXS	Illumina HiSeq	.	86	12	NM_003331	Q6QB10|Q96CH0	Frame_Shift_Del	DEL	ENST00000525621.1	37	CCDS12236.1																																																																																			.		0.654	TYK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389443.1		
RNPC3	55599	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	104077437	104077437	+	Missense_Mutation	SNP	T	T	G			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr1:104077437T>G	ENST00000533099.1	+	5	637	c.401T>G	c.(400-402)cTt>cGt	p.L134R	RNPC3_ENST00000524631.1_Missense_Mutation_p.L134R|RNPC3_ENST00000423855.2_Missense_Mutation_p.L134R			Q96LT9	RBM40_HUMAN	RNA-binding region (RNP1, RRM) containing 3	134	Necessary for interaction with PDCD7.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Lung(183;0.111)|Epithelial(280;0.122)|all cancers(265;0.125)|Colorectal(144;0.163)		AAAAAAGAACTTGGTTATTTA	0.343																																					p.L134R		.											.	.	.	0			c.T401G						.						152.0	145.0	147.0					1																	104077437		692	1589	2281	SO:0001583	missense	55599	exon4			AAGAACTTGGTTA	AB058742, AY099329	CCDS781.1	1p21.1	2013-07-16			ENSG00000185946	ENSG00000185946		"""RNA binding motif (RRM) containing"""	18666	protein-coding gene	gene with protein product	"""U11/U12 snRNP 65K"""					14974681, 15146077	Standard	NM_017619		Approved	KIAA1839, FLJ20008, RBM40, SNRNP65	uc010oun.2	Q96LT9	OTTHUMG00000166613	ENST00000533099.1:c.401T>G	1.37:g.104077437T>G	ENSP00000432886:p.Leu134Arg	Somatic	40	0		WXS	Illumina HiSeq	.	50	25	NM_017619	A8K1C9|D3DT74|Q5TZ87|Q96FK7|Q96JI8|Q9NSU7|Q9NXX2	Missense_Mutation	SNP	ENST00000533099.1	37	CCDS781.1	.	.	.	.	.	.	.	.	.	.	T	5.391	0.257269	0.10239	.	.	ENSG00000185946	ENST00000524631;ENST00000531883;ENST00000533099;ENST00000423855	T;T;T;T	0.22743	2.3;1.94;2.31;2.31	5.73	1.7	0.24286	.	.	.	.	.	T	0.02267	0.0070	N	0.14661	0.345	0.09310	N	1	B;B	0.23735	0.09;0.09	B;B	0.19148	0.024;0.024	T	0.44034	-0.9354	9	0.15499	T	0.54	.	0.2118	0.00157	0.3092:0.2592:0.1597:0.2719	.	134;134	A8K1C9;Q96LT9	.;RBM40_HUMAN	R	134	ENSP00000437278:L134R;ENSP00000431344:L134R;ENSP00000432886:L134R;ENSP00000391432:L134R	ENSP00000391432:L134R	L	+	2	0	RNPC3	.	0.006000	0.16342	0.729000	0.30791	0.887000	0.51463	0.330000	0.19715	0.517000	0.28361	0.524000	0.50904	CTT	.		0.343	RNPC3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390812.1	NM_017619	
ABCC12	94160	hgsc.bcm.edu	37	16	48138174	48138174	+	Missense_Mutation	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr16:48138174C>T	ENST00000311303.3	-	20	3124	c.2779G>A	c.(2779-2781)Gca>Aca	p.A927T	ABCC12_ENST00000448542.1_Intron|ABCC12_ENST00000416054.1_3'UTR	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	927	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.A927T(1)		NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				AAGTTCTCTGCGTGAAACGGC	0.488																																					p.A927T		.											ABCC12,rectum,carcinoma,0,1	ABCC12	0	1	Substitution - Missense(1)	large_intestine(1)	c.G2779A						.						170.0	160.0	164.0					16																	48138174		2201	4300	6501	SO:0001583	missense	94160	exon20			TCTCTGCGTGAAA	AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"""ATP binding cassette transporters / subfamily C"""	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.2779G>A	16.37:g.48138174C>T	ENSP00000311030:p.Ala927Thr	Somatic	36	0		WXS	Illumina HiSeq	.	29	2	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.050415	0.55218	.	.	ENSG00000140798	ENST00000311303;ENST00000449939	D	0.89681	-2.55	5.55	3.61	0.41365	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.308605	0.37857	N	0.001905	T	0.80639	0.4661	L	0.31526	0.94	0.80722	D	1	B	0.31989	0.35	B	0.34180	0.177	T	0.73742	-0.3887	10	0.18710	T	0.47	.	8.941	0.35729	0.0:0.8273:0.0:0.1727	.	927	Q96J65	MRP9_HUMAN	T	927;845	ENSP00000311030:A927T	ENSP00000311030:A927T	A	-	1	0	ABCC12	46695675	0.939000	0.31865	0.327000	0.25402	0.960000	0.62799	1.982000	0.40638	1.336000	0.45506	0.655000	0.94253	GCA	.		0.488	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	
NPSR1	387129	hgsc.bcm.edu	37	7	34797615	34797615	+	Intron	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr7:34797615C>T	ENST00000360581.1	+	3	408				NPSR1_ENST00000359791.1_Intron|NPSR1-AS1_ENST00000419766.1_RNA|NPSR1_ENST00000381542.1_Intron|NPSR1_ENST00000531252.1_Intron|NPSR1_ENST00000381553.3_Intron|NPSR1_ENST00000381539.3_Intron	NM_207172.1	NP_997055.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1							cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	agcattcatcctctggaatga	0.453																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	404744	.			TTCATCCTCTGGA	AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"""GPCR / Class A : Neuropeptide receptors : S"""	23631	protein-coding gene	gene with protein product		608595	"""G protein-coupled receptor 154"""	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000360581.1:c.281-20459C>T	7.37:g.34797615C>T		Somatic	60	0		WXS	Illumina HiSeq	.	74	4	.	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	RNA	SNP	ENST00000360581.1	37	CCDS5444.1																																																																																			.		0.453	NPSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216837.1	NM_207173	
OR6B1	135946	hgsc.bcm.edu;bcgsc.ca	37	7	143701151	143701151	+	Missense_Mutation	SNP	T	T	C			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr7:143701151T>C	ENST00000408922.2	+	1	130	c.62T>C	c.(61-63)tTg>tCg	p.L21S		NM_001005281.1	NP_001005281.1	O95007	OR6B1_HUMAN	olfactory receptor, family 6, subfamily B, member 1	21						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(3)|large_intestine(3)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	27	Melanoma(164;0.0783)					CCTGGGAGCTTGAGTATGCGG	0.493																																					p.L21S		.											.	.	.	0			c.T62C						.						110.0	102.0	104.0					7																	143701151		1959	4169	6128	SO:0001583	missense	135946	exon1			GGAGCTTGAGTAT		CCDS43667.1	7q33-q35	2012-08-09			ENSG00000221813	ENSG00000221813		"""GPCR / Class A : Olfactory receptors"""	8354	protein-coding gene	gene with protein product							Standard	NM_001005281		Approved	OR7-3	uc003wdt.1	O95007	OTTHUMG00000157765	ENST00000408922.2:c.62T>C	7.37:g.143701151T>C	ENSP00000386151:p.Leu21Ser	Somatic	63	0		WXS	Illumina HiSeq	.	54	4	NM_001005281	A4D2G2|B9EH47|Q6IFP6|Q96R38	Missense_Mutation	SNP	ENST00000408922.2	37	CCDS43667.1	.	.	.	.	.	.	.	.	.	.	T	0.770	-0.766213	0.02974	.	.	ENSG00000221813	ENST00000408922	T	0.00441	7.41	5.37	0.656	0.17844	.	1.364740	0.06269	U	0.695290	T	0.00210	0.0006	N	0.12961	0.28	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.34004	-0.9846	10	0.23891	T	0.37	.	1.646	0.02762	0.1116:0.2557:0.211:0.4216	.	21	O95007	OR6B1_HUMAN	S	21	ENSP00000386151:L21S	ENSP00000386151:L21S	L	+	2	0	OR6B1	143332084	0.000000	0.05858	0.000000	0.03702	0.290000	0.27261	-0.601000	0.05687	0.561000	0.29186	0.455000	0.32223	TTG	.		0.493	OR6B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349566.1		
HTT	3064	hgsc.bcm.edu	37	4	3076696	3076696	+	Silent	SNP	T	T	G			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr4:3076696T>G	ENST00000355072.5	+	1	289	c.144T>G	c.(142-144)ccT>ccG	p.P48P	HTT-AS_ENST00000503893.1_RNA	NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	48	Poly-Pro.				anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		cgccgccgcctcctcagcttc	0.771																																					p.P48P		.											.	.	.	0			c.T144G						.																																			SO:0001819	synonymous_variant	3064	exon1			GCCGCCTCCTCAG	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.144T>G	4.37:g.3076696T>G		Somatic	6	0		WXS	Illumina HiSeq	.	14	6	NM_002111	Q9UQB7	Silent	SNP	ENST00000355072.5	37	CCDS43206.1																																																																																			.		0.771	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
SMURF1	57154	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	98636132	98636132	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr7:98636132G>T	ENST00000361125.1	-	15	1964	c.1645C>A	c.(1645-1647)Cct>Act	p.P549T	AC004893.11_ENST00000360902.1_RNA|AC004893.11_ENST00000468960.2_RNA|SMURF1_ENST00000361368.2_Missense_Mutation_p.P523T	NM_020429.2	NP_065162.1	Q9HCE7	SMUF1_HUMAN	SMAD specific E3 ubiquitin protein ligase 1	549	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of ossification (GO:0030279)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein export from nucleus (GO:0006611)|protein localization to cell surface (GO:0034394)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activin binding (GO:0048185)|I-SMAD binding (GO:0070411)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|urinary_tract(1)	25	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			TCCAGTACAGGCGTGATGTCG	0.517																																					p.P549T		.											.	.	.	0			c.C1645A						.						129.0	102.0	112.0					7																	98636132		2203	4300	6503	SO:0001583	missense	57154	exon15			GTACAGGCGTGAT	AB046845	CCDS34689.1, CCDS34690.1	7q21.1-q31.1	2004-07-29			ENSG00000198742	ENSG00000198742			16807	protein-coding gene	gene with protein product		605568				10458166	Standard	NM_020429		Approved	KIAA1625	uc003upu.2	Q9HCE7	OTTHUMG00000150272	ENST00000361125.1:c.1645C>A	7.37:g.98636132G>T	ENSP00000354621:p.Pro549Thr	Somatic	37	0		WXS	Illumina HiSeq	.	42	4	NM_020429	A4D279|B7ZMB6|B9EGV3|O75853|Q547Q3|Q9UJT8	Missense_Mutation	SNP	ENST00000361125.1	37	CCDS34690.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.920925	0.33908	.	.	ENSG00000198742	ENST00000361368;ENST00000361125	T;T	0.56444	0.46;0.46	5.5	4.62	0.57501	HECT (4);	0.057146	0.64402	D	0.000001	T	0.39886	0.1095	N	0.20530	0.585	0.37954	D	0.932743	B;B;B	0.21225	0.053;0.04;0.04	B;B;B	0.29440	0.038;0.102;0.063	T	0.43393	-0.9394	10	0.66056	D	0.02	.	10.7787	0.46365	0.1452:0.0:0.8548:0.0	.	523;549;523	Q9HCE7-2;Q9HCE7;B9EGV3	.;SMUF1_HUMAN;.	T	523;549	ENSP00000355326:P523T;ENSP00000354621:P549T	ENSP00000354621:P549T	P	-	1	0	SMURF1	98474068	1.000000	0.71417	0.792000	0.32020	0.484000	0.33280	4.054000	0.57434	1.471000	0.48121	0.563000	0.77884	CCT	.		0.517	SMURF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335001.2	NM_020429	
OTOP1	133060	hgsc.bcm.edu	37	4	4204211	4204211	+	Missense_Mutation	SNP	G	G	A	rs200612216		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr4:4204211G>A	ENST00000296358.4	-	4	718	c.694C>T	c.(694-696)Cgg>Tgg	p.R232W		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	232					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)		p.R232W(2)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GTGATGAGCCGTTCCTTGTGC	0.507																																					p.R232W		.											OTOP1,NS,carcinoma,0,3	OTOP1	0	2	Substitution - Missense(2)	prostate(1)|liver(1)	c.C694T						.						144.0	123.0	130.0					4																	4204211		2203	4300	6503	SO:0001583	missense	133060	exon4			TGAGCCGTTCCTT	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.694C>T	4.37:g.4204211G>A	ENSP00000296358:p.Arg232Trp	Somatic	39	0		WXS	Illumina HiSeq	.	50	2	NM_177998	A1L476	Missense_Mutation	SNP	ENST00000296358.4	37	CCDS3372.1	.	.	.	.	.	.	.	.	.	.	G	11.92	1.781817	0.31502	.	.	ENSG00000163982	ENST00000296358	T	0.09817	2.94	5.28	4.35	0.52113	.	0.000000	0.85682	D	0.000000	T	0.06690	0.0171	N	0.14661	0.345	0.80722	D	1	P	0.35328	0.495	B	0.32583	0.148	T	0.26224	-1.0109	10	0.72032	D	0.01	.	10.6877	0.45852	0.0:0.0:0.5681:0.4319	.	232	Q7RTM1	OTOP1_HUMAN	W	232	ENSP00000296358:R232W	ENSP00000296358:R232W	R	-	1	2	OTOP1	4255112	1.000000	0.71417	0.547000	0.28179	0.267000	0.26476	2.487000	0.45268	2.462000	0.83206	0.603000	0.83216	CGG	.		0.507	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998	
PPM1H	57460	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	12	63042370	63042370	+	Silent	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr12:63042370G>A	ENST00000228705.6	-	10	1744	c.1444C>T	c.(1444-1446)Ctg>Ttg	p.L482L	PPM1H_ENST00000551214.1_5'UTR|snoU13_ENST00000459527.1_RNA	NM_020700.1	NP_065751.1	Q9ULR3	PPM1H_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1H	482	PP2C-like.						phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)	18			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)		CTGTCCTTCAGCACACCCCGG	0.512																																					p.L482L		.											.	.	.	0			c.C1444T						.						62.0	66.0	65.0					12																	63042370		2088	4234	6322	SO:0001819	synonymous_variant	57460	exon10			CCTTCAGCACACC	AB032983	CCDS44934.1	12q14.1	2012-04-17	2010-03-05	2004-03-26	ENSG00000111110	ENSG00000111110	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	18583	protein-coding gene	gene with protein product	"""neurite extension-related protein phosphatase related to PP2C"""		"""ras homolog gene family, member C like 1"", ""protein phosphatase 1H (PP2C domain containing)"""	ARHCL1			Standard	NM_020700		Approved	KIAA1157, FLJ13253, NERPP-2C	uc001srk.3	Q9ULR3	OTTHUMG00000169990	ENST00000228705.6:c.1444C>T	12.37:g.63042370G>A		Somatic	35	0		WXS	Illumina HiSeq	.	58	4	NM_020700	B1Q2A9|B2RXG4|Q6PI86	Silent	SNP	ENST00000228705.6	37	CCDS44934.1																																																																																			.		0.512	PPM1H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406760.2	NM_020700	
KIAA1109	84162	hgsc.bcm.edu	37	4	123107280	123107280	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr4:123107280G>T	ENST00000264501.4	+	7	821	c.448G>T	c.(448-450)Gag>Tag	p.E150*	KIAA1109_ENST00000388738.3_Nonsense_Mutation_p.E150*|KIAA1109_ENST00000455637.1_Nonsense_Mutation_p.E150*			Q2LD37	K1109_HUMAN	KIAA1109	150					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.E150*(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						ACGCCTTCAAGAGTTGTTTGG	0.383																																					p.E150X		.											KIAA1109,NS,carcinoma,0,1	KIAA1109	0	1	Substitution - Nonsense(1)	lung(1)	c.G448T						.						108.0	105.0	106.0					4																	123107280		1817	4083	5900	SO:0001587	stop_gained	84162	exon5			CTTCAAGAGTTGT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.448G>T	4.37:g.123107280G>T	ENSP00000264501:p.Glu150*	Somatic	146	0		WXS	Illumina HiSeq	.	67	2	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Nonsense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	G	38	6.831629	0.97869	.	.	ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637	.	.	.	4.94	4.94	0.65067	.	0.125066	0.29692	U	0.011450	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	18.1682	0.89736	0.0:0.0:1.0:0.0	.	.	.	.	X	150	.	ENSP00000264501:E150X	E	+	1	0	KIAA1109	123326730	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	9.605000	0.98321	2.281000	0.76405	0.467000	0.42956	GAG	.		0.383	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
MATK	4145	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	3778217	3778217	+	Silent	SNP	G	G	A	rs373868622		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:3778217G>A	ENST00000310132.6	-	14	1886	c.1488C>T	c.(1486-1488)gcC>gcT	p.A496A	MATK_ENST00000585778.1_Silent_p.A495A|MATK_ENST00000395040.2_Silent_p.A455A|MATK_ENST00000395045.2_Silent_p.A497A	NM_139355.2	NP_647612.1	P42679	MATK_HUMAN	megakaryocyte-associated tyrosine kinase	496			A -> T (in dbSNP:rs35351680). {ECO:0000269|PubMed:17344846}.	ARRPPFRKLAEKLARELRSAGAPASVSGQDADGSTSPRSQE P -> PAGHPSANWPRSWPGSYAVQVPQPPSQGRTPTVHLA PKPGALTPPGGPWPQRTERVESAAWGH (in Ref. 1; AAA16703). {ECO:0000305}.	cell proliferation (GO:0008283)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	26		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGAGCCGTCGGCGTCCTGCC	0.736													g|||	1	0.000199681	0.0008	0.0	5008	,	,		13245	0.0		0.0	False		,,,				2504	0.0				p.A497A		.											.	.	.	0			c.C1491T						.	A	,,	2,4346		0,2,2172	10.0	11.0	11.0		1491,1365,1488	-5.1	0.0	19		11	4,8488		0,4,4242	no	coding-synonymous,coding-synonymous,coding-synonymous	MATK	NM_002378.3,NM_139354.2,NM_139355.2	,,	0,6,6414	AA,AG,GG		0.0471,0.046,0.0467	,,	497/509,455/467,496/508	3778217	6,12834	2174	4246	6420	SO:0001819	synonymous_variant	4145	exon14			GCCGTCGGCGTCC	L18974	CCDS12113.1, CCDS12114.1, CCDS42468.1	19p13.3	2013-02-14						"""SH2 domain containing"""	6906	protein-coding gene	gene with protein product	"""Csk-homologous kinase"", ""tyrosine-protein kinase CTK"", ""protein kinase HYL"", ""hematopoietic consensus tyrosine-lacking kinase"", ""tyrosylprotein kinase"", ""hydroxyaryl-protein kinase"", ""Csk-type protein tyrosine kinase"", ""HYL tyrosine kinase"", ""tyrosine kinase MATK"", ""leukocyte carboxyl-terminal src kinase related"""	600038				8288563, 7530249	Standard	NM_139355		Approved	HYLTK, CTK, HYL, Lsk, CHK, HHYLTK, DKFZp434N1212, MGC1708, MGC2101	uc002lyt.3	P42679		ENST00000310132.6:c.1488C>T	19.37:g.3778217G>A		Somatic	27	0		WXS	Illumina HiSeq	.	32	14	NM_002378	B3KNZ9|Q9NST8	Silent	SNP	ENST00000310132.6	37	CCDS12114.1																																																																																			.		0.736	MATK-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453639.1	NM_139355	
KIF3A	11127	hgsc.bcm.edu	37	5	132070088	132070088	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr5:132070088G>T	ENST00000378746.4	-	2	307	c.89C>A	c.(88-90)tCa>tAa	p.S30*	KIF3A_ENST00000378735.1_Nonsense_Mutation_p.S30*|KIF3A_ENST00000403231.1_Nonsense_Mutation_p.S30*	NM_007054.5	NP_008985.3	Q9Y496	KIF3A_HUMAN	kinesin family member 3A	30	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterior/posterior pattern specification (GO:0009952)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|organelle organization (GO:0006996)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of receptor-mediated endocytosis (GO:0048260)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|neuron projection (GO:0043005)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|spectrin binding (GO:0030507)			endometrium(1)|kidney(4)|large_intestine(8)|lung(3)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	25		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GTAGCACATTGATTTCTCTCT	0.408																																					p.S30X		.											.	.	.	0			c.C89A						.						205.0	201.0	203.0					5																	132070088		2203	4300	6503	SO:0001587	stop_gained	11127	exon2			CACATTGATTTCT	AF041853	CCDS34235.1, CCDS75295.1, CCDS75296.1	5q31	2012-08-01			ENSG00000131437	ENSG00000131437		"""Kinesins"""	6319	protein-coding gene	gene with protein product	"""kinesin family protein 3A"""	604683				1054846	Standard	XM_005271868		Approved	FLA10, KLP-20	uc003kxo.3	Q9Y496	OTTHUMG00000059725	ENST00000378746.4:c.89C>A	5.37:g.132070088G>T	ENSP00000368020:p.Ser30*	Somatic	75	0		WXS	Illumina HiSeq	.	81	3	NM_007054	A8MSW9|Q59EN1|Q86XE9|Q9Y6V4	Nonsense_Mutation	SNP	ENST00000378746.4	37	CCDS34235.1	.	.	.	.	.	.	.	.	.	.	G	34	5.369474	0.95900	.	.	ENSG00000131437	ENST00000378746;ENST00000378735;ENST00000541316;ENST00000403231;ENST00000428744	.	.	.	5.72	5.72	0.89469	.	0.322570	0.36740	N	0.002421	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	.	19.8691	0.96843	0.0:0.0:1.0:0.0	.	.	.	.	X	30;30;30;30;29	.	ENSP00000368009:S30X	S	-	2	0	KIF3A	132097987	0.938000	0.31826	0.674000	0.29902	0.955000	0.61496	3.466000	0.53071	2.706000	0.92434	0.313000	0.20887	TCA	.		0.408	KIF3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132788.3	NM_007054	
TTC17	55761	hgsc.bcm.edu	37	11	43465625	43465625	+	Missense_Mutation	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr11:43465625G>A	ENST00000039989.4	+	18	2545	c.2531G>A	c.(2530-2532)cGt>cAt	p.R844H	TTC17_ENST00000299240.6_Missense_Mutation_p.R901H|TTC17_ENST00000526774.1_3'UTR	NM_018259.5	NP_060729.2	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	844					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(27)|ovary(5)|prostate(3)|skin(3)	53						CAGGTCAAACGTGTAAAGAAA	0.368																																					p.R844H		.											TTC17,right_upper_lobe,carcinoma,0,1	TTC17	0	0			c.G2531A						.						80.0	79.0	80.0					11																	43465625		2203	4300	6503	SO:0001583	missense	55761	exon18			TCAAACGTGTAAA	AK001540	CCDS31466.1	11p11.2	2013-01-10			ENSG00000052841	ENSG00000052841		"""Tetratricopeptide (TTC) repeat domain containing"""	25596	protein-coding gene	gene with protein product						12477932	Standard	NM_018259		Approved	FLJ10890	uc001mxi.3	Q96AE7	OTTHUMG00000166398	ENST00000039989.4:c.2531G>A	11.37:g.43465625G>A	ENSP00000039989:p.Arg844His	Somatic	53	0		WXS	Illumina HiSeq	.	47	2	NM_018259	G3XAB3|Q8NEC0	Missense_Mutation	SNP	ENST00000039989.4	37	CCDS31466.1	.	.	.	.	.	.	.	.	.	.	G	32	5.120779	0.94385	.	.	ENSG00000052841	ENST00000299240;ENST00000039989	T;T	0.65364	-0.15;0.42	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.72011	0.3408	L	0.32530	0.975	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.996;0.999	T	0.71013	-0.4715	10	0.48119	T	0.1	-12.2899	18.4816	0.90813	0.0:0.0:1.0:0.0	.	901;844;901	Q8NEC0;Q96AE7;G3XAB3	.;TTC17_HUMAN;.	H	901;844	ENSP00000299240:R901H;ENSP00000039989:R844H	ENSP00000039989:R844H	R	+	2	0	TTC17	43422201	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.864000	0.87037	2.809000	0.96659	0.555000	0.69702	CGT	.		0.368	TTC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389577.2	NM_018259	
OTOGL	283310	hgsc.bcm.edu;bcgsc.ca	37	12	80626733	80626733	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr12:80626733G>T	ENST00000547103.1	+	8	652	c.646G>T	c.(646-648)Gtg>Ttg	p.V216L	OTOGL_ENST00000458043.2_Missense_Mutation_p.V216L			Q3ZCN5	OTOGL_HUMAN	otogelin-like	216	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						CTACATTCTTGTGAAAACAAC	0.403																																					p.V216L		.											.	.	.	0			c.G646T						.						92.0	87.0	88.0					12																	80626733		1857	4098	5955	SO:0001583	missense	283310	exon8			ATTCTTGTGAAAA	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"""chromosome 12 open reading frame 64"""	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.646G>T	12.37:g.80626733G>T	ENSP00000447211:p.Val216Leu	Somatic	70	0		WXS	Illumina HiSeq	.	69	4	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		.	.	.	.	.	.	.	.	.	.	G	28.2	4.900446	0.92035	.	.	ENSG00000165899	ENST00000547103;ENST00000458043	T;T	0.58797	0.31;0.31	5.92	5.92	0.95590	.	.	.	.	.	T	0.63965	0.2556	L	0.38175	1.15	0.80722	D	1	.	.	.	.	.	.	T	0.58053	-0.7704	7	0.37606	T	0.19	.	20.3172	0.98658	0.0:0.0:1.0:0.0	.	.	.	.	L	216	ENSP00000447211:V216L;ENSP00000400895:V216L	ENSP00000400895:V216L	V	+	1	0	OTOGL	79150864	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	9.476000	0.97823	2.801000	0.96364	0.650000	0.86243	GTG	.		0.403	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	
PF4V1	5197	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	74719786	74719786	+	Missense_Mutation	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr4:74719786G>A	ENST00000226524.3	+	3	436	c.262G>A	c.(262-264)Gat>Aat	p.D88N		NM_002620.2	NP_002611.1	P10720	PF4V_HUMAN	platelet factor 4 variant 1	88					cell chemotaxis (GO:0060326)|immune response (GO:0006955)	extracellular space (GO:0005615)	heparin binding (GO:0008201)			endometrium(1)|liver(2)	3	Breast(15;0.00102)		all cancers(17;0.00176)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			AATTTGCTTGGATCTGCAAGC	0.448																																					p.D88N		.											.	.	.	0			c.G262A						.						91.0	94.0	93.0					4																	74719786		2203	4300	6503	SO:0001583	missense	5197	exon3			TGCTTGGATCTGC	M26167	CCDS3561.1	4q12-q21	2008-08-15			ENSG00000109272	ENSG00000109272			8862	protein-coding gene	gene with protein product		173461				2725510	Standard	NM_002620		Approved	SCYB4V1, CXCL4V1, CXCL4L1	uc003hhg.1	P10720	OTTHUMG00000130177	ENST00000226524.3:c.262G>A	4.37:g.74719786G>A	ENSP00000226524:p.Asp88Asn	Somatic	64	0		WXS	Illumina HiSeq	.	26	20	NM_002620	A1L4S0	Missense_Mutation	SNP	ENST00000226524.3	37	CCDS3561.1	.	.	.	.	.	.	.	.	.	.	G	11.21	1.571625	0.28003	.	.	ENSG00000109272	ENST00000226524	T	0.04862	3.54	4.02	4.02	0.46733	CXC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.169661	0.49916	D	0.000130	T	0.08626	0.0214	L	0.39020	1.185	0.31260	N	0.692998	P	0.48640	0.913	P	0.50352	0.638	T	0.04885	-1.0920	10	0.15499	T	0.54	.	11.945	0.52924	0.0:0.0:1.0:0.0	.	88	P10720	PF4V_HUMAN	N	88	ENSP00000226524:D88N	ENSP00000226524:D88N	D	+	1	0	PF4V1	74938650	0.999000	0.42202	0.913000	0.36048	0.011000	0.07611	1.812000	0.38952	2.515000	0.84797	0.655000	0.94253	GAT	.		0.448	PF4V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252495.1		
DOT1L	84444	hgsc.bcm.edu	37	19	2194519	2194519	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:2194519G>T	ENST00000398665.3	+	7	630	c.594G>T	c.(592-594)atG>atT	p.M198I		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	198	DOT1. {ECO:0000255|PROSITE- ProRule:PRU00902}.				histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCCAGACCATGGACCGCGAGT	0.582																																					p.M198I		.											.	.	.	0			c.G594T						.						105.0	108.0	107.0					19																	2194519		1921	4136	6057	SO:0001583	missense	84444	exon7			GACCATGGACCGC	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"""	24948	protein-coding gene	gene with protein product	"""histone methyltransferase DOT1L"""	607375	"""DOT1-like, histone H3 methyltransferase (S. cerevisiae)"""			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.594G>T	19.37:g.2194519G>T	ENSP00000381657:p.Met198Ile	Somatic	89	0		WXS	Illumina HiSeq	.	93	4	NM_032482	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	37	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.201998	0.79127	.	.	ENSG00000104885	ENST00000398665;ENST00000221482;ENST00000452696	T;T	0.20881	2.04;2.04	4.27	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.43033	0.1229	L	0.59436	1.845	0.80722	D	1	D	0.64830	0.994	D	0.75484	0.986	T	0.41805	-0.9488	10	0.87932	D	0	-26.9195	15.8524	0.78943	0.0:0.0:1.0:0.0	.	198	Q8TEK3-2	.	I	198;198;174	ENSP00000381657:M198I;ENSP00000404284:M174I	ENSP00000221482:M198I	M	+	3	0	DOT1L	2145519	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.122000	0.94380	2.216000	0.71823	0.462000	0.41574	ATG	.		0.582	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482	
WTIP	126374	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	34981373	34981373	+	Missense_Mutation	SNP	G	G	T	rs373500546		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:34981373G>T	ENST00000590071.2	+	2	1097	c.760G>T	c.(760-762)Gac>Tac	p.D254Y	WTIP_ENST00000270288.6_Missense_Mutation_p.D478Y	NM_001080436.1	NP_001073905.1	A6NIX2	WTIP_HUMAN	Wilms tumor 1 interacting protein	254	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|negative regulation of hippo signaling (GO:0035331)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)	4	all_lung(56;5.94e-07)|Lung NSC(56;9.35e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			CTTCACCTGCGACTCGTGTGG	0.582																																					p.D254Y		.											.	.	.	0			c.G760T						.						103.0	101.0	102.0					19																	34981373		2114	4236	6350	SO:0001583	missense	126374	exon2			ACCTGCGACTCGT	AK130059	CCDS59375.1	19q13.11	2012-03-16			ENSG00000142279	ENSG00000142279			20964	protein-coding gene	gene with protein product	"""WT1-interacting protein"""	614790				14736876	Standard	NM_001080436		Approved		uc002nvm.3	A6NIX2		ENST00000590071.2:c.760G>T	19.37:g.34981373G>T	ENSP00000466953:p.Asp254Tyr	Somatic	38	0		WXS	Illumina HiSeq	.	46	5	NM_001080436		Missense_Mutation	SNP	ENST00000590071.2	37	CCDS59375.1	.	.	.	.	.	.	.	.	.	.	G	1.314	-0.601442	0.03744	.	.	ENSG00000142279	ENST00000270288	D	0.87412	-2.25	5.14	2.89	0.33648	Zinc finger, LIM-type (4);	0.237540	0.44097	D	0.000489	T	0.68568	0.3015	N	0.11201	0.11	0.32263	N	0.569858	P	0.35208	0.49	B	0.39094	0.29	T	0.69075	-0.5241	10	0.02654	T	1	.	3.864	0.09008	0.2008:0.0:0.5166:0.2825	.	478	A6NIX2	WTIP_HUMAN	Y	478	ENSP00000270288:D478Y	ENSP00000270288:D478Y	D	+	1	0	WTIP	39673213	0.996000	0.38824	0.924000	0.36721	0.181000	0.23173	2.512000	0.45485	1.370000	0.46153	0.561000	0.74099	GAC	.		0.582	WTIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459381.3	XM_059037	
KIF22	3835	hgsc.bcm.edu	37	16	29810382	29810382	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr16:29810382G>T	ENST00000160827.4	+	5	676	c.636G>T	c.(634-636)caG>caT	p.Q212H	KIF22_ENST00000400751.5_Missense_Mutation_p.Q144H|KIF22_ENST00000561482.1_Missense_Mutation_p.Q144H|KIF22_ENST00000400750.2_5'UTR|KIF22_ENST00000569382.2_Missense_Mutation_p.Q144H	NM_001256269.1|NM_007317.2	NP_001243198.1|NP_015556.1	Q14807	KIF22_HUMAN	kinesin family member 22	212	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|DNA repair (GO:0006281)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)			endometrium(1)|large_intestine(1)|lung(11)|skin(1)	14						GTCTCTCCCAGAAGCCCATCA	0.577																																					p.Q212H		.											.	.	.	0			c.G636T						.						73.0	78.0	76.0					16																	29810382		2197	4296	6493	SO:0001583	missense	3835	exon5			CTCCCAGAAGCCC	D38751	CCDS10653.1, CCDS58444.1	16p11.2	2008-03-03	2003-01-09	2003-01-10	ENSG00000079616	ENSG00000079616		"""Kinesins"""	6391	protein-coding gene	gene with protein product		603213	"""kinesin-like 4"""	KNSL4		8599929, 11416179	Standard	NM_007317		Approved	Kid, OBP-1, OBP-2	uc002dts.4	Q14807	OTTHUMG00000097771	ENST00000160827.4:c.636G>T	16.37:g.29810382G>T	ENSP00000160827:p.Gln212His	Somatic	97	0		WXS	Illumina HiSeq	.	97	4	NM_007317	B2R5M0|B7Z265|O60845|O94814|Q53F58|Q9BT46	Missense_Mutation	SNP	ENST00000160827.4	37	CCDS10653.1	.	.	.	.	.	.	.	.	.	.	G	10.06	1.246472	0.22796	.	.	ENSG00000079616	ENST00000160827;ENST00000400751	T;T	0.75260	-0.92;-0.92	5.95	3.68	0.42216	Kinesin, motor domain (4);	.	.	.	.	T	0.58637	0.2136	N	0.16790	0.44	0.80722	D	1	B;B	0.24576	0.106;0.06	B;B	0.27715	0.082;0.036	T	0.55768	-0.8089	9	0.34782	T	0.22	.	11.2049	0.48762	0.1741:0.0:0.8259:0.0	.	144;212	B7Z265;Q14807	.;KIF22_HUMAN	H	212;144	ENSP00000160827:Q212H;ENSP00000383562:Q144H	ENSP00000160827:Q212H	Q	+	3	2	KIF22	29717883	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	1.161000	0.31773	1.526000	0.49068	0.655000	0.94253	CAG	.		0.577	KIF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215012.2		
THPO	7066	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	184091269	184091269	+	Silent	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr3:184091269G>A	ENST00000204615.7	-	5	544	c.330C>T	c.(328-330)ctC>ctT	p.L110L	THPO_ENST00000421442.2_Silent_p.L110L|EIF2B5_ENST00000444495.1_Intron|THPO_ENST00000445696.2_Silent_p.L110L|THPO_ENST00000477594.1_5'Flank	NM_000460.2|NM_001177597.1|NM_001177598.1	NP_000451.1|NP_001171068.1|NP_001171069.1	P40225	TPO_HUMAN	thrombopoietin	110					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|myeloid cell differentiation (GO:0030099)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|thrombopoietin-mediated signaling pathway (GO:0038163)	extracellular space (GO:0005615)	growth factor activity (GO:0008083)			NS(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GCTGCCCCAGGAGGGATGAGA	0.597																																					p.L110L		.											.	.	.	0			c.C330T						.						85.0	73.0	77.0					3																	184091269		2203	4300	6503	SO:0001819	synonymous_variant	7066	exon5			CCCCAGGAGGGAT		CCDS3265.1, CCDS54693.1	3q27	2014-01-30	2008-07-31		ENSG00000090534	ENSG00000090534		"""Endogenous ligands"""	11795	protein-coding gene	gene with protein product	"""prepro-thrombopoietin"", ""megakaryocyte stimulating factor"", ""myeloproliferative leukemia virus oncogene ligand"", ""megakaryocyte growth and development factor"", ""MPL ligand"", ""megakaryocyte colony-stimulating factor"", ""c-mpl ligand"", ""thrombopoietin nirs variant 1"""	600044		MGDF		8202154	Standard	XM_006713738		Approved	TPO, MPLLG	uc003fol.1	P40225	OTTHUMG00000156745	ENST00000204615.7:c.330C>T	3.37:g.184091269G>A		Somatic	41	0		WXS	Illumina HiSeq	.	48	19	NM_001177598	A1L3Y0|B7ZLR8|B9EGA8|Q13020|Q15790|Q15791|Q15792	Silent	SNP	ENST00000204615.7	37	CCDS3265.1																																																																																			.		0.597	THPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345554.1	NM_000460	
ABCA7	10347	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	1052002	1052002	+	Silent	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:1052002G>A	ENST00000263094.6	+	22	3255	c.3024G>A	c.(3022-3024)gtG>gtA	p.V1008V	ABCA7_ENST00000433129.1_Silent_p.V1008V|ABCA7_ENST00000435683.2_Silent_p.V870V	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1008	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGACCGTGTGGCCGTGGTGG	0.672																																					p.V1008V		.											.	.	.	0			c.G3024A						.						76.0	50.0	59.0					19																	1052002		2192	4284	6476	SO:0001819	synonymous_variant	10347	exon22			CCGTGTGGCCGTG	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.3024G>A	19.37:g.1052002G>A		Somatic	29	0		WXS	Illumina HiSeq	.	33	12	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			.		0.672	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
UPRT	139596	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	74494297	74494297	+	Missense_Mutation	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chrX:74494297G>A	ENST00000373383.4	+	1	375	c.208G>A	c.(208-210)Ggc>Agc	p.G70S	UPRT_ENST00000531704.1_3'UTR|UPRT_ENST00000530743.1_5'Flank|UPRT_ENST00000373379.1_Missense_Mutation_p.G70S	NM_145052.3	NP_659489.1	Q96BW1	UPP_HUMAN	uracil phosphoribosyltransferase (FUR1) homolog (S. cerevisiae)	70					female pregnancy (GO:0007565)|lactation (GO:0007595)|response to insulin (GO:0032868)|UMP biosynthetic process (GO:0006222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(4)|lung(4)	18						TGGGGCCTGCGGCGGCTCCAG	0.627																																					p.G70S		.											.	.	.	0			c.G208A						.						25.0	23.0	24.0					X																	74494297		2202	4289	6491	SO:0001583	missense	139596	exon1			GCCTGCGGCGGCT	BC015116	CCDS14429.1	Xq13.3	2009-01-14			ENSG00000094841	ENSG00000094841			28334	protein-coding gene	gene with protein product		300656				12477932	Standard	NM_145052		Approved	DKFZp781E1243, MGC23937, FUR1, RP11-311P8.3	uc004ecb.2	Q96BW1	OTTHUMG00000021864	ENST00000373383.4:c.208G>A	X.37:g.74494297G>A	ENSP00000362481:p.Gly70Ser	Somatic	26	0		WXS	Illumina HiSeq	.	24	22	NM_145052	Q5JRL1|Q5JRL3|Q68DN0|Q96MW2	Missense_Mutation	SNP	ENST00000373383.4	37	CCDS14429.1	.	.	.	.	.	.	.	.	.	.	G	8.364	0.833750	0.16820	.	.	ENSG00000094841	ENST00000373383;ENST00000373379	.	.	.	5.14	-0.174	0.13319	.	0.783386	0.12136	N	0.496325	T	0.13243	0.0321	N	0.12182	0.205	0.09310	N	0.999995	B;B;B	0.27117	0.168;0.028;0.028	B;B;B	0.17979	0.02;0.011;0.007	T	0.27262	-1.0079	9	0.06757	T	0.87	-19.1505	3.3365	0.07103	0.3892:0.0:0.2777:0.3331	.	70;70;70	Q96BW1-2;A8KAF9;Q96BW1	.;.;UPP_HUMAN	S	70	.	ENSP00000362471:G70S	G	+	1	0	UPRT	74411022	0.078000	0.21339	0.000000	0.03702	0.022000	0.10575	0.309000	0.19332	-0.410000	0.07542	0.600000	0.82982	GGC	.		0.627	UPRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057278.1	NM_145052	
ZNF485	220992	hgsc.bcm.edu	37	10	44104181	44104181	+	Silent	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr10:44104181G>T	ENST00000361807.3	+	3	338	c.144G>T	c.(142-144)gtG>gtT	p.V48V	ZNF485_ENST00000374437.2_Intron|ZNF485_ENST00000374435.3_Silent_p.V48V	NM_145312.3	NP_660355.2	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	48	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16						GGAATCTGGTGTCTGTGGGTG	0.507																																					p.V48V		.											.	.	.	0			c.G144T						.						249.0	207.0	221.0					10																	44104181		2203	4300	6503	SO:0001819	synonymous_variant	220992	exon3			TCTGGTGTCTGTG	AK074679	CCDS7205.2	10q11.21	2013-01-08			ENSG00000198298	ENSG00000198298		"""Zinc fingers, C2H2-type"", ""-"""	23440	protein-coding gene	gene with protein product							Standard	NM_145312		Approved		uc010qfc.2	Q8NCK3	OTTHUMG00000018040	ENST00000361807.3:c.144G>T	10.37:g.44104181G>T		Somatic	81	0		WXS	Illumina HiSeq	.	84	4	NM_145312	B4DSE6|Q96CL0	Silent	SNP	ENST00000361807.3	37	CCDS7205.2																																																																																			.		0.507	ZNF485-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047719.2	NM_145312	
RBM25	58517	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	73576153	73576153	+	Missense_Mutation	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr14:73576153C>T	ENST00000261973.7	+	14	1930	c.1645C>T	c.(1645-1647)Cgc>Tgc	p.R549C	RBM25_ENST00000527432.1_Missense_Mutation_p.R549C|RBM25_ENST00000532483.1_3'UTR	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN	RNA binding motif protein 25	549	Arg-rich.|Glu-rich.|Necessary for nuclear speckle localization.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of apoptotic process (GO:0042981)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		AATCAGGCAGCGCCTTCTGGC	0.522																																					p.R549C		.											.	.	.	0			c.C1645T						.						96.0	94.0	95.0					14																	73576153		2203	4300	6503	SO:0001583	missense	58517	exon14			AGGCAGCGCCTTC	BX647116	CCDS32113.1	14q24.3	2013-02-12	2004-04-23	2004-04-29	ENSG00000119707	ENSG00000119707		"""RNA binding motif (RRM) containing"""	23244	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 94"""	612427	"""RNA-binding region (RNP1, RRM) containing 7"""	RNPC7		9847074, 7596406	Standard	NM_021239		Approved	S164, fSAP94, NET52, Snu71	uc001xno.3	P49756	OTTHUMG00000167540	ENST00000261973.7:c.1645C>T	14.37:g.73576153C>T	ENSP00000261973:p.Arg549Cys	Somatic	54	0		WXS	Illumina HiSeq	.	25	19	NM_021239	A0PJL9|B2RNA8|B3KT03|Q2TA72|Q5XJ17|Q6P665|Q9H6A1|Q9UEQ5|Q9UIE9	Missense_Mutation	SNP	ENST00000261973.7	37	CCDS32113.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.434001	0.83776	.	.	ENSG00000119707	ENST00000261973;ENST00000527432	T;T	0.15017	2.46;2.46	5.97	5.09	0.68999	.	0.043771	0.85682	N	0.000000	T	0.23926	0.0579	M	0.69823	2.125	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.02933	-1.1092	10	0.72032	D	0.01	.	15.368	0.74538	0.0:0.9333:0.0:0.0667	.	549	P49756	RBM25_HUMAN	C	549	ENSP00000261973:R549C;ENSP00000431150:R549C	ENSP00000261973:R549C	R	+	1	0	RBM25	72645906	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.793000	0.55484	1.535000	0.49220	0.655000	0.94253	CGC	.		0.522	RBM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394966.1	XM_027330	
CTNND2	1501	hgsc.bcm.edu	37	5	11199612	11199612	+	Silent	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr5:11199612C>T	ENST00000304623.8	-	11	2112	c.1923G>A	c.(1921-1923)ctG>ctA	p.L641L	CTNND2_ENST00000495388.2_5'UTR|CTNND2_ENST00000359640.2_Silent_p.L641L|CTNND2_ENST00000511377.1_Silent_p.L550L|CTNND2_ENST00000503622.1_Silent_p.L304L|CTNND2_ENST00000458100.2_Silent_p.L208L	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	641					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.L641L(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						GTAACCTCACCAGTGCTGGGA	0.453																																					p.L641L		.											CTNND2,NS,carcinoma,0,1	CTNND2	0	1	Substitution - coding silent(1)	lung(1)	c.G1923A						.						161.0	162.0	162.0					5																	11199612		2203	4300	6503	SO:0001819	synonymous_variant	1501	exon11			CCTCACCAGTGCT	U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"""Armadillo repeat containing"""	2516	protein-coding gene	gene with protein product	"""neural plakophilin-related arm-repeat protein"""	604275	"""catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"""			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.1923G>A	5.37:g.11199612C>T		Somatic	76	0		WXS	Illumina HiSeq	.	72	3	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Silent	SNP	ENST00000304623.8	37	CCDS3881.1																																																																																			.		0.453	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332	
CTCFL	140690	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	56099137	56099137	+	Missense_Mutation	SNP	C	C	T	rs572527047		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr20:56099137C>T	ENST00000608263.1	-	1	786	c.125G>A	c.(124-126)cGg>cAg	p.R42Q	CTCFL_ENST00000608858.1_Intron|CTCFL_ENST00000502686.2_Intron|CTCFL_ENST00000422869.2_Missense_Mutation_p.R42Q|CTCFL_ENST00000433949.3_Intron|CTCFL_ENST00000608903.1_Intron|CTCFL_ENST00000243914.3_Missense_Mutation_p.R42Q|CTCFL_ENST00000429804.3_Missense_Mutation_p.R42Q|CTCFL_ENST00000539382.1_Intron|CTCFL_ENST00000371196.2_Missense_Mutation_p.R42Q|CTCFL_ENST00000609232.1_Missense_Mutation_p.R42Q|CTCFL_ENST00000608425.1_Missense_Mutation_p.R42Q|CTCFL_ENST00000432255.2_Missense_Mutation_p.R42Q|CTCFL_ENST00000423479.3_Missense_Mutation_p.R42Q|CTCFL_ENST00000608440.1_Missense_Mutation_p.R42Q|CTCFL_ENST00000608158.1_Missense_Mutation_p.R42Q|CTCFL_ENST00000481655.2_Missense_Mutation_p.R42Q	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	42					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			ACTAGGGCTCCGATGGTCTTT	0.567													C|||	1	0.000199681	0.0	0.0	5008	,	,		19262	0.0		0.0	False		,,,				2504	0.001				p.R42Q		.											.	.	.	0			c.G125A						.						193.0	211.0	205.0					20																	56099137		2203	4300	6503	SO:0001583	missense	140690	exon1			GGGCTCCGATGGT		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"""Zinc fingers, C2H2-type"""	16234	protein-coding gene	gene with protein product	"""cancer/testis antigen 27"""	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.125G>A	20.37:g.56099137C>T	ENSP00000476783:p.Arg42Gln	Somatic	44	0		WXS	Illumina HiSeq	.	33	9	NM_001269044	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Missense_Mutation	SNP	ENST00000608263.1	37	CCDS13459.1	.	.	.	.	.	.	.	.	.	.	C	7.221	0.597317	0.13875	.	.	ENSG00000124092	ENST00000423479;ENST00000243914;ENST00000371196;ENST00000429804;ENST00000433949;ENST00000422109;ENST00000426658;ENST00000432255;ENST00000422869	T;T;T;T;T;T;T;T;T	0.09073	3.02;3.05;3.05;3.24;3.07;3.41;3.08;3.72;3.07	3.81	-7.41	0.01392	.	3.940590	0.00725	N	0.000911	T	0.02571	0.0078	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B;B;B;B	0.13145	0.0;0.0;0.001;0.007;0.001;0.003;0.0;0.0	B;B;B;B;B;B;B;B	0.04013	0.0;0.0;0.001;0.001;0.001;0.001;0.0;0.0	T	0.37798	-0.9690	10	0.11485	T	0.65	0.5628	1.718	0.02905	0.2202:0.1213:0.135:0.5235	.	42;42;42;42;42;42;42;42	A6XGM3;A6XGM0;A6XGM9;A6XGM8;A6XGM2;E7EUE3;A6XGL8;Q8NI51	.;.;.;.;.;.;.;CTCFL_HUMAN	Q	42	ENSP00000415579:R42Q;ENSP00000243914:R42Q;ENSP00000360239:R42Q;ENSP00000415329:R42Q;ENSP00000392034:R42Q;ENSP00000413713:R42Q;ENSP00000403369:R42Q;ENSP00000409344:R42Q;ENSP00000399061:R42Q	ENSP00000243914:R42Q	R	-	2	0	CTCFL	55532543	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.911000	0.01583	-1.226000	0.02574	-0.742000	0.03525	CGG	.		0.567	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618	
SYNPO2L	79933	hgsc.bcm.edu;bcgsc.ca	37	10	75406952	75406952	+	Missense_Mutation	SNP	A	A	G	rs200429699		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr10:75406952A>G	ENST00000394810.2	-	4	2607	c.2458T>C	c.(2458-2460)Ttt>Ctt	p.F820L	SYNPO2L_ENST00000372873.4_Missense_Mutation_p.F596L	NM_001114133.1	NP_001107605.1	Q9H987	SYP2L_HUMAN	synaptopodin 2-like	820	Pro-rich.					cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)				breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Prostate(51;0.0112)					TGGGGGAAAAAGGGAGAGAGC	0.577													A|||	1	0.000199681	0.0	0.0	5008	,	,		15267	0.0		0.001	False		,,,				2504	0.0				p.F820L		.											SYNPO2L_ENST00000394810,NS,carcinoma,+1,2	SYNPO2L_ENST00000394810	+1	0			c.T2458C						.						62.0	74.0	70.0					10																	75406952		2202	4300	6502	SO:0001583	missense	79933	exon4			GGAAAAAGGGAGA	AK022983	CCDS7331.1, CCDS44438.1	10q22.3	2007-12-19			ENSG00000166317	ENSG00000166317			23532	protein-coding gene	gene with protein product							Standard	XM_005270158		Approved	FLJ12921	uc001jut.4	Q9H987	OTTHUMG00000018471	ENST00000394810.2:c.2458T>C	10.37:g.75406952A>G	ENSP00000378289:p.Phe820Leu	Somatic	51	0		WXS	Illumina HiSeq	.	26	4	NM_001114133	A5PKV9|Q68A20	Missense_Mutation	SNP	ENST00000394810.2	37	CCDS44438.1	.	.	.	.	.	.	.	.	.	.	A	19.36	3.813125	0.70912	.	.	ENSG00000166317	ENST00000372873;ENST00000394810	T;T	0.22539	1.95;2.26	4.98	4.98	0.66077	.	0.119748	0.64402	D	0.000019	T	0.23766	0.0575	L	0.54323	1.7	0.44500	D	0.997447	P;P	0.45531	0.666;0.86	B;P	0.44561	0.162;0.453	T	0.03597	-1.1021	10	0.12103	T	0.63	-5.368	14.8374	0.70194	1.0:0.0:0.0:0.0	.	820;596	Q9H987;Q9H987-2	SYP2L_HUMAN;.	L	596;820	ENSP00000361964:F596L;ENSP00000378289:F820L	ENSP00000361964:F596L	F	-	1	0	SYNPO2L	75076958	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.139000	0.94554	2.090000	0.63153	0.402000	0.26972	TTT	.		0.577	SYNPO2L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316562.2	NM_024875	
ABCC4	10257	hgsc.bcm.edu;bcgsc.ca	37	13	95816668	95816668	+	Silent	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr13:95816668G>T	ENST00000376887.4	-	16	2253	c.2139C>A	c.(2137-2139)gtC>gtA	p.V713V	ABCC4_ENST00000431522.1_Silent_p.V713V|ABCC4_ENST00000412704.1_Intron|ABCC4_ENST00000536256.1_Silent_p.V638V	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	713					blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	GGAAAATGAAGACAATCCAGT	0.383																																					p.V713V		.											.	.	.	0			c.C2139A						.						107.0	99.0	102.0					13																	95816668		2203	4300	6503	SO:0001819	synonymous_variant	10257	exon16			AATGAAGACAATC	U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257		"""ATP binding cassette transporters / subfamily C"""	55	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter (ABC superfamily)"", ""bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4)"", ""multidrug resistance-associated protein 4"", ""multispecific organic anion transporter B"""	605250				8894702, 9661885	Standard	NM_005845		Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.2139C>A	13.37:g.95816668G>T		Somatic	117	0		WXS	Illumina HiSeq	.	91	4	NM_005845	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Silent	SNP	ENST00000376887.4	37	CCDS9474.1																																																																																			.		0.383	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845	
C18orf54	162681	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	51888024	51888024	+	Missense_Mutation	SNP	C	C	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr18:51888024C>A	ENST00000300091.5	+	3	627	c.295C>A	c.(295-297)Ctt>Att	p.L99I	C18orf54_ENST00000578138.1_Intron|C18orf54_ENST00000382911.4_Missense_Mutation_p.L99I	NM_173529.4	NP_775800.3	Q8IYD9	LAS2_HUMAN	chromosome 18 open reading frame 54	99						extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	15				Colorectal(16;0.0206)|READ - Rectum adenocarcinoma(59;0.186)		TTTTGAAAACCTTGATCACAA	0.318																																					p.L99I		.											.	.	.	0			c.C295A						.						59.0	55.0	56.0					18																	51888024		2203	4298	6501	SO:0001583	missense	162681	exon3			GAAAACCTTGATC	AK126503	CCDS11956.1, CCDS74223.1	18q21	2012-10-24			ENSG00000166845	ENSG00000166845			13796	protein-coding gene	gene with protein product	"""lung adenoma susceptibility protein 2"""	613258					Standard	XM_005258201		Approved	MGC33382, LAS2	uc031rij.1	Q8IYD9	OTTHUMG00000132703	ENST00000300091.5:c.295C>A	18.37:g.51888024C>A	ENSP00000300091:p.Leu99Ile	Somatic	113	0		WXS	Illumina HiSeq	.	77	21	NM_173529	I7HFJ6|Q6MZU3|Q6ZTL6	Missense_Mutation	SNP	ENST00000300091.5	37	CCDS11956.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.824967	0.32237	.	.	ENSG00000166845	ENST00000300091;ENST00000382911	D;D	0.97811	-4.55;-4.55	5.52	-0.238	0.13055	.	0.818073	0.10856	N	0.626597	D	0.95626	0.8578	M	0.73598	2.24	0.09310	N	1	B;B	0.32829	0.253;0.386	B;B	0.32677	0.107;0.15	D	0.90903	0.4770	10	0.72032	D	0.01	-2.6227	3.969	0.09444	0.0:0.2774:0.356:0.3666	.	99;99	Q8IYD9-2;Q8IYD9	.;CR054_HUMAN	I	99	ENSP00000300091:L99I;ENSP00000372368:L99I	ENSP00000300091:L99I	L	+	1	0	C18orf54	50142022	0.001000	0.12720	0.600000	0.28864	0.813000	0.45954	-0.364000	0.07583	0.022000	0.15160	0.557000	0.71058	CTT	.		0.318	C18orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256001.1	NM_173529	
RPL7A	6130	hgsc.bcm.edu;ucsc.edu	37	9	136216982	136216982	+	Intron	SNP	T	T	C			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr9:136216982T>C	ENST00000323345.6	+	4	445				MED22_ENST00000371999.1_5'Flank|SNORD36A_ENST00000362874.1_RNA|MED22_ENST00000344469.5_5'Flank|SURF1_ENST00000495952.1_5'Flank|RPL7A_ENST00000463740.1_Intron|RPL7A_ENST00000315731.4_Intron|MED22_ENST00000491289.1_5'Flank|MED22_ENST00000343730.5_5'Flank|SNORD24_ENST00000383884.1_RNA|MED22_ENST00000471524.1_5'Flank|SNORD36B_ENST00000363961.1_RNA|SNORD36C_ENST00000516733.1_RNA|MED22_ENST00000476080.1_5'Flank	NM_000972.2	NP_000963.1	P62424	RL7A_HUMAN	ribosomal protein L7a						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(145;4.93e-07)|Epithelial(140;4.09e-06)|all cancers(34;3.78e-05)		GGCCTGAAATTACTGTGAAGA	0.517																																					.		.											.	.	.	0			.						.						65.0	65.0	65.0					9																	136216982		876	1991	2867	SO:0001627	intron_variant	26814	.			TGAAATTACTGTG	BC005128	CCDS6965.1	9q34	2011-04-06			ENSG00000148303	ENSG00000148303		"""L ribosomal proteins"""	10364	protein-coding gene	gene with protein product	"""surfeit 3"", ""PLA-X polypeptide"", ""surfeit locus protein 3"", ""60S ribosomal protein L7a"", "";"", ""thyroid hormone receptor uncoupling protein"""	185640				2403926, 2966065	Standard	NM_000972		Approved	SURF3, TRUP, L7A	uc004cde.1	P62424	OTTHUMG00000020864	ENST00000323345.6:c.415+75T>C	9.37:g.136216982T>C		Somatic	39	0		WXS	Illumina HiSeq	.	25	9	.	P11518|Q5T8U4	RNA	SNP	ENST00000323345.6	37	CCDS6965.1																																																																																			.		0.517	RPL7A-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054869.1	NM_000972	
PXDN	7837	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	1668821	1668821	+	Silent	SNP	A	A	G			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr2:1668821A>G	ENST00000252804.4	-	11	1367	c.1317T>C	c.(1315-1317)ccT>ccC	p.P439P	PXDN_ENST00000483018.1_5'Flank	NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	439	Ig-like C2-type 3.				extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		CTCTGTCCTGAGGCGTCACAG	0.537																																					p.P439P		.											.	.	.	0			c.T1317C						.						45.0	48.0	47.0					2																	1668821		1936	4147	6083	SO:0001819	synonymous_variant	7837	exon11			GTCCTGAGGCGTC	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"""Immunoglobulin superfamily / I-set domain containing"""	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.1317T>C	2.37:g.1668821A>G		Somatic	72	0		WXS	Illumina HiSeq	.	76	17	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Silent	SNP	ENST00000252804.4	37	CCDS46221.1	.	.	.	.	.	.	.	.	.	.	A	0.569	-0.842102	0.02671	.	.	ENSG00000130508	ENST00000433670	.	.	.	5.55	-11.1	0.00147	.	.	.	.	.	T	0.31544	0.0800	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46275	-0.9203	4	.	.	.	-22.2517	1.4007	0.02270	0.1402:0.2257:0.2639:0.3702	.	.	.	.	P	435	.	.	L	-	2	0	PXDN	1647828	0.008000	0.16893	0.000000	0.03702	0.052000	0.14988	-0.810000	0.04505	-3.562000	0.00141	-2.409000	0.00222	CTC	.		0.537	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455	
ABCC6P2	730013	hgsc.bcm.edu	37	16	14916703	14916703	+	IGR	SNP	C	C	A	rs557836550	byFrequency	TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr16:14916703C>A								NPIPA2 (57433 upstream) : NOMO1 (10834 downstream)																							TGCCTCCCCCCACCATTGCCT	0.542																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	730013	.			TCCCCCCACCATT																													16.37:g.14916703C>A		Somatic	81	0		WXS	Illumina HiSeq	.	64	13	.		RNA	SNP		37																																																																																				.	0	0.542								
DPY19L2P1	554236	hgsc.bcm.edu	37	7	35189650	35189650	+	IGR	SNP	A	A	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr7:35189650A>T								DPY19L2P1 (42304 upstream) : TBX20 (52391 downstream)																							CATGTTTGAAATTCTAGCTAT	0.249																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	554236	.			TTTGAAATTCTAG																													7.37:g.35189650A>T		Somatic	17	0		WXS	Illumina HiSeq	.	57	10	.		RNA	SNP		37																																																																																				.	0	0.249								
MUC16	94025	hgsc.bcm.edu	37	19	9090831	9090831	+	Silent	SNP	A	A	G			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:9090831A>G	ENST00000397910.4	-	1	1187	c.984T>C	c.(982-984)ccT>ccC	p.P328P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	328	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)				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						TCATGGAAAAAGGGATAGCTG	0.522																																					p.P328P		.											MUC16_ENST00000397910,bladder,carcinoma,0,2	MUC16_ENST00000397910	0	0			c.T984C						.						96.0	95.0	96.0					19																	9090831		2041	4195	6236	SO:0001819	synonymous_variant	94025	exon1			GGAAAAAGGGATA	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.984T>C	19.37:g.9090831A>G		Somatic	31	1		WXS	Illumina HiSeq	.	34	2	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			.		0.522	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
SPATA18	132671	hgsc.bcm.edu	37	4	52945942	52945942	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr4:52945942G>T	ENST00000295213.4	+	9	1586	c.1212G>T	c.(1210-1212)aaG>aaT	p.K404N	SPATA18_ENST00000419395.2_Missense_Mutation_p.K372N	NM_145263.2	NP_660306.1	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18	404					cellular response to DNA damage stimulus (GO:0006974)|mitochondrial protein catabolic process (GO:0035694)|mitochondrion degradation by induced vacuole formation (GO:0035695)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial outer membrane (GO:0005741)		p.K404N(2)		breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)			TCAATCCCAAGATTTCATTCC	0.443																																					p.K404N		.											SPATA18_ENST00000295213,NS,carcinoma,0,4	SPATA18_ENST00000295213	0	2	Substitution - Missense(2)	lung(2)	c.G1212T						.						289.0	270.0	277.0					4																	52945942		2203	4300	6503	SO:0001583	missense	132671	exon9			TCCCAAGATTTCA	BC025396	CCDS3489.1, CCDS75124.1	4q11	2012-01-23	2012-01-23		ENSG00000163071	ENSG00000163071			29579	protein-coding gene	gene with protein product		612814	"""spermatogenesis associated 18 homolog (rat)"""			21300779	Standard	XR_245253		Approved	FLJ32906	uc003gzl.3	Q8TC71	OTTHUMG00000128698	ENST00000295213.4:c.1212G>T	4.37:g.52945942G>T	ENSP00000295213:p.Lys404Asn	Somatic	65	1		WXS	Illumina HiSeq	.	60	3	NM_145263	B4E2R0|E5RLK1|Q8IY48|Q8N7D7	Missense_Mutation	SNP	ENST00000295213.4	37	CCDS3489.1	.	.	.	.	.	.	.	.	.	.	G	18.15	3.559194	0.65538	.	.	ENSG00000163071	ENST00000295213;ENST00000419395	T;T	0.34859	1.34;3.69	5.4	5.4	0.78164	.	0.318068	0.38326	N	0.001736	T	0.52322	0.1727	L	0.55481	1.735	0.43647	D	0.996057	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.85130	0.973;0.973;0.997	T	0.51474	-0.8701	10	0.66056	D	0.02	-28.9994	9.989	0.41858	0.089:0.0:0.911:0.0	.	372;404;404	Q8TC71-2;Q8TC71;Q96M13	.;MIEAP_HUMAN;.	N	404;372	ENSP00000295213:K404N;ENSP00000415309:K372N	ENSP00000295213:K404N	K	+	3	2	SPATA18	52640699	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	2.347000	0.44036	2.814000	0.96858	0.655000	0.94253	AAG	.		0.443	SPATA18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250597.2	NM_145263	
INHBB	3625	hgsc.bcm.edu	37	2	121107289	121107289	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr2:121107289G>T	ENST00000295228.3	+	2	1109	c.1063G>T	c.(1063-1065)Gtg>Ttg	p.V355L		NM_002193.2	NP_002184.2	P09529	INHBB_HUMAN	inhibin, beta B	355					activin receptor signaling pathway (GO:0032924)|cell differentiation (GO:0030154)|cellular response to insulin stimulus (GO:0032869)|cellular response to leptin stimulus (GO:0044320)|cellular response to starvation (GO:0009267)|defense response (GO:0006952)|fat cell differentiation (GO:0045444)|growth (GO:0040007)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of hepatocyte growth factor biosynthetic process (GO:0048178)|negative regulation of insulin secretion (GO:0046676)|oocyte development (GO:0048599)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|response to mechanical stimulus (GO:0009612)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	cytokine activity (GO:0005125)|hormone activity (GO:0005179)|host cell surface receptor binding (GO:0046789)|protein homodimerization activity (GO:0042803)			NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(4)|pancreas(2)|skin(2)	15		Prostate(154;0.122)				CACGGCTGTGGTGAACCAGTA	0.617																																					p.V355L		.											INHBB,caecum,carcinoma,0,1	INHBB	0	0			c.G1063T						.						49.0	47.0	48.0					2																	121107289		2203	4300	6503	SO:0001583	missense	3625	exon2			GCTGTGGTGAACC		CCDS2132.1	2q14.2	2014-01-30	2007-07-30		ENSG00000163083	ENSG00000163083		"""Endogenous ligands"""	6067	protein-coding gene	gene with protein product		147390	"""inhibin, beta B (activin AB beta polypeptide)"""			3345731	Standard	NM_002193		Approved		uc002tmn.2	P09529	OTTHUMG00000131437	ENST00000295228.3:c.1063G>T	2.37:g.121107289G>T	ENSP00000295228:p.Val355Leu	Somatic	37	0		WXS	Illumina HiSeq	.	42	3	NM_002193	Q53T31|Q8N1D3	Missense_Mutation	SNP	ENST00000295228.3	37	CCDS2132.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.516631	0.44763	.	.	ENSG00000163083	ENST00000295228	D	0.84589	-1.87	4.57	4.57	0.56435	Transforming growth factor-beta, C-terminal (3);	0.000000	0.64402	D	0.000001	T	0.76219	0.3957	N	0.12853	0.265	0.51767	D	0.999939	B	0.28880	0.226	B	0.34991	0.193	T	0.74393	-0.3680	10	0.34782	T	0.22	-23.1343	16.2785	0.82657	0.0:0.0:1.0:0.0	.	355	P09529	INHBB_HUMAN	L	355	ENSP00000295228:V355L	ENSP00000295228:V355L	V	+	1	0	INHBB	120823759	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.556000	0.73932	2.368000	0.80403	0.462000	0.41574	GTG	.		0.617	INHBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254234.1		
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45994302	45994302	+	Missense_Mutation	SNP	T	T	C	rs200473430|rs201123486		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr21:45994302T>C	ENST00000400374.3	+	1	697	c.667T>C	c.(667-669)Tcc>Ccc	p.S223P	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_5'Flank	NM_198687.1	NP_941960.1	P60372	KR104_HUMAN	keratin associated protein 10-4	223	36 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(1)	18						CACCTCCTCCTCCTGCCAGCA	0.637																																					p.S223P		.											KRTAP10-4,NS,carcinoma,0,1	KRTAP10-4	0	0			c.T667C						.						59.0	65.0	63.0					21																	45994302		2203	4299	6502	SO:0001583	missense	386672	exon1			TCCTCCTCCTGCC	AB076351	CCDS42957.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000215454	ENSG00000215454		"""Keratin associated proteins"""	20521	protein-coding gene	gene with protein product			"""keratin associated protein 18-4"""	KRTAP18-4			Standard	NM_198687		Approved	KRTAP18.4, KAP10.4	uc002zfk.1	P60372	OTTHUMG00000057641	ENST00000400374.3:c.667T>C	21.37:g.45994302T>C	ENSP00000383225:p.Ser223Pro	Somatic	42	1		WXS	Illumina HiSeq	.	53	3	NM_198687	Q08AS0	Missense_Mutation	SNP	ENST00000400374.3	37	CCDS42957.1	.	.	.	.	.	.	.	.	.	.	N	8.649	0.897850	0.17686	.	.	ENSG00000215454	ENST00000400374	T	0.01388	4.95	2.9	-3.25	0.05079	.	.	.	.	.	T	0.00440	0.0014	N	0.00368	-1.59	0.20926	N	0.999826	B	0.02656	0.0	B	0.04013	0.001	T	0.45425	-0.9262	9	0.18276	T	0.48	.	4.3087	0.10960	0.0:0.2984:0.1843:0.5173	.	223	P60372	KR104_HUMAN	P	223	ENSP00000383225:S223P	ENSP00000383225:S223P	S	+	1	0	KRTAP10-4	44818730	0.000000	0.05858	0.609000	0.28983	0.851000	0.48451	-2.984000	0.00661	-0.677000	0.05231	-0.552000	0.04208	TCC	.		0.637	KRTAP10-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128045.1	NM_198687	
GTDC1	79712	hgsc.bcm.edu	37	2	144709619	144709619	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr2:144709619G>T	ENST00000392869.2	-	10	1375	c.1223C>A	c.(1222-1224)cCt>cAt	p.P408H	GTDC1_ENST00000241391.5_Missense_Mutation_p.P323H|GTDC1_ENST00000344850.4_Missense_Mutation_p.P408H|GTDC1_ENST00000409214.1_Missense_Mutation_p.P408H|GTDC1_ENST00000542155.1_Missense_Mutation_p.P408H|GTDC1_ENST00000392867.3_Missense_Mutation_p.P323H|AC016910.1_ENST00000422799.1_RNA|GTDC1_ENST00000409298.1_Missense_Mutation_p.P290H|GTDC1_ENST00000463875.2_Missense_Mutation_p.P279H	NM_001284234.1	NP_001271163.1	Q4AE62	GTDC1_HUMAN	glycosyltransferase-like domain containing 1	408					biosynthetic process (GO:0009058)		transferase activity, transferring glycosyl groups (GO:0016757)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(17)|ovary(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.0914)		AAGCTGTTCAGGTGTAGAATA	0.323																																					p.P408H		.											.	.	.	0			c.C1223A						.						83.0	87.0	86.0					2																	144709619		2203	4297	6500	SO:0001583	missense	79712	exon11			TGTTCAGGTGTAG	AY281366	CCDS2185.1, CCDS33300.1, CCDS63029.1, CCDS74582.1, CCDS74583.1	2q22.3	2013-02-22			ENSG00000121964	ENSG00000121964		"""Glycosyltransferase group 1 domain containing"""	20887	protein-coding gene	gene with protein product	"""mannosyltransferase-like"""	610165				15068588, 21821951	Standard	NM_024659		Approved	FLJ11753, Hmat-Xa	uc010fnn.3	Q4AE62	OTTHUMG00000131835	ENST00000392869.2:c.1223C>A	2.37:g.144709619G>T	ENSP00000376608:p.Pro408His	Somatic	75	0		WXS	Illumina HiSeq	.	86	4	NM_001006636	A8K5P2|D3DP81|Q53SM7|Q53TC5|Q6P7E7|Q6PJB6|Q6WKW6|Q9HAE5	Missense_Mutation	SNP	ENST00000392869.2	37	CCDS33300.1	.	.	.	.	.	.	.	.	.	.	G	15.32	2.797709	0.50208	.	.	ENSG00000121964	ENST00000392869;ENST00000409214;ENST00000392867;ENST00000409298;ENST00000542155;ENST00000241391;ENST00000344850;ENST00000463875	T;T;T;T;T;T;T;T	0.81415	0.81;0.81;0.89;-1.49;0.81;0.89;0.81;0.78	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	D	0.88731	0.6516	M	0.63428	1.95	0.80722	D	1	D;D;D;D	0.89917	1.0;0.996;1.0;1.0	D;D;D;D	0.97110	0.999;0.927;0.999;1.0	D	0.88218	0.2895	10	0.49607	T	0.09	-13.8718	19.3137	0.94202	0.0:0.0:1.0:0.0	.	408;323;290;408	G1UFN1;Q4AE62-2;B8ZZ45;Q4AE62	.;.;.;GTDC1_HUMAN	H	408;408;323;290;408;323;408;279	ENSP00000376608:P408H;ENSP00000386581:P408H;ENSP00000376606:P323H;ENSP00000386691:P290H;ENSP00000438323:P408H;ENSP00000241391:P323H;ENSP00000339750:P408H;ENSP00000437964:P279H	ENSP00000241391:P323H	P	-	2	0	GTDC1	144426089	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.399000	0.97285	2.634000	0.89283	0.650000	0.86243	CCT	.		0.323	GTDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254779.2	NM_024659	
APBB1	322	hgsc.bcm.edu	37	11	6432092	6432092	+	Missense_Mutation	SNP	C	C	A	rs145320037		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr11:6432092C>A	ENST00000609360.1	-	2	585	c.486G>T	c.(484-486)gaG>gaT	p.E162D	APBB1_ENST00000389906.2_Missense_Mutation_p.E162D|APBB1_ENST00000311051.3_Missense_Mutation_p.E162D|APBB1_ENST00000299402.6_Missense_Mutation_p.E162D	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)	162	Glu-rich.				apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)	p.E162D(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		catcatcatcctcctcctcct	0.637																																					p.E162D	GBM(147;1810 2556 5672 39622)	.											APBB1,NS,carcinoma,0,1	APBB1	0	1	Substitution - Missense(1)	prostate(1)	c.G486T						.						35.0	35.0	35.0					11																	6432092		2201	4296	6497	SO:0001583	missense	322	exon2			ATCATCCTCCTCC	L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213		ENST00000609360.1:c.486G>T	11.37:g.6432092C>A	ENSP00000477213:p.Glu162Asp	Somatic	24	0		WXS	Illumina HiSeq	.	25	2	NM_001164	A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Missense_Mutation	SNP	ENST00000609360.1	37		.	.	.	.	.	.	.	.	.	.	C	0.439	-0.899741	0.02472	.	.	ENSG00000166313	ENST00000299402;ENST00000311051;ENST00000389906	T;T;T	0.14893	2.47;2.47;2.47	4.85	-4.93	0.03066	.	0.650451	0.13993	N	0.348689	T	0.05318	0.0141	N	0.08118	0	0.27333	N	0.956714	B	0.10296	0.003	B	0.10450	0.005	T	0.38134	-0.9675	10	0.12766	T	0.61	-7.4359	4.4462	0.11598	0.2593:0.2348:0.0:0.5059	.	162	O00213-2	.	D	162	ENSP00000299402:E162D;ENSP00000311912:E162D;ENSP00000374556:E162D	ENSP00000299402:E162D	E	-	3	2	APBB1	6388668	0.040000	0.19996	0.894000	0.35097	0.055000	0.15305	-0.394000	0.07296	-1.017000	0.03367	-0.556000	0.04195	GAG	0.000		0.637	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1	NM_001164	
TLK2	11011	hgsc.bcm.edu	37	17	60679483	60679483	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr17:60679483G>T	ENST00000326270.9	+	20	2135	c.1867G>T	c.(1867-1869)Gat>Tat	p.D623Y	TLK2_ENST00000542523.1_Missense_Mutation_p.D569Y|TLK2_ENST00000346027.5_Missense_Mutation_p.D601Y|TLK2_ENST00000582809.1_Missense_Mutation_p.D452Y|TLK2_ENST00000343388.7_Missense_Mutation_p.D569Y	NM_001284333.1	NP_001271262.1	Q86UE8	TLK2_HUMAN	tousled-like kinase 2	623	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|negative regulation of autophagy (GO:0010507)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	intermediate filament (GO:0005882)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(4)|large_intestine(6)|liver(2)|lung(10)|prostate(1)|stomach(1)|urinary_tract(1)	39						CATGGATGATGATAGCTACAA	0.388																																					p.D601Y		.											TLK2_ENST00000346027,right_upper_lobe,carcinoma,0,3	TLK2_ENST00000346027	0	0			c.G1801T						.						99.0	92.0	95.0					17																	60679483		2203	4297	6500	SO:0001583	missense	11011	exon19			GATGATGATAGCT	AB004884	CCDS11633.1, CCDS45753.1, CCDS62283.1	17q23	2008-07-18							11842	protein-coding gene	gene with protein product		608439				9427565, 10523312	Standard	NM_006852		Approved	PKU-ALPHA, MGC44450	uc002izz.4	Q86UE8		ENST00000326270.9:c.1867G>T	17.37:g.60679483G>T	ENSP00000316512:p.Asp623Tyr	Somatic	58	0		WXS	Illumina HiSeq	.	62	3	NM_006852	D3DU07|Q9UKI7|Q9Y4F7	Missense_Mutation	SNP	ENST00000326270.9	37		.	.	.	.	.	.	.	.	.	.	G	15.18	2.756303	0.49362	.	.	ENSG00000146872	ENST00000346027;ENST00000343388;ENST00000326270;ENST00000542523	T;T;T;T	0.20332	2.08;2.08;2.08;2.08	5.78	5.78	0.91487	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.41143	0.1146	L	0.39397	1.21	0.80722	D	1	D;D;D;D	0.89917	1.0;0.997;0.996;0.997	D;D;D;D	0.91635	0.999;0.973;0.964;0.984	T	0.12293	-1.0553	10	0.87932	D	0	.	18.996	0.92813	0.0:0.0:1.0:0.0	.	623;569;601;601	Q86UE8;Q86UE8-3;Q86UE8-2;D3DU05	TLK2_HUMAN;.;.;.	Y	601;569;623;569	ENSP00000275780:D601Y;ENSP00000340800:D569Y;ENSP00000316512:D623Y;ENSP00000442311:D569Y	ENSP00000316512:D623Y	D	+	1	0	TLK2	58033215	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.726000	0.93360	0.561000	0.74099	GAT	.		0.388	TLK2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000445140.1	NM_006852	
KIAA0355	9710	hgsc.bcm.edu;bcgsc.ca	37	19	34832636	34832636	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:34832636G>T	ENST00000299505.6	+	10	2670	c.1797G>T	c.(1795-1797)agG>agT	p.R599S		NM_014686.3	NP_055501.2	O15063	K0355_HUMAN	KIAA0355	599										breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	41	Esophageal squamous(110;0.162)					ATTTCCCCAGGACTACAGACC	0.448																																					p.R599S		.											.	.	.	0			c.G1797T						.						66.0	66.0	66.0					19																	34832636		2203	4300	6503	SO:0001583	missense	9710	exon10			CCCCAGGACTACA		CCDS12436.1	19q13.12	2012-11-29			ENSG00000166398	ENSG00000166398			29016	protein-coding gene	gene with protein product						9205841	Standard	NM_014686		Approved		uc002nvd.4	O15063	OTTHUMG00000180505	ENST00000299505.6:c.1797G>T	19.37:g.34832636G>T	ENSP00000299505:p.Arg599Ser	Somatic	60	0		WXS	Illumina HiSeq	.	65	4	NM_014686	Q2M3W4	Missense_Mutation	SNP	ENST00000299505.6	37	CCDS12436.1	.	.	.	.	.	.	.	.	.	.	G	15.39	2.820293	0.50633	.	.	ENSG00000166398	ENST00000299505	T	0.24350	1.86	5.43	4.38	0.52667	.	0.254953	0.43919	D	0.000511	T	0.34250	0.0891	N	0.24115	0.695	0.49213	D	0.999763	D	0.57899	0.981	D	0.69142	0.962	T	0.16247	-1.0409	10	0.87932	D	0	-16.9448	11.6544	0.51309	0.0913:0.0:0.9087:0.0	.	599	O15063	K0355_HUMAN	S	599	ENSP00000299505:R599S	ENSP00000299505:R599S	R	+	3	2	KIAA0355	39524476	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	3.549000	0.53681	1.330000	0.45394	0.655000	0.94253	AGG	.		0.448	KIAA0355-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451678.4	NM_014686	
PRKCD	5580	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	53217486	53217486	+	Missense_Mutation	SNP	A	A	C			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr3:53217486A>C	ENST00000394729.2	+	8	1004	c.676A>C	c.(676-678)Aac>Cac	p.N226H	PRKCD_ENST00000330452.3_Missense_Mutation_p.N226H	NM_212539.1	NP_997704.1	Q05655	KPCD_HUMAN	protein kinase C, delta	226					activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular senescence (GO:0090398)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-10 production (GO:0032613)|interleukin-12 production (GO:0032615)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|mRNA metabolic process (GO:0016071)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of filopodium assembly (GO:0051490)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein binding (GO:0032091)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil activation (GO:0042119)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of glucosylceramide catabolic process (GO:2000753)|positive regulation of phospholipid scramblase activity (GO:1900163)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of sphingomyelin catabolic process (GO:2000755)|positive regulation of superoxide anion generation (GO:0032930)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of receptor activity (GO:0010469)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|termination of signal transduction (GO:0023021)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|insulin receptor substrate binding (GO:0043560)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Ovarian(412;0.0728)		OV - Ovarian serous cystadenocarcinoma(275;3.58e-08)|BRCA - Breast invasive adenocarcinoma(193;0.000142)|Kidney(197;0.00153)|KIRC - Kidney renal clear cell carcinoma(197;0.00173)	Ingenol Mebutate(DB05013)|Tamoxifen(DB00675)	AGAACGCTTCAACATCGACAT	0.587																																					p.N226H		.											.	.	.	0			c.A676C						.						156.0	125.0	135.0					3																	53217486		2203	4300	6503	SO:0001583	missense	5580	exon8			CGCTTCAACATCG		CCDS2870.1	3p21.31	2009-07-10			ENSG00000163932	ENSG00000163932	2.7.11.1		9399	protein-coding gene	gene with protein product		176977				8188219	Standard	NM_006254		Approved		uc003dgm.3	Q05655	OTTHUMG00000133659	ENST00000394729.2:c.676A>C	3.37:g.53217486A>C	ENSP00000378217:p.Asn226His	Somatic	62	0		WXS	Illumina HiSeq	.	43	31	NM_212539	B0KZ81|B2R834|Q15144|Q86XJ6	Missense_Mutation	SNP	ENST00000394729.2	37	CCDS2870.1	.	.	.	.	.	.	.	.	.	.	A	15.31	2.794825	0.50102	.	.	ENSG00000163932	ENST00000394729;ENST00000330452	D;D	0.83837	-1.77;-1.77	5.06	5.06	0.68205	.	0.218173	0.56097	D	0.000040	T	0.81545	0.4845	M	0.73962	2.25	0.49687	D	0.999814	B	0.12630	0.006	B	0.15484	0.013	T	0.79344	-0.1842	10	0.56958	D	0.05	.	10.4572	0.44557	0.8368:0.1632:0.0:0.0	.	226	Q05655	KPCD_HUMAN	H	226	ENSP00000378217:N226H;ENSP00000331602:N226H	ENSP00000331602:N226H	N	+	1	0	PRKCD	53192526	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.142000	0.71750	1.914000	0.55421	0.460000	0.39030	AAC	.		0.587	PRKCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257818.1		
ZNF234	10780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	44660536	44660536	+	Missense_Mutation	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:44660536C>T	ENST00000426739.2	+	6	625	c.367C>T	c.(367-369)Cgg>Tgg	p.R123W	ZNF234_ENST00000592437.1_Missense_Mutation_p.R123W	NM_006630.2	NP_006621.1	Q14588	ZN234_HUMAN	zinc finger protein 234	123	KRNB.				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)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)	23		Prostate(69;0.0435)				AAGTATTTCTCGGTTCCCCAG	0.413																																					p.R123W		.											.	.	.	0			c.C367T						.						57.0	59.0	58.0					19																	44660536		1957	4159	6116	SO:0001583	missense	10780	exon6			ATTTCTCGGTTCC	X78927	CCDS46101.1	19q13	2013-01-08				ENSG00000263002		"""Zinc fingers, C2H2-type"", ""-"""	13027	protein-coding gene	gene with protein product		604750		ZNF269		7865130	Standard	NM_006630		Approved	HZF4	uc002oyl.4	Q14588		ENST00000426739.2:c.367C>T	19.37:g.44660536C>T	ENSP00000400878:p.Arg123Trp	Somatic	72	0		WXS	Illumina HiSeq	.	73	24	NM_006630	A8K1C8|Q96IR4|Q9NS45|Q9NYT7	Missense_Mutation	SNP	ENST00000426739.2	37	CCDS46101.1	.	.	.	.	.	.	.	.	.	.	C	10.82	1.459553	0.26248	.	.	ENSG00000167380	ENST00000426739	T	0.05786	3.39	3.12	-0.302	0.12796	.	.	.	.	.	T	0.02418	0.0074	N	0.08118	0	0.09310	N	1	P	0.35107	0.484	B	0.15870	0.014	T	0.42531	-0.9446	9	0.72032	D	0.01	.	4.7632	0.13118	0.0:0.5761:0.1935:0.2304	.	123	Q14588	ZN234_HUMAN	W	123	ENSP00000400878:R123W	ENSP00000400878:R123W	R	+	1	2	ZNF226	49352376	0.000000	0.05858	0.000000	0.03702	0.211000	0.24417	0.337000	0.19841	0.031000	0.15407	0.591000	0.81541	CGG	.		0.413	ZNF234-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460586.2		
MT-ND2	4536	hgsc.bcm.edu;broad.mit.edu	37	M	2833	2833	+	5'Flank	SNP	A	A	C			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chrM:2833A>C	ENST00000361453.3	+	0	0				MT-TN_ENST00000387400.1_RNA|MT-TV_ENST00000387342.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TF_ENST00000387314.1_RNA|MT-ND1_ENST00000361390.2_5'Flank|MT-TI_ENST00000387365.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TA_ENST00000387392.1_RNA			P03891	NU2M_HUMAN	mitochondrially encoded NADH dehydrogenase 2						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|lung(1)	3						CCTCGGAGCAGAACCCAACCT	0.428																																					.		.											.	.	.	0			.						.																																			SO:0001631	upstream_gene_variant	6053	.			AGCAGAACCCAAC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198763	ENSG00000198763	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7456	protein-coding gene	gene with protein product	"""complex I ND2 subunit"", ""NADH-ubiquinone oxidoreductase chain 2"""	516001	"""NADH dehydrogenase 2"""	MTND2			Standard			Approved	ND2, NAD2		P03891			M.37:g.2833A>C	Exception_encountered	Somatic	525	0		WXS	Illumina HiSeq	.	562	129	.	Q34769|Q9TGI0|Q9TGI1|Q9TGI2|Q9TGI3|Q9TGI4	RNA	SNP	ENST00000361453.3	37																																																																																				.		0.428	MT-ND2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024027	
ACAD8	27034	hgsc.bcm.edu	37	11	134128487	134128487	+	Missense_Mutation	SNP	G	G	T	rs35423297		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr11:134128487G>T	ENST00000281182.4	+	4	565	c.459G>T	c.(457-459)gaG>gaT	p.E153D	ACAD8_ENST00000524547.1_Intron|ACAD8_ENST00000543332.1_Missense_Mutation_p.E55D|ACAD8_ENST00000537423.1_Missense_Mutation_p.E76D|ACAD8_ENST00000374752.4_Intron	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8	153					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|lipid metabolic process (GO:0006629)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)	p.E153D(1)		endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)	Flavin adenine dinucleotide(DB03147)	GTACCATGGAGAAGTTTGCTT	0.488																																					p.E153D	GBM(65;238 1125 33403 41853 48889)	.											ACAD8,rectum,carcinoma,0,1	ACAD8	0	1	Substitution - Missense(1)	large_intestine(1)	c.G459T						.						129.0	90.0	103.0					11																	134128487		2201	4297	6498	SO:0001583	missense	27034	exon4			CATGGAGAAGTTT	AF126245	CCDS8498.1	11q25	2014-09-17	2010-04-30		ENSG00000151498	ENSG00000151498			87	protein-coding gene	gene with protein product		604773	"""acyl-Coenzyme A dehydrogenase family, member 8"""			10524212	Standard	NM_014384		Approved		uc001qhk.3	Q9UKU7	OTTHUMG00000167177	ENST00000281182.4:c.459G>T	11.37:g.134128487G>T	ENSP00000281182:p.Glu153Asp	Somatic	61	0		WXS	Illumina HiSeq	.	18	2	NM_014384	B7Z5W4|Q6ZWP6|Q9BUS8	Missense_Mutation	SNP	ENST00000281182.4	37	CCDS8498.1	.	.	.	.	.	.	.	.	.	.	G	13.52	2.260296	0.39995	.	.	ENSG00000151498	ENST00000281182;ENST00000537423;ENST00000543332;ENST00000537915	D;D;D	0.99201	-5.55;-5.55;-5.55	5.56	5.56	0.83823	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.099177	0.64402	D	0.000002	D	0.96355	0.8811	L	0.37507	1.11	0.43988	D	0.996683	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.001	B;B;B;B;B	0.10450	0.003;0.005;0.001;0.001;0.005	D	0.91859	0.5498	10	0.37606	T	0.19	.	5.7791	0.18295	0.1166:0.0:0.6944:0.189	.	94;76;55;55;153	B7Z767;B7Z5W4;B7Z9L5;B7Z7F1;Q9UKU7	.;.;.;.;ACAD8_HUMAN	D	153;76;55;115	ENSP00000281182:E153D;ENSP00000443763:E76D;ENSP00000438302:E55D	ENSP00000281182:E153D	E	+	3	2	ACAD8	133633697	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.909000	0.39917	2.605000	0.88082	0.655000	0.94253	GAG	.		0.488	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384	
DPY19L3	147991	hgsc.bcm.edu	37	19	32968452	32968452	+	Silent	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:32968452G>A	ENST00000342179.5	+	17	1937	c.1722G>A	c.(1720-1722)gtG>gtA	p.V574V	DPY19L3_ENST00000392250.2_Silent_p.V574V|DPY19L3_ENST00000586987.1_Silent_p.V574V	NM_207325.2	NP_997208.2	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3 (C. elegans)	574						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(4)|pancreas(1)	32	Esophageal squamous(110;0.162)					GAAAGGCTGTGTTTGCGGGAA	0.478																																					p.V574V		.											.	.	.	0			c.G1722A						.						106.0	97.0	100.0					19																	32968452		2203	4300	6503	SO:0001819	synonymous_variant	147991	exon17			GGCTGTGTTTGCG		CCDS12422.1	19q13.11	2008-02-05				ENSG00000178904			27120	protein-coding gene	gene with protein product		613894					Standard	NM_207325		Approved		uc002ntg.3	Q6ZPD9		ENST00000342179.5:c.1722G>A	19.37:g.32968452G>A		Somatic	90	0		WXS	Illumina HiSeq	.	99	4	NM_001172774	Q68DC7|Q6ZTB7|Q6ZTS2	Silent	SNP	ENST00000342179.5	37	CCDS12422.1																																																																																			.		0.478	DPY19L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450311.1	NM_207325	
COL6A3	1293	hgsc.bcm.edu	37	2	238283545	238283545	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr2:238283545G>T	ENST00000295550.4	-	8	3641	c.3189C>A	c.(3187-3189)gaC>gaA	p.D1063E	COL6A3_ENST00000353578.4_Missense_Mutation_p.D857E|COL6A3_ENST00000409809.1_Missense_Mutation_p.D857E|COL6A3_ENST00000346358.4_Missense_Mutation_p.D863E|COL6A3_ENST00000392004.3_Missense_Mutation_p.D857E|COL6A3_ENST00000472056.1_Missense_Mutation_p.D456E|COL6A3_ENST00000347401.3_Missense_Mutation_p.D862E|COL6A3_ENST00000392003.2_Missense_Mutation_p.D656E	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1063	Nonhelical region.|VWFA 6. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CGCGGACCCGGTCCTGGCCCA	0.592																																					p.D1063E		.											COL6A3_ENST00000392004,NS,carcinoma,0,2	COL6A3_ENST00000392004	0	0			c.C3189A						.						57.0	57.0	57.0					2																	238283545		2203	4300	6503	SO:0001583	missense	1293	exon8			GACCCGGTCCTGG	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.3189C>A	2.37:g.238283545G>T	ENSP00000295550:p.Asp1063Glu	Somatic	27	0		WXS	Illumina HiSeq	.	23	2	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	G	16.22	3.060470	0.55432	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000392003	D;D;D;D;D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69;-1.69;-1.69;-1.69;-1.69	5.33	1.16	0.20824	von Willebrand factor, type A (3);	0.103755	0.41712	D	0.000839	D	0.87075	0.6087	M	0.62266	1.93	0.44012	D	0.996729	D;D;P;D;P	0.63880	0.993;0.97;0.868;0.991;0.722	D;P;P;D;B	0.71414	0.973;0.868;0.491;0.937;0.393	D	0.84811	0.0790	10	0.52906	T	0.07	.	9.8847	0.41255	0.2959:0.0:0.7041:0.0	.	456;656;857;857;1063	E9PFQ6;A8MT30;E9PGQ9;P12111-2;P12111	.;.;.;.;CO6A3_HUMAN	E	1063;862;857;456;857;863;857;656	ENSP00000295550:D1063E;ENSP00000315609:D862E;ENSP00000315873:D857E;ENSP00000418285:D456E;ENSP00000386844:D857E;ENSP00000295546:D863E;ENSP00000375861:D857E;ENSP00000375860:D656E	ENSP00000295550:D1063E	D	-	3	2	COL6A3	237948284	1.000000	0.71417	0.514000	0.27761	0.827000	0.46813	2.739000	0.47409	0.246000	0.21394	0.655000	0.94253	GAC	.		0.592	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
SNIP1	79753	hgsc.bcm.edu	37	1	38006254	38006254	+	Missense_Mutation	SNP	G	G	A	rs143428642		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr1:38006254G>A	ENST00000296215.6	-	3	502	c.430C>T	c.(430-432)Cgg>Tgg	p.R144W	SNIP1_ENST00000468040.1_5'UTR	NM_024700.3	NP_078976.2	Q8TAD8	SNIP1_HUMAN	Smad nuclear interacting protein 1	144	Arg-rich.				I-kappaB kinase/NF-kappaB signaling (GO:0007249)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R144W(1)		breast(2)|cervix(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(586;0.0393)				GAATGGCCCCGGTGTCTGTCC	0.607																																					p.R144W		.											SNIP1,rectum,carcinoma,0,1	SNIP1	0	1	Substitution - Missense(1)	large_intestine(1)	c.C430T						.	G	TRP/ARG	4,4402	8.1+/-20.4	0,4,2199	129.0	131.0	130.0		430	3.3	1.0	1	dbSNP_134	130	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SNIP1	NM_024700.2	101	0,5,6498	AA,AG,GG		0.0116,0.0908,0.0384	probably-damaging	144/397	38006254	5,13001	2203	4300	6503	SO:0001583	missense	79753	exon3			GGCCCCGGTGTCT		CCDS419.1	1p34.3	2010-07-06			ENSG00000163877	ENSG00000163877			30587	protein-coding gene	gene with protein product		608241				10887155, 15378006	Standard	NM_024700		Approved		uc001cbi.4	Q8TAD8	OTTHUMG00000004225	ENST00000296215.6:c.430C>T	1.37:g.38006254G>A	ENSP00000296215:p.Arg144Trp	Somatic	48	0		WXS	Illumina HiSeq	.	48	3	NM_024700	Q96SP9|Q9H9T7	Missense_Mutation	SNP	ENST00000296215.6	37	CCDS419.1	.	.	.	.	.	.	.	.	.	.	G	16.01	3.000786	0.54254	9.08E-4	1.16E-4	ENSG00000163877	ENST00000296215;ENST00000436196	T	0.15256	2.44	5.25	3.34	0.38264	.	0.401658	0.24638	N	0.036829	T	0.11707	0.0285	L	0.27053	0.805	0.58432	D	0.999992	B	0.22541	0.071	B	0.12156	0.007	T	0.07424	-1.0773	10	0.87932	D	0	-12.1472	8.5955	0.33712	0.0754:0.0:0.6288:0.2958	.	144	Q8TAD8	SNIP1_HUMAN	W	144;128	ENSP00000296215:R144W	ENSP00000296215:R144W	R	-	1	2	SNIP1	37778841	0.895000	0.30542	1.000000	0.80357	0.678000	0.39670	1.070000	0.30653	0.734000	0.32515	-0.150000	0.13652	CGG	0.000		0.607	SNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012169.2	NM_024700	
CSDC2	27254	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	22	41970815	41970815	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr22:41970815G>T	ENST00000306149.7	+	4	922	c.378G>T	c.(376-378)aaG>aaT	p.K126N		NM_014460.3	NP_055275.1	Q9Y534	CSDC2_HUMAN	cold shock domain containing C2, RNA binding	126	CSD.				mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			prostate(2)|upper_aerodigestive_tract(1)	3						AGAACCAGAAGTTCCAGGCCG	0.637																																					p.K126N	NSCLC(181;294 2110 12667 14717 31090)	.											.	.	.	0			c.G378T						.						92.0	65.0	74.0					22																	41970815		2203	4300	6503	SO:0001583	missense	27254	exon4			CCAGAAGTTCCAG	AL834417	CCDS14019.1	22q13.2	2006-02-24			ENSG00000172346	ENSG00000172346			30359	protein-coding gene	gene with protein product						8573167, 12767259	Standard	NM_014460		Approved	PIPPin	uc003bak.1	Q9Y534	OTTHUMG00000150967	ENST00000306149.7:c.378G>T	22.37:g.41970815G>T	ENSP00000302485:p.Lys126Asn	Somatic	68	0		WXS	Illumina HiSeq	.	56	4	NM_014460	Q8ND37	Missense_Mutation	SNP	ENST00000306149.7	37	CCDS14019.1	.	.	.	.	.	.	.	.	.	.	g	27.4	4.827392	0.90955	.	.	ENSG00000172346	ENST00000306149	.	.	.	5.02	5.02	0.67125	Cold shock protein (1);Nucleic acid-binding, OB-fold-like (1);Cold-shock protein, DNA-binding (1);Nucleic acid-binding, OB-fold (1);	0.000000	0.85682	D	0.000000	T	0.80149	0.4570	M	0.87269	2.87	0.80722	D	1	D	0.71674	0.998	D	0.79108	0.992	T	0.82874	-0.0241	9	0.72032	D	0.01	.	11.9414	0.52903	0.079:0.0:0.921:0.0	.	126	Q9Y534	CSDC2_HUMAN	N	126	.	ENSP00000302485:K126N	K	+	3	2	CSDC2	40300761	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.635000	0.67841	2.604000	0.88044	0.651000	0.88453	AAG	.		0.637	CSDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320689.1	NM_014460	
CFAP44	55779	hgsc.bcm.edu	37	3	113010415	113010415	+	Missense_Mutation	SNP	C	C	T	rs549546748		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr3:113010415C>T	ENST00000393845.2	-	35	5620	c.5554G>A	c.(5554-5556)Gca>Aca	p.A1852T	WDR52_ENST00000308346.6_3'UTR	NM_001164496.1	NP_001157968.1														breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						CAAAGGTCTGCGGGCTGTATC	0.438													C|||	1	0.000199681	0.0	0.0	5008	,	,		19977	0.0		0.0	False		,,,				2504	0.001				p.A1852T		.											.	.	.	0			c.G5554A						.						205.0	199.0	201.0					3																	113010415		692	1591	2283	SO:0001583	missense	55779	exon35			GGTCTGCGGGCTG																												ENST00000393845.2:c.5554G>A	3.37:g.113010415C>T	ENSP00000377428:p.Ala1852Thr	Somatic	78	0		WXS	Illumina HiSeq	.	61	4	NM_001164496		Missense_Mutation	SNP	ENST00000393845.2	37	CCDS54624.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.73|10.73	1.432321|1.432321	0.25813|0.25813	.|.	.|.	ENSG00000206530|ENSG00000206530	ENST00000393845|ENST00000465636	T|.	0.10668|.	2.85|.	5.23|5.23	-10.5|-10.5	0.00291|0.00291	.|.	0.528659|.	0.14262|.	U|.	0.330761|.	T|T	0.10766|0.10766	0.0263|0.0263	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.10965|0.10965	-1.0607|-1.0607	10|5	0.32370|.	T|.	0.25|.	0.0741|0.0741	1.8868|1.8868	0.03240|0.03240	0.2161:0.2926:0.3423:0.149|0.2161:0.2926:0.3423:0.149	.|.	1852|.	Q96MT7-2|.	.|.	T|H	1852|988	ENSP00000377428:A1852T|.	ENSP00000377428:A1852T|.	A|R	-|-	1|2	0|0	WDR52|WDR52	114493105|114493105	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.017000|0.017000	0.09413|0.09413	-1.819000|-1.819000	0.01716|0.01716	-2.099000|-2.099000	0.00849|0.00849	-0.459000|-0.459000	0.05422|0.05422	GCA|CGC	.		0.438	WDR52-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
C14orf159	80017	hgsc.bcm.edu	37	14	91666203	91666203	+	Silent	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr14:91666203C>T	ENST00000523771.1	+	11	1986	c.1383C>T	c.(1381-1383)gaC>gaT	p.D461D	C14orf159_ENST00000518868.1_Silent_p.D466D|C14orf159_ENST00000525393.2_Silent_p.D337D|C14orf159_ENST00000256324.10_Silent_p.D466D|C14orf159_ENST00000523816.1_Silent_p.D461D|C14orf159_ENST00000412671.2_Silent_p.D466D|C14orf159_ENST00000521077.2_Silent_p.D466D|C14orf159_ENST00000428926.2_Silent_p.D461D|C14orf159_ENST00000522322.1_Silent_p.D461D|C14orf159_ENST00000520328.1_Silent_p.D449D			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	461						mitochondrion (GO:0005739)		p.D461D(1)		NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		ACCCCATTGACGATCTTTTTC	0.483																																					p.D466D		.											C14orf159,colon,carcinoma,0,2	C14orf159	0	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C1398T						.						185.0	173.0	177.0					14																	91666203		2203	4300	6503	SO:0001819	synonymous_variant	80017	exon11			CATTGACGATCTT	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.1383C>T	14.37:g.91666203C>T		Somatic	79	0		WXS	Illumina HiSeq	.	33	2	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Silent	SNP	ENST00000523771.1	37	CCDS32141.1	.	.	.	.	.	.	.	.	.	.	C	0.657	-0.807161	0.02819	.	.	ENSG00000133943	ENST00000522816	.	.	.	5.25	-3.47	0.04753	.	.	.	.	.	T	0.62865	0.2463	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60239	-0.7302	4	.	.	.	.	13.4582	0.61212	0.0:0.1255:0.0:0.8745	.	.	.	.	M	62	.	.	T	+	2	0	C14orf159	90735956	0.066000	0.20996	0.000000	0.03702	0.082000	0.17680	-0.774000	0.04684	-0.945000	0.03681	0.563000	0.77884	ACG	.		0.483	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	
PPP1R13B	23368	hgsc.bcm.edu	37	14	104202439	104202439	+	Missense_Mutation	SNP	G	G	T	rs371359449		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr14:104202439G>T	ENST00000202556.9	-	16	3414	c.3132C>A	c.(3130-3132)gaC>gaA	p.D1044E	PPP1R13B_ENST00000423488.2_3'UTR|PPP1R13B_ENST00000555391.1_5'UTR	NM_015316.2	NP_056131.2	Q96KQ4	ASPP1_HUMAN	protein phosphatase 1, regulatory subunit 13B	1044	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.D1044D(1)		endometrium(6)|kidney(2)|large_intestine(7)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)				TGGTGAGGGCGTCCCCTTCGT	0.607																																					p.D1044E		.											PPP1R13B,colon,carcinoma,0,1	PPP1R13B	0	1	Substitution - coding silent(1)	large_intestine(1)	c.C3132A						.						120.0	125.0	124.0					14																	104202439		2130	4225	6355	SO:0001583	missense	23368	exon16			GAGGGCGTCCCCT	AB018314	CCDS41997.1	14q32.33	2013-01-10	2011-10-04		ENSG00000088808	ENSG00000088808		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	14950	protein-coding gene	gene with protein product		606455	"""protein phosphatase 1, regulatory (inhibitor) subunit 13B"""			9872452	Standard	NM_015316		Approved	p53BP2-like, KIAA0771, p85, ASPP1	uc001yof.1	Q96KQ4	OTTHUMG00000171647	ENST00000202556.9:c.3132C>A	14.37:g.104202439G>T	ENSP00000202556:p.Asp1044Glu	Somatic	58	0		WXS	Illumina HiSeq	.	47	2	NM_015316	B2RMX5|O94870	Missense_Mutation	SNP	ENST00000202556.9	37	CCDS41997.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.178155	0.78564	.	.	ENSG00000088808	ENST00000202556	T	0.59364	0.27	5.39	-7.32	0.01436	Src homology-3 domain (5);	0.045961	0.85682	D	0.000000	T	0.53899	0.1825	N	0.20483	0.58	0.80722	D	1	D	0.59357	0.985	D	0.69824	0.966	T	0.65261	-0.6211	10	0.37606	T	0.19	.	15.8601	0.79014	0.3628:0.0:0.6372:0.0	.	1044	Q96KQ4	ASPP1_HUMAN	E	1044	ENSP00000202556:D1044E	ENSP00000202556:D1044E	D	-	3	2	PPP1R13B	103272192	0.978000	0.34361	0.785000	0.31869	0.972000	0.66771	0.261000	0.18442	-1.423000	0.02002	-1.056000	0.02311	GAC	.		0.607	PPP1R13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414591.1	NM_015316	
DRD5	1816	hgsc.bcm.edu	37	4	9784785	9784785	+	Missense_Mutation	SNP	T	T	G			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr4:9784785T>G	ENST00000304374.2	+	1	1528	c.1132T>G	c.(1132-1134)Ttc>Gtc	p.F378V		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	378					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)	p.F378V(4)		NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	GTGCAGCCACTTCTGCTCCCG	0.562																																					p.F378V		.											DRD5,NS,carcinoma,0,4	DRD5	0	4	Substitution - Missense(4)	skin(2)|NS(1)|endometrium(1)	c.T1132G						.						63.0	55.0	57.0					4																	9784785		2203	4300	6503	SO:0001583	missense	1816	exon1			AGCCACTTCTGCT	X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"""GPCR / Class A : Dopamine receptors"""	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.1132T>G	4.37:g.9784785T>G	ENSP00000306129:p.Phe378Val	Somatic	27	0		WXS	Illumina HiSeq	.	27	2	NM_000798	B2R9S3|Q8NEQ8	Missense_Mutation	SNP	ENST00000304374.2	37	CCDS3405.1	.	.	.	.	.	.	.	.	.	.	t	1.422	-0.572511	0.03882	.	.	ENSG00000169676	ENST00000304374	T	0.36878	1.23	4.73	-0.492	0.12041	.	1.972870	0.02341	N	0.074845	T	0.21103	0.0508	N	0.17474	0.49	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10109	-1.0644	10	0.16420	T	0.52	.	4.5978	0.12338	0.0:0.3044:0.1738:0.5218	.	378	P21918	DRD5_HUMAN	V	378	ENSP00000306129:F378V	ENSP00000306129:F378V	F	+	1	0	DRD5	9393883	0.067000	0.21026	0.022000	0.16811	0.197000	0.23852	0.558000	0.23469	-0.022000	0.13986	-2.216000	0.00297	TTC	.		0.562	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1		
SH3BP1	23616	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	38049853	38049853	+	Missense_Mutation	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr22:38049853G>A	ENST00000357436.4	+	17	1979	c.1666G>A	c.(1666-1668)Gcc>Acc	p.A556T	SH3BP1_ENST00000599616.1_Missense_Mutation_p.A492T|Z83844.1_ENST00000456099.1_RNA	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	556					signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Melanoma(58;0.0574)					GGAGACAGCTGCCCCAGTGGA	0.662																																					p.A556T		.											.	.	.	0			c.G1666A						.						37.0	38.0	37.0					22																	38049853		2200	4300	6500	SO:0001583	missense	23616	exon17			ACAGCTGCCCCAG		CCDS13952.2	22q13.1	2011-07-04			ENSG00000100092	ENSG00000100092		"""Rho GTPase activating proteins"""	10824	protein-coding gene	gene with protein product						10591208, 12029088	Standard	NM_018957		Approved	ARHGAP43	uc003ati.3	Q9Y3L3	OTTHUMG00000030996	ENST00000357436.4:c.1666G>A	22.37:g.38049853G>A	ENSP00000350018:p.Ala556Thr	Somatic	122	0		WXS	Illumina HiSeq	.	178	114	NM_018957	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Missense_Mutation	SNP	ENST00000357436.4	37	CCDS13952.2	.	.	.	.	.	.	.	.	.	.	G	9.635	1.137372	0.21123	.	.	ENSG00000100092	ENST00000357436;ENST00000397014	T	0.16196	2.36	5.45	-1.57	0.08506	.	0.723885	0.12742	N	0.442969	T	0.07458	0.0188	N	0.17082	0.46	0.09310	N	1	B;B;B;B	0.15141	0.012;0.0;0.0;0.012	B;B;B;B	0.12156	0.007;0.001;0.001;0.007	T	0.41662	-0.9496	10	0.12766	T	0.61	.	5.0885	0.14696	0.4066:0.1424:0.451:0.0	.	470;492;556;470	E7EUD3;Q6ZT62;Q9Y3L3;Q6ZTJ5	.;.;3BP1_HUMAN;.	T	556;470	ENSP00000350018:A556T	ENSP00000350018:A556T	A	+	1	0	SH3BP1	36379799	0.000000	0.05858	0.000000	0.03702	0.647000	0.38526	-0.127000	0.10547	-0.287000	0.09064	-0.137000	0.14449	GCC	.		0.662	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957	
OR8B3	390271	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	11	124266860	124266860	+	Silent	SNP	A	A	G			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr11:124266860A>G	ENST00000354597.3	-	1	404	c.388T>C	c.(388-390)Ttg>Ctg	p.L130L		NM_001005467.1	NP_001005467.1	Q8NGG8	OR8B3_HUMAN	olfactory receptor, family 8, subfamily B, member 3	130						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		TTATACAGCAATGGATTACAG	0.458																																					p.L130L		.											.	.	.	0			c.T388C						.						49.0	43.0	45.0					11																	124266860		2201	4299	6500	SO:0001819	synonymous_variant	390271	exon1			ACAGCAATGGATT	AB065827	CCDS31709.1	11q24.1	2012-08-09			ENSG00000196661	ENSG00000196661		"""GPCR / Class A : Olfactory receptors"""	8472	protein-coding gene	gene with protein product							Standard	NM_001005467		Approved		uc010saj.2	Q8NGG8	OTTHUMG00000165983	ENST00000354597.3:c.388T>C	11.37:g.124266860A>G		Somatic	54	0		WXS	Illumina HiSeq	.	42	24	NM_001005467	Q6IFQ8|Q8NGH1	Silent	SNP	ENST00000354597.3	37	CCDS31709.1																																																																																			.		0.458	OR8B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387291.1	NM_001005467	
LRCH2	57631	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	114357150	114357150	+	Silent	SNP	T	T	C			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chrX:114357150T>C	ENST00000317135.8	-	20	2148	c.2118A>G	c.(2116-2118)gcA>gcG	p.A706A	LRCH2_ENST00000538422.1_Silent_p.A689A	NM_020871.3	NP_065922.3	Q5VUJ6	LRCH2_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 2	706	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.									breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	19						TTCGACATTTTGCCATGCTCA	0.328																																					p.A706A		.											.	.	.	0			c.A2118G						.						88.0	75.0	79.0					X																	114357150		1813	4077	5890	SO:0001819	synonymous_variant	57631	exon20			ACATTTTGCCATG	AB040928	CCDS48155.1, CCDS59175.1	Xq24	2008-02-05			ENSG00000130224	ENSG00000130224			29292	protein-coding gene	gene with protein product						10819331	Standard	NM_020871		Approved	KIAA1495	uc010nqe.3	Q5VUJ6	OTTHUMG00000022233	ENST00000317135.8:c.2118A>G	X.37:g.114357150T>C		Somatic	110	0		WXS	Illumina HiSeq	.	97	34	NM_020871	F5H2T1|Q08AD5|Q9HA88|Q9P233	Silent	SNP	ENST00000317135.8	37	CCDS48155.1																																																																																			.		0.328	LRCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057971.2	NM_020871	
THPO	7066	hgsc.bcm.edu	37	3	184090560	184090560	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr3:184090560G>T	ENST00000204615.7	-	6	1017	c.803C>A	c.(802-804)aCc>aAc	p.T268N	THPO_ENST00000421442.2_Missense_Mutation_p.D229E|EIF2B5_ENST00000444495.1_Intron|THPO_ENST00000445696.2_Missense_Mutation_p.T264N|THPO_ENST00000477594.1_5'Flank	NM_000460.2|NM_001177597.1|NM_001177598.1	NP_000451.1|NP_001171068.1|NP_001171069.1	P40225	TPO_HUMAN	thrombopoietin	268					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|myeloid cell differentiation (GO:0030099)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|thrombopoietin-mediated signaling pathway (GO:0038163)	extracellular space (GO:0005615)	growth factor activity (GO:0008083)			NS(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GGCTCCTAGGGTCCTGCGTGA	0.562																																					p.T268N		.											THPO,NS,carcinoma,0,1	THPO	0	0			c.C803A						.						165.0	174.0	171.0					3																	184090560		2203	4300	6503	SO:0001583	missense	7066	exon6			CCTAGGGTCCTGC		CCDS3265.1, CCDS54693.1	3q27	2014-01-30	2008-07-31		ENSG00000090534	ENSG00000090534		"""Endogenous ligands"""	11795	protein-coding gene	gene with protein product	"""prepro-thrombopoietin"", ""megakaryocyte stimulating factor"", ""myeloproliferative leukemia virus oncogene ligand"", ""megakaryocyte growth and development factor"", ""MPL ligand"", ""megakaryocyte colony-stimulating factor"", ""c-mpl ligand"", ""thrombopoietin nirs variant 1"""	600044		MGDF		8202154	Standard	XM_006713738		Approved	TPO, MPLLG	uc003fol.1	P40225	OTTHUMG00000156745	ENST00000204615.7:c.803C>A	3.37:g.184090560G>T	ENSP00000204615:p.Thr268Asn	Somatic	33	0		WXS	Illumina HiSeq	.	49	2	NM_000460	A1L3Y0|B7ZLR8|B9EGA8|Q13020|Q15790|Q15791|Q15792	Missense_Mutation	SNP	ENST00000204615.7	37	CCDS3265.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.782|6.782	0.513301|0.513301	0.12944|0.12944	.|.	.|.	ENSG00000090534|ENSG00000090534	ENST00000421442|ENST00000204615;ENST00000445696;ENST00000353488	T|T;T	0.38077|0.36340	1.16|1.26;1.27	4.59|4.59	3.55|3.55	0.40652|0.40652	.|Four-helical cytokine, core (1);	.|0.504141	.|0.16767	.|N	.|0.200344	T|T	0.26048|0.26048	0.0635|0.0635	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	B|P;P	0.33238|0.48503	0.403|0.911;0.856	B|P;B	0.22601|0.44561	0.04|0.453;0.266	T|T	0.08472|0.08472	-1.0720|-1.0720	9|10	0.19147|0.87932	T|D	0.46|0	-9.6195|-9.6195	6.5569|6.5569	0.22466|0.22466	0.169:0.0:0.831:0.0|0.169:0.0:0.831:0.0	.|.	229|264;268	F8W6L1|P40225-2;P40225	.|.;TPO_HUMAN	E|N	229|268;264;229	ENSP00000411704:D229E|ENSP00000204615:T268N;ENSP00000410763:T264N	ENSP00000411704:D229E|ENSP00000204615:T268N	D|T	-|-	3|2	2|0	THPO|THPO	185573254|185573254	0.059000|0.059000	0.20769|0.20769	0.070000|0.070000	0.20053|0.20053	0.414000|0.414000	0.31173|0.31173	0.882000|0.882000	0.28186|0.28186	0.891000|0.891000	0.36235|0.36235	0.467000|0.467000	0.42956|0.42956	GAC|ACC	.		0.562	THPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345554.1	NM_000460	
CCDC132	55610	hgsc.bcm.edu	37	7	92970748	92970748	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr7:92970748G>T	ENST00000305866.5	+	23	2196	c.2068G>T	c.(2068-2070)Gct>Tct	p.A690S	CCDC132_ENST00000541136.1_Missense_Mutation_p.A501S|CCDC132_ENST00000474412.1_3'UTR|CCDC132_ENST00000544910.1_Missense_Mutation_p.A660S|CCDC132_ENST00000535481.1_Missense_Mutation_p.A410S	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	690						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			GGAAGTTTCAGCTGATCCTAC	0.378																																					p.A690S		.											.	.	.	0			c.G2068T						.						94.0	95.0	95.0					7																	92970748		1956	4144	6100	SO:0001583	missense	55610	exon23			GTTTCAGCTGATC	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.2068G>T	7.37:g.92970748G>T	ENSP00000307666:p.Ala690Ser	Somatic	82	0		WXS	Illumina HiSeq	.	98	4	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	37	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	G	2.068	-0.413856	0.04799	.	.	ENSG00000004766	ENST00000305866;ENST00000544910;ENST00000541136;ENST00000535481	.	.	.	5.55	2.67	0.31697	.	0.165508	0.53938	D	0.000055	T	0.14098	0.0341	N	0.02011	-0.69	0.31730	N	0.637157	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.20338	-1.0278	9	0.10902	T	0.67	-23.076	7.5405	0.27735	0.1333:0.0:0.6294:0.2373	.	410;660;690	B4DS55;F5H5U7;Q96JG6	.;.;CC132_HUMAN	S	690;660;501;410	.	ENSP00000307666:A690S	A	+	1	0	CCDC132	92808684	0.631000	0.27164	0.932000	0.37286	0.219000	0.24729	0.867000	0.27968	0.792000	0.33850	0.655000	0.94253	GCT	.		0.378	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667	
B3GNT6	192134	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	76751719	76751719	+	Missense_Mutation	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr11:76751719C>T	ENST00000533140.1	+	2	1262	c.1124C>T	c.(1123-1125)gCg>gTg	p.A375V	B3GNT6_ENST00000354301.5_Missense_Mutation_p.A374V|B3GNT6_ENST00000421061.1_Missense_Mutation_p.A253V			O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase)	0					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)			central_nervous_system(1)|kidney(2)|lung(4)|prostate(1)	8						CACAGCCCCGCGCTCAGCTGT	0.657																																					p.A374V		.											.	.	.	0			c.C1121T						.						15.0	17.0	16.0					11																	76751719		2142	4246	6388	SO:0001583	missense	192134	exon5			GCCCCGCGCTCAG	AB073740	CCDS53681.1	11q13.4	2013-02-19			ENSG00000198488	ENSG00000198488		"""Beta 3-glycosyltransferases"""	24141	protein-coding gene	gene with protein product		615315				11821425	Standard	NM_138706		Approved	B3Gn-T6	uc021qnp.1	Q6ZMB0		ENST00000533140.1:c.1124C>T	11.37:g.76751719C>T	ENSP00000435352:p.Ala375Val	Somatic	45	0		WXS	Illumina HiSeq	.	45	17	NM_138706	Q4TTN0	Missense_Mutation	SNP	ENST00000533140.1	37	CCDS53681.1	.	.	.	.	.	.	.	.	.	.	C	11.76	1.733869	0.30684	.	.	ENSG00000198488	ENST00000533140;ENST00000354301;ENST00000421061	T;T;T	0.42513	0.97;0.97;0.97	2.9	-1.47	0.08772	.	0.669611	0.15074	U	0.282008	T	0.26666	0.0652	L	0.36672	1.1	0.09310	N	1	B	0.16166	0.016	B	0.15870	0.014	T	0.14337	-1.0476	10	0.33940	T	0.23	.	6.2067	0.20606	0.2562:0.3848:0.359:0.0	.	374	Q6ZMB0	B3GN6_HUMAN	V	375;374;253	ENSP00000435352:A375V;ENSP00000346256:A374V;ENSP00000403463:A253V	ENSP00000346256:A374V	A	+	2	0	B3GNT6	76429367	0.000000	0.05858	0.021000	0.16686	0.110000	0.19582	0.027000	0.13621	-0.325000	0.08577	0.462000	0.41574	GCG	.		0.657	B3GNT6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000382740.2	NM_138706	
SLIT2	9353	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	20535338	20535338	+	Splice_Site	SNP	T	T	C			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr4:20535338T>C	ENST00000504154.1	+	18	2084	c.1832T>C	c.(1831-1833)tTg>tCg	p.L611S	SLIT2_ENST00000503823.1_Splice_Site_p.L603S|SLIT2_ENST00000273739.5_Splice_Site_p.L615S|SLIT2_ENST00000503837.1_Splice_Site_p.L607S	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	611					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						CTCAAAACTTTGTAAGTATTT	0.388																																					p.L611S		.											.	.	.	0			c.T1832C						.						141.0	140.0	141.0					4																	20535338		2203	4300	6503	SO:0001630	splice_region_variant	9353	exon18			AAACTTTGTAAGT	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.1832+1T>C	4.37:g.20535338T>C		Somatic	123	0		WXS	Illumina HiSeq	.	144	18	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	37	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.488389	0.84854	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.80566	-1.39;-1.39;-1.39;-1.39	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.93996	0.8077	H	0.99042	4.41	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.993;0.996	D	0.96375	0.9277	10	0.87932	D	0	.	15.1788	0.72938	0.0:0.0:0.0:1.0	.	603;611	O94813-3;O94813	.;SLIT2_HUMAN	S	603;611;615;607;607	ENSP00000427548:L603S;ENSP00000422591:L611S;ENSP00000273739:L615S;ENSP00000422261:L607S	ENSP00000273739:L615S	L	+	2	0	SLIT2	20144436	1.000000	0.71417	0.985000	0.45067	0.964000	0.63967	7.942000	0.87708	1.998000	0.58463	0.459000	0.35465	TTG	.		0.388	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		Missense_Mutation
PNCK	139728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	152936621	152936621	+	Silent	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chrX:152936621G>A	ENST00000370150.1	-	8	817	c.639C>T	c.(637-639)taC>taT	p.Y213Y	PNCK_ENST00000393831.2_Silent_p.Y236Y|PNCK_ENST00000340888.3_Silent_p.Y213Y|PNCK_ENST00000370142.1_Silent_p.Y236Y|PNCK_ENST00000475172.1_5'Flank|PNCK_ENST00000370145.4_Silent_p.Y230Y|PNCK_ENST00000447676.2_Silent_p.Y296Y			Q6P2M8	KCC1B_HUMAN	pregnancy up-regulated nonubiquitous CaM kinase	213	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			breast(2)|lung(3)|skin(1)	6	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CGCTCTCGTCGTAGAAGGGGG	0.592													G|||	1	0.000264901	0.0	0.0014	3775	,	,		12507	0.0		0.0	False		,,,				2504	0.0				p.Y296Y		.											.	.	.	0			c.C888T						.						55.0	55.0	55.0					X																	152936621		2203	4300	6503	SO:0001819	synonymous_variant	139728	exon8			CTCGTCGTAGAAG	BC033746	CCDS35503.2, CCDS48189.1	Xq28	2013-10-14	2013-10-14		ENSG00000130822	ENSG00000130822			13415	protein-coding gene	gene with protein product		300680	"""pregnancy upregulated non-ubiquitously expressed CaM kinase"", ""pregnancy up-regulated non-ubiquitously expressed CaM kinase"""			12477932	Standard	NM_001039582		Approved	MGC45419, CaMK1b	uc011myu.2	Q6P2M8	OTTHUMG00000024216	ENST00000370150.1:c.639C>T	X.37:g.152936621G>A		Somatic	31	0		WXS	Illumina HiSeq	.	31	7	NM_001039582	B4DJR8|B4E1A6|B7WPG0|D3DWU7|Q8N4R0	Silent	SNP	ENST00000370150.1	37																																																																																				.		0.592	PNCK-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000061044.2	NM_198452	
RASAL3	64926	hgsc.bcm.edu	37	19	15572380	15572380	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:15572380G>T	ENST00000343625.7	-	3	452	c.367C>A	c.(367-369)Cag>Aag	p.Q123K		NM_022904.1	NP_075055.1	Q86YV0	RASL3_HUMAN	RAS protein activator like 3	123	Pro-rich.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)	Ras GTPase activator activity (GO:0005099)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|skin(1)	18						TCAGGGATCTGTGGGGTAGGG	0.617																																					p.Q123K		.											RASAL3,NS,carcinoma,0,1	RASAL3	0	0			c.C367A						.						10.0	13.0	12.0					19																	15572380		1924	4117	6041	SO:0001583	missense	64926	exon3			GGATCTGTGGGGT		CCDS46006.1	19p13.12	2008-12-18			ENSG00000105122	ENSG00000105122			26129	protein-coding gene	gene with protein product						12477932	Standard	NM_022904		Approved	FLJ21438	uc002nbe.2	Q86YV0		ENST00000343625.7:c.367C>A	19.37:g.15572380G>T	ENSP00000341905:p.Gln123Lys	Somatic	50	0		WXS	Illumina HiSeq	.	40	3	NM_022904	Q8N2T9|Q9H735	Missense_Mutation	SNP	ENST00000343625.7	37	CCDS46006.1	.	.	.	.	.	.	.	.	.	.	G	7.144	0.582314	0.13749	.	.	ENSG00000105122	ENST00000343625	T	0.24151	1.87	3.99	2.83	0.33086	.	0.778678	0.10033	U	0.724488	T	0.20170	0.0485	L	0.57536	1.79	0.23550	N	0.997437	B	0.25667	0.131	B	0.19946	0.027	T	0.42241	-0.9463	10	0.02654	T	1	.	8.1208	0.30969	0.0:0.0:0.7599:0.2401	.	123	Q86YV0	RASL3_HUMAN	K	123	ENSP00000341905:Q123K	ENSP00000341905:Q123K	Q	-	1	0	RASAL3	15433380	0.946000	0.32159	0.894000	0.35097	0.020000	0.10135	1.343000	0.33930	2.162000	0.67917	0.462000	0.41574	CAG	.		0.617	RASAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461331.3	NM_022904	
GPRC5C	55890	hgsc.bcm.edu	37	17	72436467	72436467	+	Silent	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr17:72436467C>T	ENST00000392627.1	+	2	1813	c.687C>T	c.(685-687)ggC>ggT	p.G229G	GPRC5C_ENST00000481232.1_Intron|GPRC5C_ENST00000392629.2_Silent_p.G196G|GPRC5C_ENST00000342648.5_Intron	NM_022036.2	NP_071319.2	Q9NQ84	GPC5C_HUMAN	G protein-coupled receptor, class C, group 5, member C	184					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|vesicle (GO:0031982)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	17						GGGGCAGTGGCGAGGGCGGCC	0.622																																					p.G229G		.											GPRC5C_ENST00000392629,caecum,carcinoma,0,2	GPRC5C_ENST00000392629	0	0			c.C687T						.						47.0	47.0	47.0					17																	72436467		2203	4300	6503	SO:0001819	synonymous_variant	55890	exon2			CAGTGGCGAGGGC	AF207989	CCDS11699.1, CCDS42378.1	17q25	2014-01-30	2014-01-30		ENSG00000170412	ENSG00000170412		"""GPCR / Class C : Orphans"""	13309	protein-coding gene	gene with protein product		605949	"""G protein-coupled receptor, family C, group 5, member C"""			10945465	Standard	NM_022036		Approved	RAIG-3	uc002jkr.3	Q9NQ84	OTTHUMG00000067613	ENST00000392627.1:c.687C>T	17.37:g.72436467C>T		Somatic	35	0		WXS	Illumina HiSeq	.	33	2	NM_022036	B5BUN4|Q2NL85|Q9NZG5	Silent	SNP	ENST00000392627.1	37	CCDS11699.1																																																																																			.		0.622	GPRC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145094.2		
ZNF786	136051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	148769283	148769283	+	Missense_Mutation	SNP	T	T	G			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr7:148769283T>G	ENST00000491431.1	-	4	645	c.581A>C	c.(580-582)gAa>gCa	p.E194A	ZNF786_ENST00000316286.9_Missense_Mutation_p.E108A|ZNF786_ENST00000451334.3_Missense_Mutation_p.E157A	NM_152411.3	NP_689624.2	Q8N393	ZN786_HUMAN	zinc finger protein 786	194					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(2)	26	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			CCAACAGCTTTCCCCGCAGAC	0.562																																					p.E194A		.											.	.	.	0			c.A581C						.						25.0	28.0	27.0					7																	148769283		1976	4148	6124	SO:0001583	missense	136051	exon4			CAGCTTTCCCCGC	AK095701, AL834510	CCDS47738.1	7q36.1	2013-01-08			ENSG00000197362	ENSG00000197362		"""Zinc fingers, C2H2-type"", ""-"""	21806	protein-coding gene	gene with protein product							Standard	NM_152411		Approved	DKFZp762I137	uc003wfh.2	Q8N393	OTTHUMG00000158975	ENST00000491431.1:c.581A>C	7.37:g.148769283T>G	ENSP00000417470:p.Glu194Ala	Somatic	61	0		WXS	Illumina HiSeq	.	70	29	NM_152411	A1A568|B4DMI1	Missense_Mutation	SNP	ENST00000491431.1	37	CCDS47738.1	.	.	.	.	.	.	.	.	.	.	T	11.56	1.675586	0.29783	.	.	ENSG00000197362	ENST00000316286;ENST00000538412;ENST00000491431;ENST00000451334	T;T;T	0.10288	2.89;3.07;2.96	4.41	3.22	0.36961	Zinc finger, C2H2-like (1);	0.402150	0.18418	N	0.141853	T	0.05914	0.0154	N	0.08118	0	0.09310	N	0.999998	B	0.25312	0.123	B	0.25614	0.062	T	0.32534	-0.9903	10	0.72032	D	0.01	-4.7483	8.5375	0.33373	0.0:0.0:0.388:0.612	.	194	Q8N393	ZN786_HUMAN	A	108;108;194;157	ENSP00000313516:E108A;ENSP00000417470:E194A;ENSP00000404984:E157A	ENSP00000313516:E108A	E	-	2	0	ZNF786	148400216	0.000000	0.05858	0.013000	0.15412	0.081000	0.17604	0.457000	0.21875	0.720000	0.32209	0.454000	0.30748	GAA	.		0.562	ZNF786-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352751.1	NM_152411	
MAEL	84944	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	166963277	166963277	+	Missense_Mutation	SNP	G	G	A	rs199624416		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr1:166963277G>A	ENST00000367872.4	+	5	738	c.494G>A	c.(493-495)cGa>cAa	p.R165Q	MAEL_ENST00000491055.1_3'UTR|MAEL_ENST00000367870.2_Missense_Mutation_p.R134Q	NM_032858.1	NP_116247.1	Q96JY0	MAEL_HUMAN	maelstrom spermatogenic transposon silencer	165					cell differentiation (GO:0030154)|cell morphogenesis (GO:0000902)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|piRNA metabolic process (GO:0034587)|regulation of organ growth (GO:0046620)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	autosome (GO:0030849)|chromatin (GO:0000785)|chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|perinuclear region of cytoplasm (GO:0048471)|piP-body (GO:0071547)|XY body (GO:0001741)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(12)|skin(4)	28						GAAATTCCACGAGGATTTCGA	0.338																																					p.R165Q		.											.	.	.	0			c.G494A						.	G	GLN/ARG	0,4406		0,0,2203	81.0	83.0	82.0		494	4.1	1.0	1		82	1,8595	1.2+/-3.3	0,1,4297	yes	missense	MAEL	NM_032858.1	43	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	165/435	166963277	1,13001	2203	4298	6501	SO:0001583	missense	84944	exon5			TTCCACGAGGATT	AK027810, DQ076156	CCDS1257.1, CCDS65712.1, CCDS72975.1	1q24.1	2013-10-11	2012-12-18		ENSG00000143194	ENSG00000143194			25929	protein-coding gene	gene with protein product	"""cancer/testis antigen 128"", ""spermatogenesis associated 35"""	611368	"""maelstrom homolog (Drosophila)"""			19693694, 18694567	Standard	NM_001286378		Approved	FLJ14904, CT128, SPATA35	uc001gdy.1	Q96JY0	OTTHUMG00000034432	ENST00000367872.4:c.494G>A	1.37:g.166963277G>A	ENSP00000356846:p.Arg165Gln	Somatic	79	0		WXS	Illumina HiSeq	.	141	20	NM_032858	B4DY43|E9JVC3|Q49AP9|Q5VZP8|Q9UIW6	Missense_Mutation	SNP	ENST00000367872.4	37	CCDS1257.1	.	.	.	.	.	.	.	.	.	.	G	19.90	3.912613	0.72983	0.0	1.16E-4	ENSG00000143194	ENST00000367872;ENST00000367870;ENST00000447624	T;T;T	0.47177	0.87;0.85;0.89	4.97	4.06	0.47325	.	0.000000	0.51477	D	0.000092	T	0.39279	0.1072	L	0.27053	0.805	0.45946	D	0.998776	D;D	0.89917	1.0;1.0	D;D	0.72625	0.978;0.978	T	0.20505	-1.0273	10	0.23891	T	0.37	.	12.345	0.55116	0.083:0.0:0.917:0.0	.	134;165	E9JVC3;Q96JY0	.;MAEL_HUMAN	Q	165;134;134	ENSP00000356846:R165Q;ENSP00000356844:R134Q;ENSP00000402143:R134Q	ENSP00000356844:R134Q	R	+	2	0	MAEL	165229901	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.950000	0.70265	1.324000	0.45282	0.591000	0.81541	CGA	0.001		0.338	MAEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083239.1	NM_032858	
ADARB2	105	hgsc.bcm.edu	37	10	1577160	1577160	+	Intron	SNP	T	T	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr10:1577160T>A	ENST00000381312.1	-	2	426				ADARB2-AS1_ENST00000381301.3_RNA	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)						mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		GCTCACCGGGTGAGAAGTCAC	0.612																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	642394	.			ACCGGGTGAGAAG	AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"""RED2 homolog (rat)"""	602065	"""adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)"", ""adenosine deaminase, RNA-specific, B2"""			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.101-155805A>T	10.37:g.1577160T>A		Somatic	120	0		WXS	Illumina HiSeq	.	94	26	.	B2RPJ5|Q5VUT6|Q5VW42	RNA	SNP	ENST00000381312.1	37	CCDS7058.1																																																																																			.		0.612	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702	
CEP152	22995	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	49030571	49030571	+	Missense_Mutation	SNP	C	C	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr15:49030571C>A	ENST00000380950.2	-	27	5195	c.5008G>T	c.(5008-5010)Gat>Tat	p.D1670Y	CEP152_ENST00000399334.3_Missense_Mutation_p.D1614Y	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	1670					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		TTTTTGAAATCTGACTTTAAT	0.408																																					p.D1670Y		.											.	.	.	0			c.G5008T						.						178.0	170.0	173.0					15																	49030571		1933	4129	6062	SO:0001583	missense	22995	exon27			TGAAATCTGACTT	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"""asterless"""	613529	"""microcephaly, primary autosomal recessive 4"""	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.5008G>T	15.37:g.49030571C>A	ENSP00000370337:p.Asp1670Tyr	Somatic	118	0		WXS	Illumina HiSeq	.	101	22	NM_001194998	E7ER66|Q17RV1|Q6NTA0	Missense_Mutation	SNP	ENST00000380950.2	37	CCDS58361.1	.	.	.	.	.	.	.	.	.	.	C	19.40	3.820890	0.71028	.	.	ENSG00000103995	ENST00000399334	T	0.60797	0.16	4.76	4.76	0.60689	.	0.000000	0.45867	D	0.000339	T	0.62913	0.2467	L	0.32530	0.975	0.80722	D	1	D	0.71674	0.998	D	0.63877	0.919	T	0.65981	-0.6036	10	0.87932	D	0	-11.8523	12.4117	0.55471	0.0:0.9161:0.0:0.0839	.	1614	O94986	CE152_HUMAN	Y	1614	ENSP00000382271:D1614Y	ENSP00000382271:D1614Y	D	-	1	0	CEP152	46817863	0.060000	0.20803	0.588000	0.28705	0.399000	0.30720	1.232000	0.32636	2.475000	0.83589	0.563000	0.77884	GAT	.		0.408	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985	
MRPL45	84311	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	36453189	36453189	+	Silent	SNP	A	A	C			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr17:36453189A>C	ENST00000312513.5	+	1	201	c.40A>C	c.(40-42)Agg>Cgg	p.R14R		NM_032351.4	NP_115727.4	Q9BRJ2	RM45_HUMAN	mitochondrial ribosomal protein L45	14						mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	13	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				TTGTTTATCGAGGTTTTTGGG	0.582																																					p.R14R		.											.	.	.	0			c.A40C						.						82.0	98.0	93.0					17																	36453189		692	1591	2283	SO:0001819	synonymous_variant	84311	exon1			TTATCGAGGTTTT	BC006235	CCDS11326.1, CCDS74047.1	17q21.2	2014-05-06			ENSG00000174100	ENSG00000278845		"""Mitochondrial ribosomal proteins / large subunits"""	16651	protein-coding gene	gene with protein product		611850				11551941, 12706105	Standard	XM_006725366		Approved	MGC11321	uc002hpy.3	Q9BRJ2	OTTHUMG00000188489	ENST00000312513.5:c.40A>C	17.37:g.36453189A>C		Somatic	80	0		WXS	Illumina HiSeq	.	98	20	NM_032351	A1L436|Q6ZMJ5	Silent	SNP	ENST00000312513.5	37	CCDS11326.1																																																																																			.		0.582	MRPL45-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256792.3	NM_032351	
GIMAP2	26157	hgsc.bcm.edu;broad.mit.edu	37	7	150389906	150389906	+	Nonsense_Mutation	SNP	C	C	T	rs550994929		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr7:150389906C>T	ENST00000223293.5	+	3	626	c.532C>T	c.(532-534)Cga>Tga	p.R178*		NM_015660.2	NP_056475.1	Q9UG22	GIMA2_HUMAN	GTPase, IMAP family member 2	178	AIG1-type G.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)	GTP binding (GO:0005525)	p.R178*(1)		kidney(1)|large_intestine(1)|lung(8)|skin(2)|urinary_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ATGTGGTGGGCGAATCTGTGC	0.478																																					p.R178X		.											GIMAP2,colon,carcinoma,0,2	GIMAP2	0	1	Substitution - Nonsense(1)	large_intestine(1)	c.C532T						.						117.0	97.0	104.0					7																	150389906		2203	4300	6503	SO:0001587	stop_gained	26157	exon3			GGTGGGCGAATCT	AL110151	CCDS5905.1	7q36.1	2014-04-04			ENSG00000106560	ENSG00000106560		"""GTPases, IMAP"""	21789	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 12"""	608085				15474311	Standard	NM_015660		Approved	DKFZp586D0824, HIMAP2, IMAP2, IAN12	uc003who.3	Q9UG22	OTTHUMG00000157488	ENST00000223293.5:c.532C>T	7.37:g.150389906C>T	ENSP00000223293:p.Arg178*	Somatic	70	0		WXS	Illumina HiSeq	.	47	3	NM_015660	Q96L25	Nonsense_Mutation	SNP	ENST00000223293.5	37	CCDS5905.1	.	.	.	.	.	.	.	.	.	.	C	32	5.155047	0.94686	.	.	ENSG00000106560	ENST00000223293	.	.	.	3.89	1.97	0.26223	.	0.150137	0.40818	N	0.001017	.	.	.	.	.	.	0.18873	N	0.999983	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.5978	0.22683	0.2064:0.5938:0.1998:0.0	.	.	.	.	X	178	.	ENSP00000223293:R178X	R	+	1	2	GIMAP2	150020839	0.000000	0.05858	0.002000	0.10522	0.697000	0.40408	-0.345000	0.07770	0.387000	0.25024	0.603000	0.83216	CGA	.		0.478	GIMAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348948.1	NM_015660	
DHX8	1659	hgsc.bcm.edu;bcgsc.ca	37	17	41597543	41597543	+	Missense_Mutation	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr17:41597543C>T	ENST00000262415.3	+	19	2917	c.2845C>T	c.(2845-2847)Cca>Tca	p.P949S	DHX8_ENST00000540306.1_Missense_Mutation_p.P949S	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	949					ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		CATGGATGCCCCACCTATGGA	0.542											OREG0024435	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P949S	NSCLC(56;1548 1661 49258 49987)	.											.	.	.	0			c.C2845T						.						142.0	125.0	131.0					17																	41597543		2203	4300	6503	SO:0001583	missense	1659	exon19			GATGCCCCACCTA	D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"""DEAH-boxes"""	2749	protein-coding gene	gene with protein product		600396	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"""	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.2845C>T	17.37:g.41597543C>T	ENSP00000262415:p.Pro949Ser	Somatic	60	0	902	WXS	Illumina HiSeq	.	74	4	NM_004941		Missense_Mutation	SNP	ENST00000262415.3	37	CCDS11464.1	.	.	.	.	.	.	.	.	.	.	C	31	5.063388	0.93898	.	.	ENSG00000067596	ENST00000540306;ENST00000262415	T;T	0.03152	4.03;4.03	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.41903	0.1179	H	0.99922	4.955	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.70579	-0.4833	10	0.87932	D	0	.	19.0419	0.93004	0.0:1.0:0.0:0.0	.	949;949	F5H658;Q14562	.;DHX8_HUMAN	S	949	ENSP00000437886:P949S;ENSP00000262415:P949S	ENSP00000262415:P949S	P	+	1	0	DHX8	38953069	1.000000	0.71417	0.992000	0.48379	0.984000	0.73092	7.659000	0.83766	2.758000	0.94735	0.561000	0.74099	CCA	.		0.542	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1		
SNX20	124460	hgsc.bcm.edu;bcgsc.ca	37	16	50707593	50707593	+	Silent	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr16:50707593G>A	ENST00000330943.4	-	4	846	c.675C>T	c.(673-675)gcC>gcT	p.A225A	SNX20_ENST00000300590.3_Intron|RP11-401P9.5_ENST00000570167.1_RNA|SNX20_ENST00000423026.2_Intron|RP11-401P9.5_ENST00000570241.2_RNA	NM_182854.2	NP_878274.1	Q7Z614	SNX20_HUMAN	sorting nexin 20	225					protein transport (GO:0015031)	endosome (GO:0005768)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)			kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|skin(2)|stomach(1)	15						CCGGGACGGCGGCCGCAGGGC	0.771																																					p.A225A		.											.	.	.	0			c.C675T						.						2.0	2.0	2.0					16																	50707593		1148	2399	3547	SO:0001819	synonymous_variant	124460	exon4			GACGGCGGCCGCA	AK055837	CCDS10745.1, CCDS10744.1, CCDS45481.1	16q12.1	2008-03-25	2008-03-25		ENSG00000167208	ENSG00000167208		"""Sorting nexins"""	30390	protein-coding gene	gene with protein product	"""selectin ligand interactor cytoplasmic 1"""	613281				18196517, 16782399	Standard	NM_182854		Approved	SLIC-1, SLIC1	uc002egk.2	Q7Z614	OTTHUMG00000133173	ENST00000330943.4:c.675C>T	16.37:g.50707593G>A		Somatic	24	0		WXS	Illumina HiSeq	.	14	9	NM_182854	A8K9D5|Q08E98|Q6P4H2|Q8IV59	Silent	SNP	ENST00000330943.4	37	CCDS10745.1																																																																																			.		0.771	SNX20-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256879.2	NM_153337	
LRRC37A16P	651250	hgsc.bcm.edu	37	17	66122043	66122043	+	IGR	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr17:66122043G>A								LINC00674 (10384 upstream) : LRRC37A16P (4347 downstream)																							aaaaaaaaaagaaaaaaggaa	0.289																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	100499466	.			AAAAAAGAAAAAA																													17.37:g.66122043G>A		Somatic	22	0		WXS	Illumina HiSeq	.	47	5	.		RNA	SNP		37																																																																																				.	0	0.289								
KCNK16	83795	hgsc.bcm.edu	37	6	39285610	39285610	+	Silent	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr6:39285610G>T	ENST00000373229.5	-	3	460	c.447C>A	c.(445-447)gcC>gcA	p.A149A	KCNK16_ENST00000507712.1_Silent_p.A84A|KCNK16_ENST00000373227.4_Silent_p.A149A|KCNK16_ENST00000425054.2_Silent_p.A149A|KCNK16_ENST00000437525.2_Silent_p.A149A	NM_032115.3	NP_115491.1	Q96T55	KCNKG_HUMAN	potassium channel, subfamily K, member 16	149				A -> V (in Ref. 2; AAP82867). {ECO:0000305}.	potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)	13						CGGCCAGATGGGCACGCAGCC	0.592																																					p.A149A		.											.	.	.	0			c.C447A						.						43.0	37.0	39.0					6																	39285610		2203	4300	6503	SO:0001819	synonymous_variant	83795	exon3			CAGATGGGCACGC	AF358909	CCDS4843.1, CCDS47420.1, CCDS47421.1, CCDS47422.1	6p21.2-p21.1	2012-03-07			ENSG00000095981	ENSG00000095981		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	14464	protein-coding gene	gene with protein product		607369				11263999, 16382106	Standard	NM_032115		Approved	K2p16.1, TALK-1, TALK1	uc003ooq.3	Q96T55	OTTHUMG00000014645	ENST00000373229.5:c.447C>A	6.37:g.39285610G>T		Somatic	83	0		WXS	Illumina HiSeq	.	75	4	NM_001135106	B5TJL9|Q2M2N9|Q5TCF3|Q6X6Z3|Q6X6Z4|Q6X6Z5|Q9H591	Silent	SNP	ENST00000373229.5	37	CCDS4843.1																																																																																			.		0.592	KCNK16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040452.2	NM_032115	
NF2	4771	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	30054251	30054251	+	Missense_Mutation	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr22:30054251C>T	ENST00000338641.4	+	7	1114	c.673C>T	c.(673-675)Cgg>Tgg	p.R225W	NF2_ENST00000361452.4_Missense_Mutation_p.R184W|NF2_ENST00000347330.5_Intron|NF2_ENST00000361676.4_Missense_Mutation_p.R183W|NF2_ENST00000397789.3_Missense_Mutation_p.R225W|NF2_ENST00000353887.4_Missense_Mutation_p.R142W|NF2_ENST00000361166.4_Missense_Mutation_p.R225W|NF2_ENST00000334961.7_Missense_Mutation_p.R142W|NF2_ENST00000403999.3_Missense_Mutation_p.R225W|NF2_ENST00000413209.2_Intron|NF2_ENST00000403435.1_Missense_Mutation_p.R225W	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	225	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(4)|p.L208fs*26(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						CTTTGCAATCCGGGTGTGTTG	0.478			"""D, Mis, N, F, S, O"""		"""meningioma, acoustic neuroma, renal """	"""meningioma, acoustic neuroma"""			Neurofibromatosis, type 2																												p.R225W		.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.,1	.	1312	5	Unknown(4)|Deletion - Frameshift(1)	soft_tissue(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)	c.C673T	GRCh37	CD045503	NF2	D		.						187.0	146.0	160.0					22																	30054251		2203	4300	6503	SO:0001583	missense	4771	exon7	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	GCAATCCGGGTGT	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"""A-kinase anchor proteins"""	7773	protein-coding gene	gene with protein product	"""moesin-ezrin-radixin like"", ""schwannomin"""	607379	"""neurofibromin 2 (bilateral acoustic neuroma)"""			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.673C>T	22.37:g.30054251C>T	ENSP00000344666:p.Arg225Trp	Somatic	72	0		WXS	Illumina HiSeq	.	52	5	NM_000268	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Missense_Mutation	SNP	ENST00000338641.4	37	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	C	17.82	3.482771	0.63962	.	.	ENSG00000186575	ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	D;D;D;D;D;D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61	5.75	3.52	0.40303	FERM domain (1);Pleckstrin homology-type (1);	0.050106	0.85682	D	0.000000	D	0.86062	0.5843	L	0.52126	1.63	0.80722	D	1	D;D;D;D;D;D	0.89917	0.998;0.998;0.999;0.999;1.0;0.999	P;P;P;P;D;P	0.66351	0.827;0.574;0.755;0.899;0.943;0.791	D	0.84854	0.0815	9	.	.	.	.	11.132	0.48351	0.2635:0.6207:0.1158:0.0	.	184;225;225;183;142;225	P35240-5;P35240;P35240-2;P35240-6;P35240-4;P35240-3	.;MERL_HUMAN;.;.;.;.	W	225;225;184;225;225;142;142;225;183;225	ENSP00000344666:R225W;ENSP00000384029:R225W;ENSP00000354897:R184W;ENSP00000384797:R225W;ENSP00000335652:R142W;ENSP00000340626:R142W;ENSP00000380891:R225W;ENSP00000355183:R183W;ENSP00000354529:R225W	.	R	+	1	2	NF2	28384251	1.000000	0.71417	1.000000	0.80357	0.494000	0.33585	1.528000	0.35985	1.396000	0.46663	0.563000	0.77884	CGG	.		0.478	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268	
WIPI1	55062	hgsc.bcm.edu	37	17	66417950	66417950	+	Silent	SNP	G	G	A	rs146678987		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr17:66417950G>A	ENST00000262139.5	-	13	1304	c.1305C>T	c.(1303-1305)tgC>tgT	p.C435C	WIPI1_ENST00000546360.1_Silent_p.C353C|MIR635_ENST00000384830.1_RNA|RP11-120M18.2_ENST00000592030.1_RNA|WIPI1_ENST00000589459.1_5'UTR|ARSG_ENST00000448504.2_3'UTR	NM_017983.5	NP_060453.3	Q5MNZ9	WIPI1_HUMAN	WD repeat domain, phosphoinositide interacting 1	435					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|autophagy (GO:0006914)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|vesicle targeting, trans-Golgi to endosome (GO:0048203)	autophagic vacuole membrane (GO:0000421)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|pre-autophagosomal structure (GO:0000407)|pre-autophagosomal structure membrane (GO:0034045)|trans-Golgi network (GO:0005802)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	18						GATTTCCACGGCACAAGATTA	0.468																																					p.C435C		.											WIPI1,NS,carcinoma,0,1	WIPI1	0	0			c.C1305T						.						201.0	168.0	179.0					17																	66417950		2203	4300	6503	SO:0001819	synonymous_variant	55062	exon13			TCCACGGCACAAG		CCDS11677.1	17q24.2	2014-02-12				ENSG00000070540		"""WD repeat domain containing"""	25471	protein-coding gene	gene with protein product		609224				15020712, 15602573	Standard	NM_017983		Approved	FLJ10055, WIPI49, Atg18, ATG18A	uc010dey.3	Q5MNZ9		ENST00000262139.5:c.1305C>T	17.37:g.66417950G>A		Somatic	41	0		WXS	Illumina HiSeq	.	53	3	NM_017983	Q8IXM5|Q9NWF8	Silent	SNP	ENST00000262139.5	37	CCDS11677.1																																																																																			.		0.468	WIPI1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448739.1	NM_017983	
PLEKHG2	64857	hgsc.bcm.edu;bcgsc.ca	37	19	39914272	39914272	+	Missense_Mutation	SNP	C	C	T	rs550247261		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:39914272C>T	ENST00000409794.3	+	18	3428	c.2578C>T	c.(2578-2580)Ccc>Tcc	p.P860S	CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000378550.1_Intron|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.P831S|PLEKHG2_ENST00000458508.2_Missense_Mutation_p.P801S|PLEKHG2_ENST00000409797.2_Intron	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	860					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CCCCTGTCTGCCCCAGGAGCA	0.672													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15276	0.0		0.0	False		,,,				2504	0.0				p.P860S		.											.	.	.	0			c.C2578T						.						28.0	27.0	28.0					19																	39914272		2200	4298	6498	SO:0001583	missense	64857	exon18			TGTCTGCCCCAGG	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.2578C>T	19.37:g.39914272C>T	ENSP00000386733:p.Pro860Ser	Somatic	80	0		WXS	Illumina HiSeq	.	67	4	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	37	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	C	10.41	1.342943	0.24339	.	.	ENSG00000090924	ENST00000409794;ENST00000425673;ENST00000458508	T;T;T	0.73152	-0.57;-0.63;-0.72	5.7	0.79	0.18613	.	1.001210	0.08058	N	0.997737	T	0.51432	0.1674	N	0.20986	0.625	0.09310	N	0.999999	B;B;B	0.27882	0.181;0.02;0.192	B;B;B	0.26770	0.073;0.014;0.048	T	0.41251	-0.9519	10	0.45353	T	0.12	.	2.0098	0.03485	0.1946:0.4984:0.1391:0.1679	.	831;860;801	Q9H7P9-3;Q9H7P9;E7ESZ3	.;PKHG2_HUMAN;.	S	860;831;801	ENSP00000386733:P860S;ENSP00000392906:P831S;ENSP00000408857:P801S	ENSP00000386733:P860S	P	+	1	0	PLEKHG2	44606112	0.000000	0.05858	0.012000	0.15200	0.581000	0.36288	0.401000	0.20948	-0.021000	0.14009	-0.150000	0.13652	CCC	.		0.672	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
PAXIP1	22976	hgsc.bcm.edu;bcgsc.ca	37	7	154760124	154760124	+	Missense_Mutation	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr7:154760124G>A	ENST00000404141.1	-	7	1941	c.1787C>T	c.(1786-1788)cCa>cTa	p.P596L	PAXIP1_ENST00000397192.1_Missense_Mutation_p.P596L|PAXIP1_ENST00000473219.1_5'UTR			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	596	Gln-rich.|Interaction with TP53BP1.				adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		CTCCACTGCTGGATCATGTCC	0.512																																					p.P596L		.											.	.	.	0			c.C1787T						.						46.0	50.0	48.0					7																	154760124		1893	3573	5466	SO:0001583	missense	22976	exon7			ACTGCTGGATCAT	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"""PAX transcription activation domain interacting protein 1 like"""	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.1787C>T	7.37:g.154760124G>A	ENSP00000384048:p.Pro596Leu	Somatic	30	0		WXS	Illumina HiSeq	.	42	4	NM_007349	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Missense_Mutation	SNP	ENST00000404141.1	37	CCDS47753.1	.	.	.	.	.	.	.	.	.	.	G	17.24	3.340078	0.60963	.	.	ENSG00000157212	ENST00000404141;ENST00000397192;ENST00000357094;ENST00000323199	T;T	0.37584	1.19;1.19	4.85	4.85	0.62838	.	0.272597	0.25214	U	0.032292	T	0.50257	0.1605	L	0.32530	0.975	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.997;0.998;0.998;0.996	T	0.54036	-0.8353	10	0.87932	D	0	-7.2556	16.1802	0.81892	0.0:0.0:1.0:0.0	.	549;505;562;596	B4DEQ6;Q6ZW49-3;Q6ZW49-1;Q6ZW49	.;.;.;PAXI1_HUMAN	L	596;596;420;549	ENSP00000384048:P596L;ENSP00000380376:P596L	ENSP00000319149:P549L	P	-	2	0	PAXIP1	154391057	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.460000	0.80816	2.245000	0.73994	0.650000	0.86243	CCA	.		0.512	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349	
NSMF	26012	hgsc.bcm.edu	37	9	140348862	140348862	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr9:140348862G>T	ENST00000371475.3	-	7	1044	c.813C>A	c.(811-813)agC>agA	p.S271R	NSMF_ENST00000371468.1_Missense_Mutation_p.S4R|NSMF_ENST00000541195.1_Missense_Mutation_p.S68R|NSMF_ENST00000265663.7_Missense_Mutation_p.S269R|NSMF_ENST00000484316.1_5'UTR|NSMF_ENST00000371482.1_5'UTR|NSMF_ENST00000392812.4_Missense_Mutation_p.S248R|NSMF_ENST00000339554.3_Missense_Mutation_p.S68R|NSMF_ENST00000437259.1_Missense_Mutation_p.S248R|NSMF_ENST00000371472.2_Missense_Mutation_p.S269R|NSMF_ENST00000371474.3_Missense_Mutation_p.S246R|NSMF_ENST00000371473.3_Missense_Mutation_p.S271R	NM_001130969.1	NP_001124441.1	Q6X4W1	NSMF_HUMAN	NMDA receptor synaptonuclear signaling and neuronal migration factor	271					cellular response to amino acid stimulus (GO:0071230)|cellular response to electrical stimulus (GO:0071257)|cellular response to gonadotropin stimulus (GO:0071371)|positive regulation of neuron migration (GO:2001224)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of dendrite morphogenesis (GO:0048814)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuronal synaptic plasticity (GO:0048168)	apical dendrite (GO:0097440)|cell junction (GO:0030054)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuron projection (GO:0043005)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium-dependent protein binding (GO:0048306)										TCACCCTCCGGCTGCCGACCA	0.682																																					p.S271R		.											.	.	.	0			c.C813A						.						23.0	29.0	27.0					9																	140348862		1895	3619	5514	SO:0001583	missense	26012	exon7			CCTCCGGCTGCCG		CCDS7044.1, CCDS48067.1, CCDS48068.1, CCDS48069.1, CCDS55357.1	9q34.3	2013-01-14	2013-01-14	2013-01-14	ENSG00000165802	ENSG00000165802			29843	protein-coding gene	gene with protein product		608137	"""nasal embryonic LHRH factor"""	NELF		11230166, 10898796	Standard	NM_015537		Approved		uc004cna.3	Q6X4W1	OTTHUMG00000020989	ENST00000371475.3:c.813C>A	9.37:g.140348862G>T	ENSP00000360530:p.Ser271Arg	Somatic	100	0		WXS	Illumina HiSeq	.	71	4	NM_001178064	Q2TB96|Q6X4V7|Q6X4V8|Q6X4V9|Q8N2M2|Q96SY1|Q9NPM4|Q9NPP3|Q9NPS3	Missense_Mutation	SNP	ENST00000371475.3	37	CCDS48069.1	.	.	.	.	.	.	.	.	.	.	G	16.39	3.110606	0.56398	.	.	ENSG00000165802	ENST00000339554;ENST00000371475;ENST00000265663;ENST00000437259;ENST00000392812;ENST00000371474;ENST00000371473;ENST00000371472;ENST00000541195;ENST00000371468	T;T;T;T;T;T;T;T;T	0.71341	-0.56;0.6;0.79;0.69;0.69;0.82;0.44;0.79;0.63	4.23	3.24	0.37175	.	0.099522	0.64402	D	0.000002	T	0.69468	0.3114	L	0.56769	1.78	0.53688	D	0.999974	P;P;P;P;P;P;P	0.42620	0.709;0.785;0.677;0.528;0.528;0.528;0.528	B;P;P;B;B;B;B	0.47645	0.409;0.553;0.452;0.329;0.329;0.309;0.309	T	0.68191	-0.5474	10	0.72032	D	0.01	-19.9225	6.8943	0.24247	0.1754:0.0:0.8246:0.0	.	248;68;52;246;271;271;269	Q6X4W1-3;F5GZW0;Q9NTU2;Q2TB96;Q6X4W1-4;Q6X4W1;Q6X4W1-2	.;.;.;.;.;NELF_HUMAN;.	R	68;271;269;248;248;246;271;269;68;4	ENSP00000342966:S68R;ENSP00000360530:S271R;ENSP00000265663:S269R;ENSP00000412007:S248R;ENSP00000376559:S248R;ENSP00000360529:S246R;ENSP00000360528:S271R;ENSP00000360527:S269R;ENSP00000444177:S68R	ENSP00000265663:S269R	S	-	3	2	NELF	139468683	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.043000	0.57354	0.581000	0.29539	0.455000	0.32223	AGC	.		0.682	NSMF-204	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015537	
C17orf77	146723	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	72588674	72588674	+	Missense_Mutation	SNP	G	G	C			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr17:72588674G>C	ENST00000392620.1	+	3	851	c.489G>C	c.(487-489)ttG>ttC	p.L163F	C17orf77_ENST00000328023.2_Missense_Mutation_p.L163F|CD300LD_ENST00000375352.1_5'Flank	NM_152460.2	NP_689673.2	Q96MU5	CQ077_HUMAN	chromosome 17 open reading frame 77	163						extracellular region (GO:0005576)				breast(2)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	11						CCCAAGCATTGAGGAGCTGCG	0.587																																					p.L163F		.											.	.	.	0			c.G489C						.						101.0	82.0	88.0					17																	72588674		2203	4300	6503	SO:0001583	missense	146723	exon3			AGCATTGAGGAGC		CCDS32721.1	17q25.1	2006-01-16			ENSG00000182352	ENSG00000182352			26480	protein-coding gene	gene with protein product							Standard	NM_152460		Approved	FLJ31882	uc002jla.1	Q96MU5	OTTHUMG00000067611	ENST00000392620.1:c.489G>C	17.37:g.72588674G>C	ENSP00000376396:p.Leu163Phe	Somatic	36	0		WXS	Illumina HiSeq	.	57	14	NM_152460		Missense_Mutation	SNP	ENST00000392620.1	37	CCDS32721.1	.	.	.	.	.	.	.	.	.	.	G	2.504	-0.314440	0.05422	.	.	ENSG00000182352	ENST00000392620;ENST00000328023	T;T	0.57107	0.42;0.42	1.32	0.301	0.15781	.	.	.	.	.	T	0.26376	0.0644	N	0.08118	0	0.09310	N	1	P	0.47484	0.896	B	0.41619	0.361	T	0.09509	-1.0671	8	.	.	.	.	3.5624	0.07887	0.2691:0.0:0.7309:0.0	.	163	Q96MU5	CQ077_HUMAN	F	163	ENSP00000376396:L163F;ENSP00000329353:L163F	.	L	+	3	2	C17orf77	70100269	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.285000	0.18883	0.126000	0.18424	0.609000	0.83330	TTG	.		0.587	C17orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145090.2	NM_152460	
DEPDC7	91614	hgsc.bcm.edu	37	11	33054930	33054930	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr11:33054930G>T	ENST00000241051.3	+	9	1557	c.1465G>T	c.(1465-1467)Gag>Tag	p.E489*	DEPDC7_ENST00000311388.3_Nonsense_Mutation_p.E480*	NM_001077242.1	NP_001070710.1	Q96QD5	DEPD7_HUMAN	DEP domain containing 7	489					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)				endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	17						TTCTGCCAAAGAGAAGAAAAA	0.333																																					p.E489X		.											.	.	.	0			c.G1465T						.						80.0	79.0	79.0					11																	33054930		1803	4059	5862	SO:0001587	stop_gained	91614	exon9			GCCAAAGAGAAGA		CCDS41632.1, CCDS41633.1	11p13	2006-03-24			ENSG00000121690	ENSG00000121690			29899	protein-coding gene	gene with protein product		612294				10568747	Standard	NM_001077242		Approved		uc001mub.3	Q96QD5	OTTHUMG00000166242	ENST00000241051.3:c.1465G>T	11.37:g.33054930G>T	ENSP00000241051:p.Glu489*	Somatic	73	0		WXS	Illumina HiSeq	.	90	4	NM_001077242	G5E941|Q8N602|Q8NCU9|Q9UGK5	Nonsense_Mutation	SNP	ENST00000241051.3	37	CCDS41632.1	.	.	.	.	.	.	.	.	.	.	G	39	7.477684	0.98309	.	.	ENSG00000121690	ENST00000241051;ENST00000311388	.	.	.	5.13	5.13	0.70059	.	0.048874	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-18.5097	18.9364	0.92588	0.0:0.0:1.0:0.0	.	.	.	.	X	489;480	.	ENSP00000241051:E489X	E	+	1	0	DEPDC7	33011506	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.547000	0.82146	2.540000	0.85666	0.460000	0.39030	GAG	.		0.333	DEPDC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388655.1	NM_139160	
ARPC2	10109	hgsc.bcm.edu	37	2	219104121	219104121	+	Missense_Mutation	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr2:219104121G>A	ENST00000295685.10	+	6	724	c.463G>A	c.(463-465)Gag>Aag	p.E155K	ARPC2_ENST00000315717.5_Missense_Mutation_p.E155K|ARPC2_ENST00000477992.1_3'UTR	NM_005731.2	NP_005722.1	O15144	ARPC2_HUMAN	actin related protein 2/3 complex, subunit 2, 34kDa	155					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural constituent of cytoskeleton (GO:0005200)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	6		Renal(207;0.0474)		Epithelial(149;1.21e-06)|all cancers(144;0.000212)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0103)		CAGGTATGTTGAGTCTAAAAA	0.413																																					p.E155K		.											ARPC2,right_lower_lobe,carcinoma,0,1	ARPC2	0	0			c.G463A						.						136.0	119.0	125.0					2																	219104121		2203	4300	6503	SO:0001583	missense	10109	exon6			TATGTTGAGTCTA	AF006085	CCDS2410.1	2q36.1	2011-07-06	2002-08-29		ENSG00000163466	ENSG00000163466		"""Actin related protein 2/3 complex subunits"""	705	protein-coding gene	gene with protein product		604224	"""actin related protein 2/3 complex, subunit 2 (34 kD)"""			9359840, 9230079	Standard	NM_005731		Approved	p34-Arc, ARC34	uc002vhd.4	O15144	OTTHUMG00000133618	ENST00000295685.10:c.463G>A	2.37:g.219104121G>A	ENSP00000295685:p.Glu155Lys	Somatic	63	0		WXS	Illumina HiSeq	.	50	2	NM_005731	Q92801|Q9P1D4	Missense_Mutation	SNP	ENST00000295685.10	37	CCDS2410.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.145695	0.57044	.	.	ENSG00000163466	ENST00000315717;ENST00000295685	.	.	.	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.51753	0.1693	L	0.33245	0.995	0.80722	D	1	B	0.17465	0.022	B	0.22753	0.041	T	0.50988	-0.8762	9	0.02654	T	1	.	20.3343	0.98733	0.0:0.0:1.0:0.0	.	155	O15144	ARPC2_HUMAN	K	155	.	ENSP00000295685:E155K	E	+	1	0	ARPC2	218812366	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.869000	0.99810	2.822000	0.97130	0.650000	0.86243	GAG	.		0.413	ARPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256777.2	NM_005731	
PROZ	8858	hgsc.bcm.edu	37	13	113814370	113814370	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr13:113814370G>T	ENST00000375547.2	+	2	120	c.113G>T	c.(112-114)tGg>tTg	p.W38L	PROZ_ENST00000342783.4_Missense_Mutation_p.W60L	NM_003891.2	NP_003882.1	P22891	PROZ_HUMAN	protein Z, vitamin K-dependent plasma glycoprotein	38					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)	p.W38L(1)		NS(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(2)|skin(2)	16	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.216)	all cancers(43;0.104)		Menadione(DB00170)	CTGGTGAGGTGGAAGCGTGCG	0.502																																					p.W60L		.											PROZ,ear,carcinoma,0,1	PROZ	0	1	Substitution - Missense(1)	skin(1)	c.G179T						.						142.0	162.0	155.0					13																	113814370		2203	4300	6503	SO:0001583	missense	8858	exon3			TGAGGTGGAAGCG	M55670	CCDS9531.1, CCDS58300.1	13q34	2008-07-18			ENSG00000126231	ENSG00000126231			9460	protein-coding gene	gene with protein product		176895				2244898, 2403355	Standard	NM_001256134		Approved	PZ	uc010agr.2	P22891	OTTHUMG00000017376	ENST00000375547.2:c.113G>T	13.37:g.113814370G>T	ENSP00000364697:p.Trp38Leu	Somatic	36	0		WXS	Illumina HiSeq	.	43	2	NM_001256134	A6NMB4|Q15213|Q5JVF5|Q5JVF6	Missense_Mutation	SNP	ENST00000375547.2	37	CCDS9531.1	.	.	.	.	.	.	.	.	.	.	G	5.333	0.246808	0.10130	.	.	ENSG00000126231	ENST00000375547;ENST00000342783	D;D	0.94687	-3.49;-3.45	4.0	2.08	0.27032	Gamma-carboxyglutamic acid-rich (GLA) domain (1);	0.842832	0.10788	U	0.634050	D	0.90800	0.7111	L	0.48362	1.52	0.23076	N	0.998331	B;B	0.28178	0.202;0.009	B;B	0.32805	0.153;0.029	D	0.84506	0.0619	10	0.87932	D	0	.	4.1865	0.10400	0.2244:0.3623:0.4133:0.0	.	60;38	P22891-2;P22891	.;PROZ_HUMAN	L	38;60	ENSP00000364697:W38L;ENSP00000344458:W60L	ENSP00000344458:W60L	W	+	2	0	PROZ	112862371	0.195000	0.23338	0.784000	0.31847	0.074000	0.17049	0.399000	0.20916	1.749000	0.51849	0.313000	0.20887	TGG	.		0.502	PROZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045845.1	NM_003891	
RYR3	6263	hgsc.bcm.edu	37	15	34102761	34102761	+	Missense_Mutation	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr15:34102761G>A	ENST00000389232.4	+	71	10178	c.10108G>A	c.(10108-10110)Gca>Aca	p.A3370T	RYR3_ENST00000415757.3_Missense_Mutation_p.A3365T	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3370					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.A3370T(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CATCGTGGCTGCACTCAAGAA	0.522																																					p.A3370T		.											RYR3,NS,carcinoma,0,1	RYR3	0	1	Substitution - Missense(1)	endometrium(1)	c.G10108A						.						78.0	96.0	90.0					15																	34102761		1964	4159	6123	SO:0001583	missense	6263	exon71			GTGGCTGCACTCA		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.10108G>A	15.37:g.34102761G>A	ENSP00000373884:p.Ala3370Thr	Somatic	53	0		WXS	Illumina HiSeq	.	43	3	NM_001036	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	14.47	2.544222	0.45280	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T	0.66099	-0.19	5.15	4.23	0.50019	.	0.000000	0.85682	D	0.000000	T	0.59059	0.2166	N	0.12746	0.255	0.53005	D	0.99996	D;P	0.71674	0.998;0.589	D;B	0.77557	0.99;0.325	T	0.56583	-0.7955	10	0.25751	T	0.34	.	9.8782	0.41216	0.154:0.0:0.846:0.0	.	3365;3370	Q15413-2;Q15413	.;RYR3_HUMAN	T	3370;3370;3365	ENSP00000373884:A3370T	ENSP00000354735:A3365T	A	+	1	0	RYR3	31890053	1.000000	0.71417	0.735000	0.30896	0.996000	0.88848	4.756000	0.62205	1.393000	0.46605	0.561000	0.74099	GCA	.		0.522	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
ARAF	369	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	47426127	47426127	+	Missense_Mutation	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chrX:47426127C>T	ENST00000377045.4	+	7	841	c.647C>T	c.(646-648)cCc>cTc	p.P216L	ARAF_ENST00000290277.6_Intron	NM_001256196.1|NM_001654.4	NP_001243125.1|NP_001645.1	P10398	ARAF_HUMAN	A-Raf proto-oncogene, serine/threonine kinase	216					cellular protein modification process (GO:0006464)|negative regulation of apoptotic process (GO:0043066)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of TOR signaling (GO:0032006)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			biliary_tract(1)|endometrium(4)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	29					Adenosine triphosphate(DB00171)	ACGTCCACTCCCAACGTCCAT	0.662																																					p.P219L		.											.	.	.	0			c.C656T						.						76.0	61.0	66.0					X																	47426127		2203	4300	6503	SO:0001583	missense	369	exon7			CCACTCCCAACGT	X04790	CCDS35232.1, CCDS59164.1, CCDS75970.1	Xp11.3-p11.23	2014-06-26	2014-06-26	2005-01-19	ENSG00000078061	ENSG00000078061			646	protein-coding gene	gene with protein product		311010	"""v-raf murine sarcoma 3611 viral oncogene homolog 1"""	ARAF1			Standard	NM_001654		Approved		uc004dic.2	P10398	OTTHUMG00000021446	ENST00000377045.4:c.647C>T	X.37:g.47426127C>T	ENSP00000366244:p.Pro216Leu	Somatic	70	0		WXS	Illumina HiSeq	.	58	48	NM_001256196	P07557|Q5H9B2|Q5H9B3	Missense_Mutation	SNP	ENST00000377045.4	37	CCDS35232.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.037064	0.93630	.	.	ENSG00000078061	ENST00000377045	T	0.76186	-1.0	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	D	0.85792	0.5779	M	0.78456	2.415	0.80722	D	1	D;D	0.64830	0.992;0.994	P;D	0.71184	0.865;0.972	D	0.87731	0.2579	10	0.87932	D	0	.	15.4172	0.74980	0.0:1.0:0.0:0.0	.	216;82	P10398;B4DV85	ARAF_HUMAN;.	L	216	ENSP00000366244:P216L	ENSP00000366244:P216L	P	+	2	0	ARAF	47311071	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.334000	0.79224	2.233000	0.73108	0.544000	0.68410	CCC	.		0.662	ARAF-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056418.1		
ANKRD45	339416	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	173628573	173628573	+	Splice_Site	SNP	C	C	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr1:173628573C>A	ENST00000333279.2	-	2	46		c.e2-1		snoU13_ENST00000459202.1_RNA	NM_198493.2	NP_940895.1	Q5TZF3	ANR45_HUMAN	ankyrin repeat domain 45											NS(2)|endometrium(2)|large_intestine(4)|lung(3)|skin(1)	12						CCAAAAATACCTATGACCAAA	0.328																																					.		.											.	.	.	0			.						.						56.0	55.0	55.0					1																	173628573		2196	4295	6491	SO:0001630	splice_region_variant	339416	.			AAATACCTATGAC		CCDS1309.1	1q25.1	2013-01-10			ENSG00000183831	ENSG00000183831		"""Ankyrin repeat domain containing"""	24786	protein-coding gene	gene with protein product	"""cancer/testis antigen 117"""						Standard	NM_198493		Approved	FLJ45235, CT117	uc001gja.1	Q5TZF3	OTTHUMG00000040546	ENST00000333279.2:c.15-1G>T	1.37:g.173628573C>A		Somatic	54	0		WXS	Illumina HiSeq	.	65	17	.	A1A4G2|Q6ZST1	Splice_Site	SNP	ENST00000333279.2	37	CCDS1309.1																																																																																			.		0.328	ANKRD45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097580.2	NM_198493	Intron
CNTNAP4	85445	hgsc.bcm.edu	37	16	76486447	76486447	+	Missense_Mutation	SNP	G	G	T	rs139625830		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr16:76486447G>T	ENST00000476707.1	+	7	1262	c.1123G>T	c.(1123-1125)Gtg>Ttg	p.V375L	CNTNAP4_ENST00000478060.1_Missense_Mutation_p.V299L|CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.V371L|CNTNAP4_ENST00000377504.4_Missense_Mutation_p.V323L			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	372					cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)				breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						ATCTATGCCCGTGACTTTTCT	0.398																																					p.V299L		.											CNTNAP4_ENST00000478060,colon,carcinoma,0,6	CNTNAP4_ENST00000478060	0	0			c.G895T						.						97.0	96.0	96.0					16																	76486447		2198	4300	6498	SO:0001583	missense	85445	exon7			ATGCCCGTGACTT	AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.1123G>T	16.37:g.76486447G>T	ENSP00000417628:p.Val375Leu	Somatic	67	0		WXS	Illumina HiSeq	.	40	2	NM_138994	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	ENST00000476707.1	37		.	.	.	.	.	.	.	.	.	.	G	14.43	2.532556	0.45073	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27	5.52	3.46	0.39613	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.210872	0.23502	N	0.047488	T	0.74419	0.3714	.	.	.	0.35424	D	0.793485	B;B;B;B	0.18610	0.003;0.003;0.029;0.008	B;B;B;B	0.23574	0.047;0.006;0.038;0.015	T	0.75744	-0.3210	9	0.59425	D	0.04	.	17.7626	0.88468	0.0:0.1471:0.8529:0.0	.	299;375;347;372	E9PFZ6;E9PDN6;Q96M80;Q9C0A0	.;.;.;CNTP4_HUMAN	L	371;323;299;375	ENSP00000306893:V371L;ENSP00000439733:V323L;ENSP00000418741:V299L;ENSP00000417628:V375L	ENSP00000306893:V371L	V	+	1	0	CNTNAP4	75043948	0.998000	0.40836	0.996000	0.52242	0.879000	0.50718	2.763000	0.47605	0.786000	0.33708	0.655000	0.94253	GTG	.		0.398	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401	
NOL12	79159	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	38084863	38084863	+	Missense_Mutation	SNP	C	C	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr22:38084863C>A	ENST00000359114.4	+	4	315	c.245C>A	c.(244-246)gCa>gAa	p.A82E	NOL12_ENST00000493862.1_3'UTR	NM_024313.2	NP_077289.1	Q9UGY1	NOL12_HUMAN	nucleolar protein 12	82						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|rRNA binding (GO:0019843)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	8	Melanoma(58;0.0574)					ACAGAGGAGGCAGATGAGCTG	0.622																																					p.A82E		.											.	.	.	0			c.C245A						.						151.0	123.0	133.0					22																	38084863		2203	4300	6503	SO:0001583	missense	79159	exon4			AGGAGGCAGATGA	Z83844	CCDS13955.1	22q13.1	2012-05-02			ENSG00000256872	ENSG00000273899			28585	protein-coding gene	gene with protein product						12477932	Standard	NM_024313		Approved	MGC3731, Nop25, RRP17	uc003atp.3	Q9UGY1	OTTHUMG00000150660	ENST00000359114.4:c.245C>A	22.37:g.38084863C>A	ENSP00000352021:p.Ala82Glu	Somatic	49	0		WXS	Illumina HiSeq	.	73	22	NM_024313		Missense_Mutation	SNP	ENST00000359114.4	37	CCDS13955.1	.	.	.	.	.	.	.	.	.	.	C	15.70	2.910003	0.52439	.	.	ENSG00000256872	ENST00000359114	D	0.83075	-1.68	5.58	4.56	0.56223	.	0.500492	0.23325	N	0.049419	T	0.73969	0.3655	L	0.40543	1.245	0.33691	D	0.613337	P	0.35551	0.509	B	0.35607	0.206	T	0.74881	-0.3513	10	0.15066	T	0.55	-0.5591	10.6891	0.45860	0.0:0.8479:0.0:0.1521	.	82	Q9UGY1	NOL12_HUMAN	E	82	ENSP00000352021:A82E	ENSP00000352021:A82E	A	+	2	0	Z83844.2	36414809	0.948000	0.32251	0.888000	0.34837	0.949000	0.60115	2.112000	0.41892	1.354000	0.45846	0.655000	0.94253	GCA	.		0.622	NOL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319476.1	NM_024313	
REXO4	57109	hgsc.bcm.edu	37	9	136279959	136279959	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr9:136279959G>T	ENST00000371942.3	-	2	597	c.398C>A	c.(397-399)cCt>cAt	p.P133H	REXO4_ENST00000478037.1_Intron|ADAMTS13_ENST00000485925.1_Intron|REXO4_ENST00000371935.2_Intron	NM_020385.2	NP_065118.2	Q9GZR2	REXO4_HUMAN	REX4, RNA exonuclease 4 homolog (S. cerevisiae)	133					regulation of transcription, DNA-templated (GO:0006355)	nucleolus (GO:0005730)|nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(4)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	15				OV - Ovarian serous cystadenocarcinoma(145;8.58e-08)|Epithelial(140;9.55e-07)|all cancers(34;1.05e-05)		GGAACCTGAAGGAACAGAGCC	0.522																																					p.P133H		.											REXO4,mucosal,malignant_melanoma,0,2	REXO4	0	0			c.C398A						.						114.0	98.0	104.0					9																	136279959		2203	4300	6503	SO:0001583	missense	57109	exon2			CCTGAAGGAACAG	AF273304	CCDS6969.1, CCDS65179.1	9q34	2008-02-05	2005-08-22	2005-08-22	ENSG00000148300	ENSG00000148300			12820	protein-coding gene	gene with protein product		602930	"""Xenopus prevents mitotic catatrophe 2 homolog"", ""XPMC2 prevents mitotic catastrophe 2 homolog (Xenopus laevis)"""	XPMC2H		9325058	Standard	NM_020385		Approved		uc004cdm.3	Q9GZR2	OTTHUMG00000020870	ENST00000371942.3:c.398C>A	9.37:g.136279959G>T	ENSP00000361010:p.Pro133His	Somatic	69	0		WXS	Illumina HiSeq	.	44	3	NM_020385	B2RAT2|Q5T8S4|Q5T8S5|Q5T8S6|Q9GZW3	Missense_Mutation	SNP	ENST00000371942.3	37	CCDS6969.1	.	.	.	.	.	.	.	.	.	.	G	13.53	2.264203	0.39995	.	.	ENSG00000148300	ENST00000453165;ENST00000371942;ENST00000445916	T;T;T	0.27402	2.1;2.13;1.67	4.92	4.92	0.64577	.	9.432040	0.00166	N	0.000000	T	0.52158	0.1717	L	0.59436	1.845	0.80722	D	1	D	0.69078	0.997	P	0.55667	0.781	T	0.18272	-1.0342	10	0.39692	T	0.17	.	15.2907	0.73865	0.0:0.0:1.0:0.0	.	133	Q9GZR2	REXO4_HUMAN	H	118;133;40	ENSP00000403272:P118H;ENSP00000361010:P133H;ENSP00000391534:P40H	ENSP00000361010:P133H	P	-	2	0	REXO4	135269780	0.101000	0.21875	0.004000	0.12327	0.025000	0.11179	2.704000	0.47118	2.266000	0.75297	0.561000	0.74099	CCT	.		0.522	REXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054899.1		
DHCR24	1718	hgsc.bcm.edu	37	1	55352654	55352654	+	Missense_Mutation	SNP	C	C	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr1:55352654C>A	ENST00000371269.3	-	1	237	c.139G>T	c.(139-141)Gat>Tat	p.D47Y	RP11-67L3.5_ENST00000415336.1_RNA|RP11-67L3.4_ENST00000433690.1_RNA|RP11-67L3.4_ENST00000455380.1_RNA|DHCR24_ENST00000535035.1_5'Flank|RP11-67L3.4_ENST00000436033.1_RNA|RP11-67L3.4_ENST00000443284.1_RNA	NM_014762.3	NP_055577.1	Q15392	DHC24_HUMAN	24-dehydrocholesterol reductase	47					amyloid precursor protein catabolic process (GO:0042987)|apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cholesterol biosynthetic process (GO:0006695)|male genitalia development (GO:0030539)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|oxidation-reduction process (GO:0055114)|plasminogen activation (GO:0031639)|protein localization (GO:0008104)|Ras protein signal transduction (GO:0007265)|regulation of neuron death (GO:1901214)|response to hormone (GO:0009725)|response to oxidative stress (GO:0006979)|skin development (GO:0043588)|small molecule metabolic process (GO:0044281)|tissue development (GO:0009888)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	delta24(24-1) sterol reductase activity (GO:0000246)|delta24-sterol reductase activity (GO:0050614)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|peptide antigen binding (GO:0042605)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			large_intestine(2)|liver(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7						TAGTAGATATCGAAGATAAGC	0.632																																					p.D47Y	Pancreas(39;516 1021 24601 30715 32780)	.											DHCR24,bladder,carcinoma,0,1	DHCR24	0	0			c.G139T						.						50.0	52.0	51.0					1																	55352654		2203	4300	6503	SO:0001583	missense	1718	exon1			AGATATCGAAGAT	AF261758	CCDS600.1	1p32.3	2008-02-05			ENSG00000116133	ENSG00000116133			2859	protein-coding gene	gene with protein product		606418				11519011	Standard	NM_014762		Approved	KIAA0018, seladin-1	uc001cyc.1	Q15392	OTTHUMG00000009989	ENST00000371269.3:c.139G>T	1.37:g.55352654C>A	ENSP00000360316:p.Asp47Tyr	Somatic	19	0		WXS	Illumina HiSeq	.	20	2	NM_014762	B7Z817|D3DQ51|Q9HBA8	Missense_Mutation	SNP	ENST00000371269.3	37	CCDS600.1	.	.	.	.	.	.	.	.	.	.	C	14.45	2.539945	0.45176	.	.	ENSG00000116133	ENST00000539536;ENST00000371269	D	0.85411	-1.98	5.3	4.37	0.52481	FAD-binding, type 2 (1);	0.045401	0.85682	D	0.000000	D	0.90435	0.7005	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.70487	0.969	D	0.88353	0.2982	10	0.13853	T	0.58	-5.39	15.2735	0.73723	0.1412:0.8588:0.0:0.0	.	47	Q15392	DHC24_HUMAN	Y	47	ENSP00000360316:D47Y	ENSP00000360316:D47Y	D	-	1	0	DHCR24	55125242	1.000000	0.71417	1.000000	0.80357	0.251000	0.25915	7.176000	0.77643	1.426000	0.47256	0.561000	0.74099	GAT	.		0.632	DHCR24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027680.1	NM_014762	
MT-ND1	4535	hgsc.bcm.edu	37	M	1440	1440	+	5'Flank	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chrM:1440G>A	ENST00000361390.2	+	0	0				MT-TV_ENST00000387342.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TF_ENST00000387314.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TL1_ENST00000386347.1_RNA			P03886	NU1M_HUMAN	mitochondrially encoded NADH dehydrogenase 1						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34					Desflurane(DB01189)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	GCAGTAAACTGAGAGTAGAGT	0.473																																					.		.											.	.	.	0			.						.																																			SO:0001631	upstream_gene_variant	6052	.			AACTAAGAGTAGA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198888	ENSG00000198888	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7455	protein-coding gene	gene with protein product	"""complex I ND1 subunit"", ""NADH-ubiquinone oxidoreductase chain 1"""	516000	"""NADH dehydrogenase 1"""	MTND1			Standard			Approved	ND1, NAD1		P03886			M.37:g.1440G>A	Exception_encountered	Somatic	19	0		WXS	Illumina HiSeq	.	7	4	.	C0JKH6|Q37523	RNA	SNP	ENST00000361390.2	37																																																																																				.		0.473	MT-ND1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024026	
SMS	6611	hgsc.bcm.edu	37	X	21996164	21996164	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chrX:21996164G>T	ENST00000404933.2	+	6	844	c.592G>T	c.(592-594)Gga>Tga	p.G198*	SMS_ENST00000379404.1_Nonsense_Mutation_p.G145*|SMS_ENST00000415881.2_Nonsense_Mutation_p.G102*	NM_004595.4	NP_004586.2	P52788	SPSY_HUMAN	spermine synthase	198	PABS. {ECO:0000255|PROSITE- ProRule:PRU00354}.				cellular nitrogen compound metabolic process (GO:0034641)|methionine metabolic process (GO:0006555)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermine biosynthetic process (GO:0006597)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	spermidine synthase activity (GO:0004766)|spermine synthase activity (GO:0016768)			endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(2)	14					Spermine(DB00127)	ACTCATTCTGGGAGGTGGAGA	0.433																																					p.G198X		.											.	.	.	0			c.G592T						.						136.0	118.0	124.0					X																	21996164		2203	4300	6503	SO:0001587	stop_gained	6611	exon6			ATTCTGGGAGGTG	AD001528	CCDS14203.1, CCDS59161.1	Xp22.1	2014-05-16			ENSG00000102172	ENSG00000102172			11123	protein-coding gene	gene with protein product		300105	"""Snyder-Robinson X-linked mental retardation syndrome"""	SRS		7546290, 9299240, 14508504	Standard	NM_004595		Approved	SPMSY, SpS, MRSR	uc004dag.4	P52788	OTTHUMG00000021239	ENST00000404933.2:c.592G>T	X.37:g.21996164G>T	ENSP00000385746:p.Gly198*	Somatic	55	0		WXS	Illumina HiSeq	.	71	3	NM_004595	A6NHA7|A6NI34|B2R9M0|O00544|Q9UQS1	Nonsense_Mutation	SNP	ENST00000404933.2	37	CCDS14203.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.34|16.34	3.094491|3.094491	0.56075|0.56075	.|.	.|.	ENSG00000102172|ENSG00000102172	ENST00000457085|ENST00000404933;ENST00000379404;ENST00000415881	.|.	.|.	.|.	5.56|5.56	5.56|5.56	0.83823|0.83823	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|.	0.77778|.	0.4181|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.80065|.	-0.1538|.	4|.	.|0.66056	.|D	.|0.02	-22.1376|-22.1376	18.5981|18.5981	0.91236|0.91236	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	V|X	289|198;145;102	.|.	.|ENSP00000368714:G145X	G|G	+|+	2|1	0|0	SMS|SMS	21906085|21906085	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.344000|0.344000	0.29017|0.29017	9.476000|9.476000	0.97823|0.97823	2.334000|2.334000	0.79466|0.79466	0.600000|0.600000	0.82982|0.82982	GGG|GGA	.		0.433	SMS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056032.1	NM_004595	
PTH2	113091	hgsc.bcm.edu;broad.mit.edu	37	19	49926533	49926533	+	Missense_Mutation	SNP	G	G	C	rs200733272|rs371950649	byFrequency	TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:49926533G>C	ENST00000270631.1	-	1	165	c.64C>G	c.(64-66)Ctg>Gtg	p.L22V	CTD-3148I10.1_ENST00000576655.1_5'Flank	NM_178449.3	NP_848544.1	Q96A98	TIP39_HUMAN	parathyroid hormone 2	22					neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)		p.L22V(2)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(262;0.0015)|GBM - Glioblastoma multiforme(486;0.044)|Lung(386;0.0785)|LUSC - Lung squamous cell carcinoma(496;0.0836)		GGCACCACcagcagcagcagc	0.692													g|||	17	0.00339457	0.003	0.0043	5008	,	,		11369	0.004		0.002	False		,,,				2504	0.0041				p.L22V		.											PTH2,NS,carcinoma,0,9	PTH2	0	2	Substitution - Missense(2)	endometrium(2)	c.C64G						.		VAL/LEU	12,4376		0,12,2182	12.0	16.0	14.0		64	3.3	0.0	19		14	11,8561		0,11,4275	no	missense	PTH2	NM_178449.3	32	0,23,6457	CC,CG,GG		0.1283,0.2735,0.1775	possibly-damaging	22/101	49926533	23,12937	2194	4286	6480	SO:0001583	missense	113091	exon1			CCACCAGCAGCAG	AY037555	CCDS12763.1	19q13.33	2013-02-28				ENSG00000142538		"""Endogenous ligands"""	30828	protein-coding gene	gene with protein product	"""tuberoinfundibular 39 residues"""	608386				11861531	Standard	NM_178449		Approved	TIP39	uc002pnn.1	Q96A98		ENST00000270631.1:c.64C>G	19.37:g.49926533G>C	ENSP00000270631:p.Leu22Val	Somatic	99	2		WXS	Illumina HiSeq	.	107	6	NM_178449	Q96DJ4	Missense_Mutation	SNP	ENST00000270631.1	37	CCDS12763.1	.	.	.	.	.	.	.	.	.	.	g	6.292	0.421904	0.11928	0.002735	0.001283	ENSG00000142538	ENST00000270631	.	.	.	4.3	3.26	0.37387	.	0.489236	0.15528	U	0.257640	T	0.26521	0.0648	L	0.27053	0.805	0.09310	N	1	P	0.46142	0.873	B	0.39419	0.299	T	0.08066	-1.0740	9	0.87932	D	0	-7.2733	12.3672	0.55234	0.0:0.1717:0.8283:0.0	.	22	Q96A98	TIP39_HUMAN	V	22	.	ENSP00000270631:L22V	L	-	1	2	PTH2	54618345	0.088000	0.21588	0.012000	0.15200	0.011000	0.07611	-0.504000	0.06375	0.947000	0.37659	-0.370000	0.07254	CTG	.		0.692	PTH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465366.1	NM_178449	
KRT3	3850	hgsc.bcm.edu	37	12	53183978	53183978	+	Missense_Mutation	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr12:53183978C>T	ENST00000417996.2	-	9	1809	c.1735G>A	c.(1735-1737)Ggc>Agc	p.G579S	KRT3_ENST00000309505.3_Missense_Mutation_p.G580S	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	579	Gly-rich.|Tail.				epithelial cell differentiation (GO:0030855)|intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|skin(1)	23						ccgctgctgccgccgccaaat	0.701																																					p.G579S		.											KRT3,colon,carcinoma,0,1	KRT3	0	0			c.G1735A						.						11.0	27.0	22.0					12																	53183978		1688	3324	5012	SO:0001583	missense	3850	exon9			TGCTGCCGCCGCC		CCDS44895.1	12q13.13	2013-01-16			ENSG00000186442	ENSG00000186442		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6440	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 3"", ""cytokeratin 3"""	148043				7510223, 16831889	Standard	NM_057088		Approved	CK3, K3	uc001say.3	P12035	OTTHUMG00000169799	ENST00000417996.2:c.1735G>A	12.37:g.53183978C>T	ENSP00000413479:p.Gly579Ser	Somatic	21	1		WXS	Illumina HiSeq	.	47	5	NM_057088	A6NIS2|Q701L8	Missense_Mutation	SNP	ENST00000417996.2	37	CCDS44895.1	.	.	.	.	.	.	.	.	.	.	T	10.70	1.423846	0.25639	.	.	ENSG00000186442	ENST00000417996;ENST00000309505	D;T	0.96967	-4.19;-0.98	4.29	2.33	0.28932	.	.	.	.	.	D	0.87815	0.6272	N	0.22421	0.69	0.09310	N	1	P	0.35807	0.522	B	0.18561	0.022	T	0.78841	-0.2045	9	0.08381	T	0.77	.	6.4219	0.21748	0.0:0.6462:0.0:0.3538	.	579	P12035	K2C3_HUMAN	S	579;580	ENSP00000413479:G579S;ENSP00000312206:G580S	ENSP00000312206:G580S	G	-	1	0	KRT3	51470245	0.003000	0.15002	0.096000	0.21009	0.109000	0.19521	-0.125000	0.10579	0.456000	0.26937	0.561000	0.74099	GGC	.		0.701	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088	
FAM35A	54537	hgsc.bcm.edu	37	10	88946934	88946934	+	Missense_Mutation	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr10:88946934C>T	ENST00000298784.1	+	8	2399	c.2285C>T	c.(2284-2286)gCa>gTa	p.A762V	FAM35A_ENST00000298786.4_Missense_Mutation_p.A831V	NM_019054.2	NP_061927.2	Q86V20	FA35A_HUMAN	family with sequence similarity 35, member A	762										endometrium(2)|kidney(2)|large_intestine(5)|lung(1)|ovary(2)|prostate(2)|skin(2)	16						AACATTTCTGCAGACTGCCTC	0.388																																					p.A762V	Ovarian(175;703 2004 25460 32514 43441)	.											.	.	.	0			c.C2285T						.						119.0	99.0	106.0					10																	88946934		2203	4298	6501	SO:0001583	missense	54537	exon8			TTTCTGCAGACTG	BC051863	CCDS7383.1	10q23.2	2010-06-02			ENSG00000122376	ENSG00000122376			28773	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_019054		Approved	MGC5560, bA163M19.1, FAM35A1	uc001kei.4	Q86V20	OTTHUMG00000018669	ENST00000298784.1:c.2285C>T	10.37:g.88946934C>T	ENSP00000298784:p.Ala762Val	Somatic	104	0		WXS	Illumina HiSeq	.	80	3	NM_019054	O95885|Q9H991	Missense_Mutation	SNP	ENST00000298784.1	37	CCDS7383.1	.	.	.	.	.	.	.	.	.	.	C	17.80	3.479003	0.63849	.	.	ENSG00000122376	ENST00000298786;ENST00000298784;ENST00000358313	T;T;T	0.29142	1.58;1.6;1.6	3.13	3.13	0.36017	.	0.137951	0.49916	U	0.000139	T	0.19525	0.0469	N	0.19112	0.55	0.25002	N	0.991464	P;P	0.40476	0.59;0.718	B;B	0.35607	0.206;0.154	T	0.14924	-1.0455	10	0.45353	T	0.12	-6.4388	14.7807	0.69764	0.0:1.0:0.0:0.0	.	485;762	Q5VSZ0;Q86V20	.;FA35A_HUMAN	V	831;762;762	ENSP00000298786:A831V;ENSP00000298784:A762V;ENSP00000351064:A762V	ENSP00000298784:A762V	A	+	2	0	FAM35A	88936914	0.996000	0.38824	0.144000	0.22314	0.805000	0.45488	4.748000	0.62148	1.775000	0.52247	0.194000	0.17425	GCA	.		0.388	FAM35A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049196.2	NM_019054	
TP53RK	112858	hgsc.bcm.edu	37	20	45315633	45315633	+	3'UTR	SNP	A	A	G			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr20:45315633A>G	ENST00000372102.3	-	0	551				RP1-28H20.3_ENST00000606362.1_lincRNA			Q96S44	PRPK_HUMAN	TP53 regulating kinase						lipopolysaccharide biosynthetic process (GO:0009103)|protein phosphorylation (GO:0006468)|tRNA processing (GO:0008033)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)	p.L174fs*23(1)		kidney(1)|large_intestine(1)|lung(4)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				CAGCTGTTCCAGGGGGGGTTT	0.493																																					p.L174P		.											.,1	.	13	1	Insertion - Frameshift(1)	lung(1)	c.T521C						.						106.0	109.0	108.0					20																	45315633		2203	4300	6503	SO:0001624	3_prime_UTR_variant	112858	exon2			TGTTCCAGGGGGG		CCDS13401.1	20q13.2	2014-05-14	2004-05-10	2004-05-12	ENSG00000172315	ENSG00000172315			16197	protein-coding gene	gene with protein product		608679	"""chromosome 20 open reading frame 64"""	C20orf64		11546806, 12914926	Standard	NM_033550		Approved	dJ101A2.2, prpk, Nori-2p, BUD32	uc002xsk.3	Q96S44	OTTHUMG00000085887	ENST00000372102.3:c.*160T>C	20.37:g.45315633A>G		Somatic	44	0		WXS	Illumina HiSeq	.	42	2	NM_033550	B3KU44|Q3T977|Q5JZ01|Q6NZ60|Q96FM7|Q9NQE6	Missense_Mutation	SNP	ENST00000372102.3	37		.	.	.	.	.	.	.	.	.	.	A	0.654	-0.808436	0.02819	.	.	ENSG00000172315	ENST00000372114	T	0.21734	1.99	5.16	1.58	0.23477	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	1.902510	0.01879	N	0.037717	T	0.13543	0.0328	N	0.13098	0.295	0.09310	N	1	B	0.09022	0.002	B	0.12156	0.007	T	0.19976	-1.0289	10	0.30078	T	0.28	0.0	5.0219	0.14365	0.4169:0.1721:0.4109:0.0	.	174	Q96S44	PRPK_HUMAN	P	174	ENSP00000361186:L174P	ENSP00000361186:L174P	L	-	2	0	TP53RK	44749040	0.000000	0.05858	0.020000	0.16555	0.028000	0.11728	-0.027000	0.12371	0.427000	0.26145	0.533000	0.62120	CTG	.		0.493	TP53RK-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000193688.1	NM_033550	
CLCN6	1185	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	11897068	11897068	+	Missense_Mutation	SNP	C	C	G			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr1:11897068C>G	ENST00000346436.6	+	19	2045	c.1993C>G	c.(1993-1995)Ctc>Gtc	p.L665V	CLCN6_ENST00000376496.3_Missense_Mutation_p.L665V|CLCN6_ENST00000312413.6_3'UTR|CLCN6_ENST00000376487.3_Missense_Mutation_p.L643V	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	665					cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)	p.L665I(1)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		ATCCAGCATCCTCACCCGGGC	0.582																																					p.L665V		.											CLCN6,trunk,malignant_melanoma,0,1	CLCN6	0	1	Substitution - Missense(1)	skin(1)	c.C1993G						.						58.0	56.0	56.0					1																	11897068		2203	4300	6503	SO:0001583	missense	1185	exon19			AGCATCCTCACCC	X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"""Ion channels / Chloride channels : Voltage-sensitive"""	2024	protein-coding gene	gene with protein product		602726	"""chloride channel 6"""			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299	ENST00000346436.6:c.1993C>G	1.37:g.11897068C>G	ENSP00000234488:p.Leu665Val	Somatic	21	0		WXS	Illumina HiSeq	.	10	6	NM_001286	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Missense_Mutation	SNP	ENST00000346436.6	37	CCDS138.1	.	.	.	.	.	.	.	.	.	.	C	10.64	1.405880	0.25378	.	.	ENSG00000011021	ENST00000346436;ENST00000376487;ENST00000376496	D;D;D	0.91295	-2.79;-2.79;-2.82	5.7	4.78	0.61160	.	0.199442	0.42548	N	0.000694	D	0.83622	0.5294	L	0.29908	0.895	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.78198	-0.2297	10	0.39692	T	0.17	-26.6802	9.4136	0.38507	0.0:0.7803:0.1451:0.0746	.	643;665	F8W9R3;P51797	.;CLCN6_HUMAN	V	665;643;665	ENSP00000234488:L665V;ENSP00000365670:L643V;ENSP00000365679:L665V	ENSP00000234488:L665V	L	+	1	0	CLCN6	11819655	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	2.249000	0.43169	1.414000	0.47017	0.561000	0.74099	CTC	.		0.582	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286	
ZNF780B	163131	hgsc.bcm.edu	37	19	40540576	40540576	+	Silent	SNP	G	G	A	rs376431224		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:40540576G>A	ENST00000434248.1	-	5	2255	c.2190C>T	c.(2188-2190)tgC>tgT	p.C730C	ZNF780B_ENST00000221355.6_Silent_p.C582C	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	730					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)			endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					AGGCCTTTCCGCATTCTTTAC	0.403																																					p.C730C		.											ZNF780B_ENST00000434248,NS,carcinoma,0,2	ZNF780B_ENST00000434248	0	0			c.C2190T						.	G		1,4391	2.1+/-5.4	0,1,2195	57.0	62.0	60.0		2190	1.4	0.2	19		60	0,8594		0,0,4297	no	coding-synonymous	ZNF780B	NM_001005851.2		0,1,6492	AA,AG,GG		0.0,0.0228,0.0077		730/834	40540576	1,12985	2196	4297	6493	SO:0001819	synonymous_variant	163131	exon5			CTTTCCGCATTCT	AK127063	CCDS46077.1	19q13.2	2013-01-08	2006-08-15	2006-08-15	ENSG00000128000	ENSG00000128000		"""Zinc fingers, C2H2-type"", ""-"""	33109	protein-coding gene	gene with protein product			"""zinc finger protein 779"""	ZNF779			Standard	NM_001005851		Approved		uc002omu.3	Q9Y6R6	OTTHUMG00000155118	ENST00000434248.1:c.2190C>T	19.37:g.40540576G>A		Somatic	66	0		WXS	Illumina HiSeq	.	63	3	NM_001005851	B9EH00	Silent	SNP	ENST00000434248.1	37	CCDS46077.1																																																																																			.		0.403	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851	
KIAA1456	57604	hgsc.bcm.edu	37	8	12870249	12870249	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr8:12870249G>T	ENST00000524591.2	+	4	700	c.211G>T	c.(211-213)Gac>Tac	p.D71Y	KIAA1456_ENST00000447063.2_Missense_Mutation_p.D71Y	NM_001099677.1|NM_020844.2	NP_001093147.1|NP_065895.2	Q9P272	K1456_HUMAN	KIAA1456	71							methyltransferase activity (GO:0008168)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7						CGTGGGCTGTGACTACTGTGG	0.468																																					p.D71Y		.											.	.	.	0			c.G211T						.						140.0	139.0	140.0					8																	12870249		1959	4154	6113	SO:0001583	missense	57604	exon4			GGCTGTGACTACT	BC035082	CCDS47808.1	8p22	2013-10-04	2011-02-23	2011-02-23	ENSG00000250305	ENSG00000250305			26725	protein-coding gene	gene with protein product		615666	"""chromosome 8 open reading frame 79"""	C8orf79		23381944	Standard	NM_020844		Approved	FLJ36980	uc010lsq.3	Q8N9K7	OTTHUMG00000165477	ENST00000524591.2:c.211G>T	8.37:g.12870249G>T	ENSP00000432695:p.Asp71Tyr	Somatic	96	0		WXS	Illumina HiSeq	.	86	4	NM_020844	Q96AW6	Missense_Mutation	SNP	ENST00000524591.2	37	CCDS47808.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.882577	0.91740	.	.	ENSG00000250305	ENST00000447063;ENST00000524591;ENST00000532376	T;T	0.74002	-0.8;-0.8	5.73	5.73	0.89815	Methyltransferase type 11 (1);	.	.	.	.	D	0.91643	0.7359	H	0.97131	3.945	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.93532	0.6870	9	0.87932	D	0	.	20.2886	0.98538	0.0:0.0:1.0:0.0	.	71;71	E9PK20;Q9P272	.;K1456_HUMAN	Y	71	ENSP00000443288:D71Y;ENSP00000432695:D71Y	ENSP00000443288:D71Y	D	+	1	0	AC135352.2	12914620	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.882000	0.98803	0.655000	0.94253	GAC	.		0.468	KIAA1456-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383262.2	NM_001099677	
TTC41P	253724	hgsc.bcm.edu	37	12	104251050	104251050	+	IGR	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr12:104251050G>T								RP11-650K20.3 (12608 upstream) : RP11-642P15.1 (56754 downstream)																							ATTAAAGTTTGCATCAAAGAA	0.358																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			AAGTTTGCATCAA																													12.37:g.104251050G>T		Somatic	82	0		WXS	Illumina HiSeq	.	85	3	.		RNA	SNP		37																																																																																				.	0	0.358								
PTH1R	5745	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	3	46940168	46940168	+	Missense_Mutation	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr3:46940168C>T	ENST00000313049.5	+	7	858	c.655C>T	c.(655-657)Cgc>Tgc	p.R219C	PTH1R_ENST00000490109.1_3'UTR|PTH1R_ENST00000430002.2_Missense_Mutation_p.R219C|PTH1R_ENST00000449590.1_Missense_Mutation_p.R219C|PTH1R_ENST00000418619.1_Missense_Mutation_p.R219C			Q03431	PTH1R_HUMAN	parathyroid hormone 1 receptor	219					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|bone mineralization (GO:0030282)|bone resorption (GO:0045453)|cell maturation (GO:0048469)|chondrocyte differentiation (GO:0002062)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cell proliferation (GO:0008285)|osteoblast development (GO:0002076)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of inositol phosphate biosynthetic process (GO:0060732)|skeletal system development (GO:0001501)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	parathyroid hormone receptor activity (GO:0004991)|peptide hormone binding (GO:0017046)|protein self-association (GO:0043621)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(5)|skin(2)|stomach(1)|urinary_tract(2)	19					Preotact(DB05829)|Teriparatide(DB06285)	GCACTGCACGCGCAACTACAT	0.652																																					p.R219C		.											.	.	.	0			c.C655T						.						55.0	48.0	50.0					3																	46940168		2203	4300	6503	SO:0001583	missense	5745	exon8			TGCACGCGCAACT		CCDS2747.1	3p22-p21.1	2012-08-10	2008-11-18	2008-11-18	ENSG00000160801	ENSG00000160801		"""GPCR / Class B : Parathyroid hormone receptors"""	9608	protein-coding gene	gene with protein product		168468	"""parathyroid hormone receptor 1"""	PTHR, PTHR1		8020952	Standard	NM_001184744		Approved		uc021wxg.1	Q03431	OTTHUMG00000133515	ENST00000313049.5:c.655C>T	3.37:g.46940168C>T	ENSP00000321999:p.Arg219Cys	Somatic	19	0		WXS	Illumina HiSeq	.	15	7	NM_001184744	Q2M1U3	Missense_Mutation	SNP	ENST00000313049.5	37	CCDS2747.1	.	.	.	.	.	.	.	.	.	.	C	19.82	3.897650	0.72639	.	.	ENSG00000160801	ENST00000449590;ENST00000418619;ENST00000427125;ENST00000430002;ENST00000313049;ENST00000313063	T;T;T;T;T	0.37058	1.22;1.22;1.22;1.22;1.22	4.71	3.8	0.43715	GPCR, family 2-like (1);	.	.	.	.	T	0.68879	0.3049	H	0.97077	3.935	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.75082	-0.3443	9	0.87932	D	0	.	9.3578	0.38177	0.1725:0.681:0.1465:0.0	.	219	Q03431	PTH1R_HUMAN	C	219;219;219;219;219;417	ENSP00000402723:R219C;ENSP00000411424:R219C;ENSP00000400977:R219C;ENSP00000413774:R219C;ENSP00000321999:R219C	ENSP00000321999:R219C	R	+	1	0	PTH1R	46915172	0.692000	0.27719	0.959000	0.39883	0.981000	0.71138	1.372000	0.34261	0.902000	0.36520	0.561000	0.74099	CGC	.		0.652	PTH1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257481.1	NM_000316	
PBRM1	55193	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	52662939	52662939	+	Nonsense_Mutation	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr3:52662939G>A	ENST00000296302.7	-	12	1415	c.1414C>T	c.(1414-1416)Cga>Tga	p.R472*	PBRM1_ENST00000356770.4_Nonsense_Mutation_p.R440*|PBRM1_ENST00000337303.4_Nonsense_Mutation_p.R472*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.R472*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.R472*|PBRM1_ENST00000409767.1_Nonsense_Mutation_p.R472*|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.R472*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.R472*			Q86U86	PB1_HUMAN	polybromo 1	472					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TTTAGAACTCGCTTGTAGATG	0.318			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																p.R472X		.		Rec	yes		3	3p21	55193	polybromo 1		E	.	.	.	0			c.C1414T						.						101.0	95.0	97.0					3																	52662939		2203	4300	6503	SO:0001587	stop_gained	55193	exon13			GAACTCGCTTGTA	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.1414C>T	3.37:g.52662939G>A	ENSP00000296302:p.Arg472*	Somatic	74	0		WXS	Illumina HiSeq	.	41	11	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	G	37	6.182101	0.97352	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	.	.	.	5.4	1.45	0.22620	.	0.136047	0.50627	D	0.000116	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	-21.0362	11.5495	0.50713	0.0:0.1018:0.3723:0.5259	.	.	.	.	X	440;472;472;472;472;472;472;472;472;416	.	ENSP00000296302:R472X	R	-	1	2	PBRM1	52637979	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	2.206000	0.42779	-0.016000	0.14127	-0.309000	0.09137	CGA	.		0.318	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	
CHD1L	9557	hgsc.bcm.edu;bcgsc.ca	37	1	146724303	146724303	+	Silent	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr1:146724303G>T	ENST00000369258.4	+	2	173	c.153G>T	c.(151-153)ctG>ctT	p.L51L	CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000431239.1_Silent_p.L51L|CHD1L_ENST00000361293.5_Intron|RP11-337C18.10_ENST00000606856.1_RNA|CHD1L_ENST00000369259.3_Intron	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	51					ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					CTTACCAGCTGGAGGGAGTAA	0.488																																					p.L51L		.											.	.	.	0			c.G153T						.						141.0	129.0	133.0					1																	146724303		2203	4300	6503	SO:0001819	synonymous_variant	9557	exon2			CCAGCTGGAGGGA	AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.153G>T	1.37:g.146724303G>T		Somatic	64	0		WXS	Illumina HiSeq	.	71	4	NM_004284	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Silent	SNP	ENST00000369258.4	37	CCDS927.1	.	.	.	.	.	.	.	.	.	.	G	8.814	0.935970	0.18206	.	.	ENSG00000131778	ENST00000254086	.	.	.	5.23	2.34	0.29019	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	4.7462	0.13038	0.1799:0.0:0.6481:0.1719	.	.	.	.	X	14	.	ENSP00000254086:G14X	G	+	1	0	CHD1L	145190927	1.000000	0.71417	0.979000	0.43373	0.833000	0.47200	2.889000	0.48601	0.223000	0.20920	-0.136000	0.14681	GGA	.		0.488	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284	
GPR110	266977	hgsc.bcm.edu	37	6	46977650	46977650	+	Silent	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr6:46977650G>T	ENST00000371253.2	-	11	1736	c.1521C>A	c.(1519-1521)tcC>tcA	p.S507S	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Silent_p.S310S	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	507					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	29						GAATAACCGTGGATATCACAG	0.413																																					p.S507S		.											.	.	.	0			c.C1521A						.						72.0	74.0	73.0					6																	46977650		2203	4300	6503	SO:0001819	synonymous_variant	266977	exon11			AACCGTGGATATC	AB083618	CCDS4920.1, CCDS34471.1	6p21.1	2014-08-08			ENSG00000153292	ENSG00000153292		"""-"", ""GPCR / Class B : Orphans"""	18990	protein-coding gene	gene with protein product						12435584, 14623098	Standard	XM_005249006		Approved	hGPCR36, PGR19	uc003oyt.3	Q5T601	OTTHUMG00000014795	ENST00000371253.2:c.1521C>A	6.37:g.46977650G>T		Somatic	71	0		WXS	Illumina HiSeq	.	78	4	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Silent	SNP	ENST00000371253.2	37	CCDS34471.1																																																																																			.		0.413	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840	
RBFA	79863	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	77802202	77802202	+	Missense_Mutation	SNP	A	A	C			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr18:77802202A>C	ENST00000306735.5	+	5	697	c.559A>C	c.(559-561)Aat>Cat	p.N187H	RP11-795F19.5_ENST00000564012.1_Intron|RP11-795F19.5_ENST00000569722.1_Intron|RBFA_ENST00000262197.7_Intron	NM_024805.2	NP_079081.2	Q8N0V3	RBFA_HUMAN	ribosome binding factor A (putative)	187					rRNA processing (GO:0006364)	mitochondrion (GO:0005739)				endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|urinary_tract(1)	15						AGACAAGGGAAATGCAGCTCT	0.403																																					p.N187H		.											.	.	.	0			c.A559C						.						95.0	83.0	87.0					18																	77802202		2203	4300	6503	SO:0001583	missense	79863	exon5			AAGGGAAATGCAG	BC014195	CCDS12021.1, CCDS54194.1	18q23	2010-10-21	2010-10-21	2010-10-21	ENSG00000101546	ENSG00000101546			26120	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 22"""	C18orf22		12477932	Standard	NM_024805		Approved	FLJ21172, HsT169	uc002lns.3	Q8N0V3	OTTHUMG00000132923	ENST00000306735.5:c.559A>C	18.37:g.77802202A>C	ENSP00000305696:p.Asn187His	Somatic	73	0		WXS	Illumina HiSeq	.	39	10	NM_024805	Q6PF07|Q8WZ65|Q9H776	Missense_Mutation	SNP	ENST00000306735.5	37	CCDS12021.1	.	.	.	.	.	.	.	.	.	.	A	7.266	0.606155	0.14002	.	.	ENSG00000101546	ENST00000306735	T	0.41758	0.99	5.18	-6.99	0.01605	K homology domain-like, alpha/beta (1);Ribosome-binding factor A domain (1);	1.621700	0.03356	N	0.196890	T	0.19287	0.0463	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.12837	0.008	T	0.11494	-1.0585	10	0.15066	T	0.55	-9.5546	3.0609	0.06199	0.2341:0.117:0.4373:0.2116	.	187	Q8N0V3	RBFA_HUMAN	H	187	ENSP00000305696:N187H	ENSP00000305696:N187H	N	+	1	0	RBFA	75903190	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.277000	0.08502	-1.470000	0.01888	0.477000	0.44152	AAT	.		0.403	RBFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256436.2	NM_024805	
HADHB	3032	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	26512787	26512787	+	Splice_Site	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr2:26512787G>A	ENST00000317799.5	+	16	1495	c.1391G>A	c.(1390-1392)gGc>gAc	p.G464D	HADHB_ENST00000494615.1_3'UTR|HADHB_ENST00000405867.3_Splice_Site_p.G341D|HADHB_ENST00000537713.1_Splice_Site_p.G449D|HADHB_ENST00000545822.1_Splice_Site_p.G442D	NM_000183.2	NP_000174.1	P55084	ECHB_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit	464					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrial envelope (GO:0005740)|mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acyltransferase activity (GO:0003988)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCTTTACAGGGCCATGCTATG	0.418																																					p.G464D		.											.	.	.	0			c.G1391A						.						185.0	172.0	177.0					2																	26512787		2203	4300	6503	SO:0001630	splice_region_variant	3032	exon16			TACAGGGCCATGC		CCDS1722.1, CCDS62871.1, CCDS62872.1	2p23	2010-04-30	2010-04-30		ENSG00000138029	ENSG00000138029	2.3.1.16		4803	protein-coding gene	gene with protein product	"""mitochondrial trifunctional protein, beta subunit"""	143450	"""hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit"""			9605857	Standard	NM_000183		Approved	MTPB	uc002rgz.3	P55084	OTTHUMG00000096978	ENST00000317799.5:c.1390-1G>A	2.37:g.26512787G>A		Somatic	60	0		WXS	Illumina HiSeq	.	68	13	NM_000183	B2RB16|B4E2W0|O14969|Q53TA6|Q96C77|Q9H3F5|Q9T2V8	Missense_Mutation	SNP	ENST00000317799.5	37	CCDS1722.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.679168	0.88542	.	.	ENSG00000138029	ENST00000317799;ENST00000405867;ENST00000537713;ENST00000545822	D;D;D;D	0.95377	-3.69;-3.69;-3.69;-3.69	5.62	5.62	0.85841	Thiolase-like, subgroup (1);Thiolase-like (1);Thiolase, C-terminal (1);	0.162618	0.53938	D	0.000058	D	0.98988	0.9655	H	0.99825	4.815	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.999;1.0	D	0.98917	1.0782	10	0.87932	D	0	-12.8745	16.4413	0.83901	0.0:0.0:1.0:0.0	.	449;442;341;464	F5GZQ3;B4E2W0;B5MD38;P55084	.;.;.;ECHB_HUMAN	D	464;341;449;442	ENSP00000325136:G464D;ENSP00000385411:G341D;ENSP00000444295:G449D;ENSP00000442665:G442D	ENSP00000325136:G464D	G	+	2	0	HADHB	26366291	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.707000	0.74654	2.657000	0.90304	0.650000	0.86243	GGC	.		0.418	HADHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214050.2	NM_000183	Missense_Mutation
FMO6P	388714	hgsc.bcm.edu	37	1	171116726	171116726	+	Intron	SNP	C	C	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr1:171116726C>A	ENST00000236166.3	+	4	594							O60774	FMO6_HUMAN	flavin containing monooxygenase 6 pseudogene							endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)										TTCATAATTTCTGAAAATCAG	0.358																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	388714	.			TAATTTCTGAAAA	AK130511		1q24.3	2011-08-04	2006-12-04	2006-12-04	ENSG00000117507	ENSG00000117507			24024	pseudogene	pseudogene			"""flavin containing monooxygenase 6"""	FMO6		15077013	Standard	NR_002601		Approved		uc001ghj.1	O60774	OTTHUMG00000035503	ENST00000236166.3:c.485-39C>A	1.37:g.171116726C>A		Somatic	70	0		WXS	Illumina HiSeq	.	90	18	.		RNA	SNP	ENST00000236166.3	37																																																																																				.		0.358	FMO6P-003	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000385941.4	XM_371326	
TTLL6	284076	hgsc.bcm.edu	37	17	46862554	46862554	+	Missense_Mutation	SNP	G	G	T	rs148198060		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr17:46862554G>T	ENST00000393382.3	-	13	1912	c.1771C>A	c.(1771-1773)Cca>Aca	p.P591T	TTLL6_ENST00000433608.2_Missense_Mutation_p.P284T	NM_001130918.1	NP_001124390.1			tubulin tyrosine ligase-like family, member 6											endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						AATGTCAATGGCTGGATGTAC	0.498																																					p.P591T		.											TTLL6_ENST00000393382,NS,carcinoma,0,2	TTLL6_ENST00000393382	0	0			c.C1771A						.						89.0	80.0	83.0					17																	46862554		2203	4300	6503	SO:0001583	missense	284076	exon13			TCAATGGCTGGAT	AK093127	CCDS11537.2, CCDS45724.1	17q21.32	2013-02-14			ENSG00000170703	ENSG00000170703		"""Tubulin tyrosine ligase-like family"""	26664	protein-coding gene	gene with protein product		610849				15890843	Standard	NM_173623		Approved	FLJ35808	uc021tzm.1	Q8N841	OTTHUMG00000156978	ENST00000393382.3:c.1771C>A	17.37:g.46862554G>T	ENSP00000377043:p.Pro591Thr	Somatic	45	0		WXS	Illumina HiSeq	.	47	2	NM_001130918		Missense_Mutation	SNP	ENST00000393382.3	37	CCDS45724.1	.	.	.	.	.	.	.	.	.	.	G	13.03	2.115090	0.37339	.	.	ENSG00000170703	ENST00000440941;ENST00000305326;ENST00000433608;ENST00000393382	.	.	.	4.61	2.63	0.31362	.	13.783700	0.00166	N	0.000000	T	0.58793	0.2147	M	0.61703	1.905	0.09310	N	1	P;P;D	0.64830	0.931;0.931;0.994	P;P;P	0.60949	0.554;0.554;0.881	T	0.25012	-1.0144	9	0.49607	T	0.09	.	6.4609	0.21956	0.2136:0.0:0.7864:0.0	.	543;344;284	Q8N841;D3DTW0;G5E937	TTLL6_HUMAN;.;.	T	591;284;269;543	.	ENSP00000302547:P284T	P	-	1	0	TTLL6	44217553	0.909000	0.30893	0.521000	0.27850	0.011000	0.07611	1.570000	0.36439	1.309000	0.44985	0.561000	0.74099	CCA	.		0.498	TTLL6-003	KNOWN	downstream_ATG|non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346939.3	NM_173623	
CTNNA3	29119	hgsc.bcm.edu	37	10	68381522	68381522	+	Silent	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr10:68381522G>T	ENST00000433211.2	-	10	1476	c.1302C>A	c.(1300-1302)tcC>tcA	p.S434S	CTNNA3_ENST00000373744.4_Silent_p.S434S	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						TTGTTGACATGGAACAAGCAA	0.333																																					p.S434S		.											CTNNA3_ENST00000433211,NS,carcinoma,0,2	CTNNA3_ENST00000433211	0	0			c.C1302A						.						84.0	79.0	81.0					10																	68381522		2203	4299	6502	SO:0001819	synonymous_variant	29119	exon10			TGACATGGAACAA	AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230			2511	protein-coding gene	gene with protein product		607667				12596047, 11590244	Standard	XM_005269717		Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.1302C>A	10.37:g.68381522G>T		Somatic	60	0		WXS	Illumina HiSeq	.	70	2	NM_013266		Silent	SNP	ENST00000433211.2	37	CCDS7269.1																																																																																			.		0.333	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266	
TBC1D32	221322	hgsc.bcm.edu	37	6	121481233	121481233	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr6:121481233G>T	ENST00000398212.2	-	24	2745	c.2696C>A	c.(2695-2697)cCt>cAt	p.P899H	TBC1D32_ENST00000275159.6_Missense_Mutation_p.P940H|TBC1D32_ENST00000398197.2_5'UTR	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	899					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)	p.P899R(1)									CATTGGCCAAGGATATGGATT	0.308																																					p.P899H		.											C6orf170,NS,carcinoma,0,1	C6orf170	0	1	Substitution - Missense(1)	lung(1)	c.C2696A						.						111.0	104.0	106.0					6																	121481233		1820	4083	5903	SO:0001583	missense	221322	exon24			GGCCAAGGATATG	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.2696C>A	6.37:g.121481233G>T	ENSP00000381270:p.Pro899His	Somatic	35	0		WXS	Illumina HiSeq	.	44	2	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	G	18.90	3.721529	0.68959	.	.	ENSG00000146350	ENST00000275159;ENST00000398212	T;T	0.29397	1.57;1.57	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.50154	0.1599	M	0.71581	2.175	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.54423	-0.8296	10	0.72032	D	0.01	.	18.7188	0.91686	0.0:0.0:1.0:0.0	.	940;899	Q96NH3-4;Q96NH3	.;BROMI_HUMAN	H	940;899	ENSP00000275159:P940H;ENSP00000381270:P899H	ENSP00000275159:P940H	P	-	2	0	C6orf170	121522932	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.567000	0.67378	2.479000	0.83701	0.460000	0.39030	CCT	.		0.308	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
PLXNA4	91584	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	132193245	132193245	+	Missense_Mutation	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr7:132193245G>A	ENST00000359827.3	-	2	1170	c.208C>T	c.(208-210)Cgg>Tgg	p.R70W	PLXNA4_ENST00000423507.2_Missense_Mutation_p.R70W|PLXNA4_ENST00000378539.5_Missense_Mutation_p.R70W|PLXNA4_ENST00000321063.4_Missense_Mutation_p.R70W			Q9HCM2	PLXA4_HUMAN	plexin A4	70	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						TTGTAAATCCGATTGACGGCC	0.577																																					p.R70W		.											.	.	.	0			c.C208T						.						57.0	61.0	59.0					7																	132193245		2203	4300	6503	SO:0001583	missense	91584	exon2			AAATCCGATTGAC	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.208C>T	7.37:g.132193245G>A	ENSP00000352882:p.Arg70Trp	Somatic	89	0		WXS	Illumina HiSeq	.	98	41	NM_001105543	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	G	13.52	2.263105	0.39995	.	.	ENSG00000221866	ENST00000321063;ENST00000359827;ENST00000423507;ENST00000378539	T;T;T;T	0.12361	2.69;2.69;2.69;2.69	5.39	3.52	0.40303	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.64402	U	0.000010	T	0.23451	0.0567	M	0.74389	2.26	0.58432	D	0.999999	P;P;P	0.45594	0.862;0.771;0.683	B;P;B	0.49252	0.371;0.604;0.17	T	0.00888	-1.1526	10	0.62326	D	0.03	.	8.3567	0.32335	0.075:0.0:0.3683:0.5567	.	70;70;70	Q9HCM2-2;A4D1N6;Q9HCM2	.;.;PLXA4_HUMAN	W	70	ENSP00000323194:R70W;ENSP00000352882:R70W;ENSP00000392772:R70W;ENSP00000367800:R70W	ENSP00000323194:R70W	R	-	1	2	PLXNA4	131843785	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	2.044000	0.41241	0.602000	0.29896	0.462000	0.41574	CGG	.		0.577	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
MDN1	23195	hgsc.bcm.edu;bcgsc.ca	37	6	90362819	90362819	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr6:90362819G>T	ENST00000369393.3	-	94	15832	c.15717C>A	c.(15715-15717)gaC>gaA	p.D5239E	MDN1_ENST00000428876.1_Missense_Mutation_p.D5239E			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	5239					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CTGTTCTGGGGTCTTGGTCTT	0.393																																					p.D5239E		.											.	.	.	0			c.C15717A						.						273.0	266.0	268.0					6																	90362819		2203	4300	6503	SO:0001583	missense	23195	exon94			TCTGGGGTCTTGG	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.15717C>A	6.37:g.90362819G>T	ENSP00000358400:p.Asp5239Glu	Somatic	88	0		WXS	Illumina HiSeq	.	51	4	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	G	4.302	0.055245	0.08291	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.39997	1.05;1.05	6.17	1.7	0.24286	.	0.317683	0.32918	N	0.005491	T	0.09862	0.0242	L	0.48362	1.52	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.32798	-0.9893	10	0.08837	T	0.75	.	4.0762	0.09906	0.1487:0.2274:0.5076:0.1163	.	5239	Q9NU22	MDN1_HUMAN	E	5239	ENSP00000358400:D5239E;ENSP00000413970:D5239E	ENSP00000358400:D5239E	D	-	3	2	MDN1	90419540	0.000000	0.05858	0.083000	0.20561	0.006000	0.05464	-0.410000	0.07151	0.416000	0.25844	0.655000	0.94253	GAC	.		0.393	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
ZNF846	162993	hgsc.bcm.edu	37	19	9869374	9869374	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:9869374G>T	ENST00000397902.2	-	6	792	c.379C>A	c.(379-381)Cca>Aca	p.P127T	ZNF846_ENST00000586293.1_3'UTR|ZNF846_ENST00000592859.1_5'UTR|ZNF846_ENST00000588267.1_5'UTR	NM_001077624.1	NP_001071092.1	Q147U1	ZN846_HUMAN	zinc finger protein 846	127					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22						ATAAGAAATGGGTGTTCATTG	0.343																																					p.P127T		.											.	.	.	0			c.C379A						.						136.0	126.0	129.0					19																	9869374		1834	4091	5925	SO:0001583	missense	162993	exon6			GAAATGGGTGTTC	AK097652	CCDS42496.1	19p13.2	2013-01-08			ENSG00000196605	ENSG00000196605		"""Zinc fingers, C2H2-type"", ""-"""	27260	protein-coding gene	gene with protein product							Standard	NM_001077624		Approved		uc002mmb.1	Q147U1		ENST00000397902.2:c.379C>A	19.37:g.9869374G>T	ENSP00000380999:p.Pro127Thr	Somatic	33	0		WXS	Illumina HiSeq	.	64	4	NM_001077624	A8K0H1|B3KUP1	Missense_Mutation	SNP	ENST00000397902.2	37	CCDS42496.1	.	.	.	.	.	.	.	.	.	.	.	4.494	0.091603	0.08632	.	.	ENSG00000196605	ENST00000397902	T	0.14266	2.52	2.15	1.07	0.20283	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03305	0.0096	N	0.01284	-0.91	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43653	-0.9378	8	.	.	.	.	1.4914	0.02457	0.462:0.0:0.2298:0.3082	.	127	Q147U1	ZN846_HUMAN	T	127	ENSP00000380999:P127T	.	P	-	1	0	ZNF846	9730374	0.000000	0.05858	0.001000	0.08648	0.120000	0.20174	-0.302000	0.08221	0.299000	0.22661	0.558000	0.71614	CCA	.		0.343	ZNF846-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450253.1	NM_001077624	
FOXS1	2307	hgsc.bcm.edu	37	20	30433234	30433234	+	Missense_Mutation	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr20:30433234G>A	ENST00000375978.3	-	1	186	c.112C>T	c.(112-114)Cgg>Tgg	p.R38W		NM_004118.3	NP_004109.1	O43638	FOXS1_HUMAN	forkhead box S1	38					blood vessel development (GO:0001568)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|neuromuscular process controlling balance (GO:0050885)|positive regulation of multicellular organism growth (GO:0040018)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	9						AGGGTGGCCCGCTGCCCCGGT	0.647																																					p.R38W		.											.	.	.	0			c.C112T						.						60.0	57.0	58.0					20																	30433234		2203	4300	6503	SO:0001583	missense	2307	exon1			TGGCCCGCTGCCC	AF042831	CCDS13192.1	20q11.1-q11.2	2008-04-10	2008-04-10	2008-04-10	ENSG00000179772	ENSG00000179772		"""Forkhead boxes"""	3735	protein-coding gene	gene with protein product		602939	"""forkhead (Drosophila)-like 18"", ""forkhead-like 18 (Drosophila)"""	FKHL18		9325056, 17062144	Standard	NM_004118		Approved	FREAC10	uc002wwt.1	O43638	OTTHUMG00000032183	ENST00000375978.3:c.112C>T	20.37:g.30433234G>A	ENSP00000365145:p.Arg38Trp	Somatic	123	0		WXS	Illumina HiSeq	.	95	4	NM_004118	Q96D28	Missense_Mutation	SNP	ENST00000375978.3	37	CCDS13192.1	.	.	.	.	.	.	.	.	.	.	G	18.72	3.684671	0.68157	.	.	ENSG00000179772	ENST00000375978	D	0.95885	-3.84	4.51	2.32	0.28847	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.39615	N	0.001317	D	0.98086	0.9369	H	0.95816	3.725	0.49051	D	0.99974	D	0.89917	1.0	D	0.85130	0.997	D	0.98231	1.0483	10	0.87932	D	0	.	11.4611	0.50211	0.0:0.0:0.5796:0.4204	.	38	O43638	FOXS1_HUMAN	W	38	ENSP00000365145:R38W	ENSP00000365145:R38W	R	-	1	2	FOXS1	29896895	0.954000	0.32549	1.000000	0.80357	0.930000	0.56654	1.241000	0.32743	1.072000	0.40860	0.555000	0.69702	CGG	.		0.647	FOXS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078560.2	NM_004118	
Unknown	0	hgsc.bcm.edu	37	2	95464459	95464459	+	IGR	SNP	A	A	G			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr2:95464459A>G								None (None upstream) : ANKRD20A8P (15389 downstream)																							AGATAAACTTACCTGATTTAA	0.313																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	729171	.			AAACTTACCTGAT																													2.37:g.95464459A>G		Somatic	95	0		WXS	Illumina HiSeq	.	228	40	.		RNA	SNP		37																																																																																				.	0	0.313								
SPATA20	64847	hgsc.bcm.edu	37	17	48629444	48629444	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr17:48629444G>T	ENST00000356488.4	+	13	1895	c.1812G>T	c.(1810-1812)caG>caT	p.Q604H	SPATA20_ENST00000393244.3_Missense_Mutation_p.Q560H|SPATA20_ENST00000511937.1_3'UTR|SPATA20_ENST00000006658.6_Missense_Mutation_p.Q620H	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	604					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			TGCGGCTGCAGGACACACAGG	0.657																																					p.Q620H		.											.	.	.	0			c.G1860T						.						30.0	35.0	33.0					17																	48629444		2203	4299	6502	SO:0001583	missense	64847	exon14			GCTGCAGGACACA		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"""hypothetical protein FLJ21347"""	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.1812G>T	17.37:g.48629444G>T	ENSP00000348878:p.Gln604His	Somatic	92	0		WXS	Illumina HiSeq	.	94	4	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	37	CCDS58563.1	.	.	.	.	.	.	.	.	.	.	G	19.68	3.872016	0.72180	.	.	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.53423	0.62;0.62;0.62	4.77	2.77	0.32553	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);	0.059953	0.64402	D	0.000002	T	0.60586	0.2280	M	0.76433	2.335	0.54753	D	0.999986	D;P	0.54772	0.968;0.918	P;P	0.57283	0.661;0.817	T	0.62167	-0.6911	10	0.62326	D	0.03	-14.6466	10.9587	0.47372	0.1537:0.0:0.8463:0.0	.	604;620	Q8TB22;Q8TB22-2	SPT20_HUMAN;.	H	620;604;560	ENSP00000006658:Q620H;ENSP00000348878:Q604H;ENSP00000376935:Q560H	ENSP00000006658:Q620H	Q	+	3	2	SPATA20	45984443	1.000000	0.71417	0.993000	0.49108	0.989000	0.77384	4.664000	0.61540	0.438000	0.26450	-0.140000	0.14226	CAG	.		0.657	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827	
CARD10	29775	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	37900277	37900277	+	Missense_Mutation	SNP	T	T	C			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr22:37900277T>C	ENST00000403299.1	-	10	1766	c.1550A>G	c.(1549-1551)aAt>aGt	p.N517S	CARD10_ENST00000406271.3_Missense_Mutation_p.N231S|CARD10_ENST00000251973.5_Missense_Mutation_p.N517S			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	517					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					GGAGAGCCGATTGATCTCCTT	0.642																																					p.N517S		.											.	.	.	0			c.A1550G						.						60.0	56.0	57.0					22																	37900277		2188	4284	6472	SO:0001583	missense	29775	exon9			AGCCGATTGATCT	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.1550A>G	22.37:g.37900277T>C	ENSP00000384570:p.Asn517Ser	Somatic	28	0		WXS	Illumina HiSeq	.	22	8	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Missense_Mutation	SNP	ENST00000403299.1	37	CCDS13948.1	.	.	.	.	.	.	.	.	.	.	T	19.05	3.751077	0.69533	.	.	ENSG00000100065	ENST00000403299;ENST00000406271;ENST00000251973;ENST00000437756	T;T;T;T	0.38240	1.15;1.15;1.15;1.15	5.71	5.71	0.89125	.	0.226025	0.44688	D	0.000436	T	0.29556	0.0737	L	0.51422	1.61	0.37789	D	0.927303	P;B	0.52316	0.952;0.291	B;B	0.40741	0.339;0.177	T	0.27839	-1.0062	10	0.02654	T	1	-44.7599	14.8725	0.70468	0.0:0.0:0.0:1.0	.	517;231	Q9BWT7;Q8NC81	CAR10_HUMAN;.	S	517;231;517;158	ENSP00000384570:N517S;ENSP00000385799:N231S;ENSP00000251973:N517S;ENSP00000416239:N158S	ENSP00000251973:N517S	N	-	2	0	CARD10	36230223	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	5.032000	0.64140	2.317000	0.78254	0.459000	0.35465	AAT	.		0.642	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550	
MUC4	4585	hgsc.bcm.edu	37	3	195505863	195505863	+	Silent	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr3:195505863G>A	ENST00000463781.3	-	2	13047	c.12588C>T	c.(12586-12588)acC>acT	p.T4196T	MUC4_ENST00000475231.1_Silent_p.T4196T|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T4196T(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGTGTCGGTGACAGGAA	0.607																																					p.T4196T		.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4_ENST00000463781	0	1	Substitution - coding silent(1)	prostate(1)	c.C12588T						.						19.0	14.0	16.0					3																	195505863		689	1578	2267	SO:0001819	synonymous_variant	4585	exon2			AGTGTCGGTGACA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12588C>T	3.37:g.195505863G>A		Somatic	97	0		WXS	Illumina HiSeq	.	105	8	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.		0.607	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ITGA4	3676	hgsc.bcm.edu;bcgsc.ca	37	2	182395369	182395369	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr2:182395369G>T	ENST00000397033.2	+	24	3087	c.2657G>T	c.(2656-2658)aGg>aTg	p.R886M		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	886					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	ACTGATAAGAGGCTATTGGTA	0.403																																					p.R886M		.											.	.	.	0			c.G2657T						.						207.0	185.0	192.0					2																	182395369		1897	4124	6021	SO:0001583	missense	3676	exon24			ATAAGAGGCTATT		CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"""CD molecules"", ""Integrins"""	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.2657G>T	2.37:g.182395369G>T	ENSP00000380227:p.Arg886Met	Somatic	102	0		WXS	Illumina HiSeq	.	70	4	NM_000885	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	37	CCDS42788.1	.	.	.	.	.	.	.	.	.	.	G	17.25	3.341415	0.60963	.	.	ENSG00000115232	ENST00000397033	T	0.48836	0.8	5.24	3.24	0.37175	.	0.089250	0.85682	N	0.000000	T	0.58708	0.2141	M	0.61703	1.905	0.41124	D	0.985832	D	0.76494	0.999	D	0.68765	0.96	T	0.58272	-0.7665	10	0.87932	D	0	.	5.6021	0.17359	0.1043:0.0:0.6561:0.2397	.	886	P13612	ITA4_HUMAN	M	886	ENSP00000380227:R886M	ENSP00000380227:R886M	R	+	2	0	ITGA4	182103614	0.996000	0.38824	0.943000	0.38184	0.970000	0.65996	2.710000	0.47169	0.502000	0.28037	0.563000	0.77884	AGG	.		0.403	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1		
MRGPRE	116534	hgsc.bcm.edu;broad.mit.edu	37	11	3249154	3249154	+	Silent	SNP	G	G	A	rs373696773		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr11:3249154G>A	ENST00000389832.5	-	2	1182	c.876C>T	c.(874-876)gaC>gaT	p.D292D	AC109309.4_ENST00000418995.2_RNA|MRGPRE_ENST00000436689.2_Silent_p.D291D			Q86SM8	MRGRE_HUMAN	MAS-related GPR, member E	292						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	19		Medulloblastoma(188;0.00106)|all_epithelial(84;0.00111)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00529)|LUSC - Lung squamous cell carcinoma(625;0.19)		GCTCAGCCTCGTCTCCCAGCG	0.741																																					p.D292D		.											.	.	.	0			c.C876T						.	G		0,3636		0,0,1818	6.0	8.0	8.0		873	-7.1	0.0	11		8	1,7923		0,1,3961	no	coding-synonymous	MRGPRE	NM_001039165.2		0,1,5779	AA,AG,GG		0.0126,0.0,0.0087		291/312	3249154	1,11559	1818	3962	5780	SO:0001819	synonymous_variant	116534	exon2			AGCCTCGTCTCCC	AY255572	CCDS41603.1, CCDS41603.2	11p15.5	2012-08-21	2004-03-25		ENSG00000184350	ENSG00000184350		"""GPCR / Class A : Orphans"""	30694	protein-coding gene	gene with protein product		607232	"""G protein-coupled receptor 167"""	GPR167		11551509	Standard	NM_001039165		Approved	mrgE	uc001lxq.5	Q86SM8	OTTHUMG00000011708	ENST00000389832.5:c.876C>T	11.37:g.3249154G>A		Somatic	13	0		WXS	Illumina HiSeq	.	8	6	NM_001039165	Q2M1V7	Silent	SNP	ENST00000389832.5	37																																																																																				.		0.741	MRGPRE-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000032346.5	XM_171536	
CNTFR	1271	hgsc.bcm.edu	37	9	34557626	34557626	+	Missense_Mutation	SNP	A	A	G			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr9:34557626A>G	ENST00000378980.3	-	6	795	c.502T>C	c.(502-504)Tac>Cac	p.Y168H	CNTFR_ENST00000351266.4_Missense_Mutation_p.Y168H	NM_001207011.1|NM_147164.2	NP_001193940.1|NP_671693.1	P26992	CNTFR_HUMAN	ciliary neurotrophic factor receptor	168	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				brainstem development (GO:0003360)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|positive regulation of cell proliferation (GO:0008284)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|skeletal muscle organ development (GO:0060538)|suckling behavior (GO:0001967)	anchored component of membrane (GO:0031225)|CNTFR-CLCF1 complex (GO:0097059)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|cytokine binding (GO:0019955)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(4)|skin(1)	15	all_epithelial(49;0.0899)		STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.00494)		AGGTGCATGTAGCGAATGTGG	0.527																																					p.Y168H		.											CNTFR,colon,carcinoma,0,2	CNTFR	0	0			c.T502C						.						181.0	146.0	158.0					9																	34557626		2203	4300	6503	SO:0001583	missense	1271	exon6			GCATGTAGCGAAT	M73238	CCDS6558.1	9p13	2013-02-11			ENSG00000122756	ENSG00000122756		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2170	protein-coding gene	gene with protein product		118946				1648265	Standard	NM_001842		Approved		uc003zuq.2	P26992	OTTHUMG00000019821	ENST00000378980.3:c.502T>C	9.37:g.34557626A>G	ENSP00000368265:p.Tyr168His	Somatic	76	0		WXS	Illumina HiSeq	.	29	3	NM_147164	Q5U050	Missense_Mutation	SNP	ENST00000378980.3	37	CCDS6558.1	.	.	.	.	.	.	.	.	.	.	A	14.41	2.528376	0.44969	.	.	ENSG00000122756	ENST00000378980;ENST00000351266;ENST00000417345	T;T;T	0.36157	1.27;1.27;1.27	5.52	4.39	0.52855	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.248101	0.34750	N	0.003702	T	0.32102	0.0818	L	0.51422	1.61	0.30691	N	0.751336	D	0.56968	0.978	P	0.45881	0.496	T	0.38156	-0.9674	9	0.15952	T	0.53	.	8.941	0.35729	0.9126:0.0:0.0874:0.0	.	168	P26992	CNTFR_HUMAN	H	168	ENSP00000368265:Y168H;ENSP00000242338:Y168H;ENSP00000388082:Y168H	ENSP00000242338:Y168H	Y	-	1	0	CNTFR	34547626	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.631000	0.74277	2.083000	0.62718	0.533000	0.62120	TAC	.		0.527	CNTFR-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052176.1		
DOCK2	1794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	169145773	169145773	+	Missense_Mutation	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr5:169145773C>T	ENST00000256935.8	+	22	2325	c.2245C>T	c.(2245-2247)Cgg>Tgg	p.R749W	DOCK2_ENST00000540750.1_5'UTR|DOCK2_ENST00000520908.1_Missense_Mutation_p.R241W	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	749					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GTTCATTGTTCGGTCGAGGAC	0.418																																					p.R749W		.											DOCK2,NS,malignant_melanoma,0,1	DOCK2	0	0			c.C2245T						.						129.0	105.0	113.0					5																	169145773		2203	4300	6503	SO:0001583	missense	1794	exon22			ATTGTTCGGTCGA	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.2245C>T	5.37:g.169145773C>T	ENSP00000256935:p.Arg749Trp	Somatic	103	0		WXS	Illumina HiSeq	.	107	12	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	37	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.059342	0.76074	.	.	ENSG00000134516	ENST00000256935;ENST00000520908	T;T	0.26660	1.72;1.72	5.58	4.68	0.58851	.	0.000000	0.85682	D	0.000000	T	0.50956	0.1646	M	0.73598	2.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.53995	-0.8359	10	0.87932	D	0	.	14.7258	0.69343	0.256:0.744:0.0:0.0	.	241;749	E7ERW7;Q92608	.;DOCK2_HUMAN	W	749;241	ENSP00000256935:R749W;ENSP00000429283:R241W	ENSP00000256935:R749W	R	+	1	2	DOCK2	169078351	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.109000	0.57824	2.661000	0.90470	0.644000	0.83932	CGG	.		0.418	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
GALM	130589	hgsc.bcm.edu	37	2	38958894	38958894	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr2:38958894G>T	ENST00000272252.5	+	6	1046	c.794G>T	c.(793-795)aGc>aTc	p.S265I	GALM_ENST00000410063.1_Missense_Mutation_p.S117I	NM_138801.2	NP_620156.1	Q96C23	GALM_HUMAN	galactose mutarotase (aldose 1-epimerase)	265					galactose metabolic process (GO:0006012)|glucose metabolic process (GO:0006006)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aldose 1-epimerase activity (GO:0004034)|carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	14		all_hematologic(82;0.248)				CATGCTGCAAGCGGGCGGGTA	0.527																																					p.S265I		.											.	.	.	0			c.G794T						.						74.0	77.0	76.0					2																	38958894		2203	4300	6503	SO:0001583	missense	130589	exon6			CTGCAAGCGGGCG		CCDS1797.1	2p22.3	2008-02-05			ENSG00000143891	ENSG00000143891			24063	protein-coding gene	gene with protein product	"""aldose 1 epimerase"""	608883				12753898	Standard	NM_138801		Approved		uc002rqy.3	Q96C23	OTTHUMG00000102077	ENST00000272252.5:c.794G>T	2.37:g.38958894G>T	ENSP00000272252:p.Ser265Ile	Somatic	38	0		WXS	Illumina HiSeq	.	35	4	NM_138801	Q53RY1|Q8NIA2|V9HWA8	Missense_Mutation	SNP	ENST00000272252.5	37	CCDS1797.1	.	.	.	.	.	.	.	.	.	.	G	14.09	2.431980	0.43122	.	.	ENSG00000143891	ENST00000272252;ENST00000410063;ENST00000434934	T;T;T	0.54866	0.55;0.74;0.55	5.94	5.02	0.67125	Glycoside hydrolase-type carbohydrate-binding, subgroup (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.082180	0.85682	D	0.000000	T	0.81983	0.4938	H	0.96633	3.855	0.58432	D	0.999994	D	0.76494	0.999	D	0.71656	0.974	D	0.87894	0.2686	10	0.87932	D	0	-29.2819	18.4536	0.90712	0.0:0.1276:0.8724:0.0	.	265	Q96C23	GALM_HUMAN	I	265;117;145	ENSP00000272252:S265I;ENSP00000386233:S117I;ENSP00000399473:S145I	ENSP00000272252:S265I	S	+	2	0	GALM	38812398	1.000000	0.71417	0.227000	0.23927	0.110000	0.19582	4.075000	0.57584	2.812000	0.96745	0.557000	0.71058	AGC	.		0.527	GALM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219891.2	NM_138801	
SYNE1	23345	hgsc.bcm.edu	37	6	152737535	152737535	+	Missense_Mutation	SNP	C	C	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr6:152737535C>A	ENST00000367255.5	-	41	6638	c.6037G>T	c.(6037-6039)Gct>Tct	p.A2013S	SYNE1_ENST00000265368.4_Missense_Mutation_p.A2013S|SYNE1_ENST00000341594.5_Missense_Mutation_p.A2050S|SYNE1_ENST00000448038.1_Missense_Mutation_p.A2020S|SYNE1_ENST00000423061.1_Missense_Mutation_p.A2020S	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2013					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TGCTGAAGAGCTTGGCGGGTA	0.393										HNSCC(10;0.0054)																											p.A2020S		.											SYNE1_ENST00000265368,NS,carcinoma,0,2	SYNE1_ENST00000265368	0	0			c.G6058T						.						193.0	199.0	197.0					6																	152737535		2203	4300	6503	SO:0001583	missense	23345	exon41			GAAGAGCTTGGCG	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.6037G>T	6.37:g.152737535C>A	ENSP00000356224:p.Ala2013Ser	Somatic	39	0		WXS	Illumina HiSeq	.	36	2	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	13.91	2.377948	0.42105	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41	5.97	5.97	0.96955	.	0.000000	0.64402	D	0.000010	T	0.34716	0.0907	M	0.74881	2.28	0.80722	D	1	P;P;D;D	0.55385	0.953;0.952;0.962;0.971	B;B;P;P	0.50617	0.388;0.444;0.526;0.646	T	0.09400	-1.0676	10	0.13108	T	0.6	.	20.4388	0.99107	0.0:1.0:0.0:0.0	.	1996;2013;2013;2020	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	S	2013;2020;2013;2020;2050	ENSP00000356224:A2013S;ENSP00000396024:A2020S;ENSP00000265368:A2013S;ENSP00000390975:A2020S;ENSP00000341887:A2050S	ENSP00000265368:A2013S	A	-	1	0	SYNE1	152779228	0.999000	0.42202	0.305000	0.25099	0.323000	0.28346	4.034000	0.57289	2.836000	0.97738	0.655000	0.94253	GCT	.		0.393	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
MAP1B	4131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	71491937	71491937	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr5:71491937G>T	ENST00000296755.7	+	5	3053	c.2755G>T	c.(2755-2757)Gga>Tga	p.G919*		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	919					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		CGAGAAGCAGGGAGTAGACGA	0.512																																					p.G919X	Melanoma(17;367 822 11631 31730 47712)	.											.	.	.	0			c.G2755T						.						66.0	72.0	70.0					5																	71491937		2203	4300	6503	SO:0001587	stop_gained	4131	exon5			AAGCAGGGAGTAG	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.2755G>T	5.37:g.71491937G>T	ENSP00000296755:p.Gly919*	Somatic	43	0		WXS	Illumina HiSeq	.	53	16	NM_005909	A2BDK5	Nonsense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	G	38	7.246903	0.98161	.	.	ENSG00000131711	ENST00000296755	.	.	.	5.6	3.48	0.39840	.	0.269960	0.32503	N	0.006009	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	-14.7434	6.3527	0.21385	0.3757:0.0:0.6243:0.0	.	.	.	.	X	919	.	ENSP00000296755:G919X	G	+	1	0	MAP1B	71527693	0.997000	0.39634	0.980000	0.43619	0.157000	0.22087	2.574000	0.46016	1.362000	0.46000	0.591000	0.81541	GGA	.		0.512	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
SIM2	6493	hgsc.bcm.edu	37	21	38114120	38114120	+	Missense_Mutation	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr21:38114120G>A	ENST00000290399.6	+	8	1566	c.953G>A	c.(952-954)cGc>cAc	p.R318H	SIM2_ENST00000430056.3_Missense_Mutation_p.R318H	NM_005069.3	NP_005060.1	Q14190	SIM2_HUMAN	single-minded family bHLH transcription factor 2	318	PAC.				cell differentiation (GO:0030154)|embryonic pattern specification (GO:0009880)|lung development (GO:0030324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(2)	16						CACAACAGCCGCTCGTCCCGG	0.572																																					p.R318H		.											SIM2_ENST00000430056,NS,carcinoma,0,2	SIM2_ENST00000430056	0	0			c.G953A						.						52.0	43.0	46.0					21																	38114120		2202	4299	6501	SO:0001583	missense	6493	exon8			ACAGCCGCTCGTC		CCDS13646.1	21q22.2	2013-10-17	2013-10-17		ENSG00000159263	ENSG00000159263		"""Basic helix-loop-helix proteins"""	10883	protein-coding gene	gene with protein product	"""transcription factor SIM2"""	600892	"""single-minded (Drosophila) homolog 2"", ""single-minded homolog 2 (Drosophila)"""	SIM		7485157	Standard	NM_009586		Approved	MGC119447, bHLHe15	uc002yvr.2	Q14190	OTTHUMG00000086637	ENST00000290399.6:c.953G>A	21.37:g.38114120G>A	ENSP00000290399:p.Arg318His	Somatic	76	0		WXS	Illumina HiSeq	.	44	2	NM_005069	O60766|Q15470|Q15471|Q15472|Q15473|Q16532|Q2TBD8	Missense_Mutation	SNP	ENST00000290399.6	37	CCDS13646.1	.	.	.	.	.	.	.	.	.	.	G	33	5.276996	0.95459	.	.	ENSG00000159263	ENST00000290399;ENST00000430056	T;T	0.17213	2.29;2.29	5.15	5.15	0.70609	PAS fold-3 (1);	0.000000	0.85682	D	0.000000	T	0.47746	0.1462	M	0.83384	2.64	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.987	T	0.54721	-0.8251	10	0.87932	D	0	.	18.6253	0.91334	0.0:0.0:1.0:0.0	.	318;318	Q14190;Q14190-2	SIM2_HUMAN;.	H	318	ENSP00000290399:R318H;ENSP00000404176:R318H	ENSP00000290399:R318H	R	+	2	0	SIM2	37035990	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	9.563000	0.98148	2.369000	0.80426	0.655000	0.94253	CGC	.		0.572	SIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194692.1	NM_009586	
NFKBIZ	64332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	101572374	101572374	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr3:101572374G>T	ENST00000326172.5	+	5	1119	c.1004G>T	c.(1003-1005)tGc>tTc	p.C335F	NFKBIZ_ENST00000394054.2_Missense_Mutation_p.C235F|NFKBIZ_ENST00000326151.5_Intron	NM_031419.3	NP_113607.1	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	335	Required for transcriptional activity. {ECO:0000250}.				inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24						TCACAGTTTTGCCCAAACCAA	0.453																																					p.C335F		.											.	.	.	0			c.G1004T						.						123.0	122.0	122.0					3																	101572374		2203	4300	6503	SO:0001583	missense	64332	exon5			AGTTTTGCCCAAA	AF548362	CCDS2946.1, CCDS43123.1	3p12-q12	2013-01-10			ENSG00000144802	ENSG00000144802		"""Ankyrin repeat domain containing"""	29805	protein-coding gene	gene with protein product	"""IL-1 inducible nuclear ankyrin-repeat protein"""	608004				12565889, 16513645	Standard	NM_031419		Approved	MAIL, FLJ34463, INAP	uc003dvp.3	Q9BYH8	OTTHUMG00000159194	ENST00000326172.5:c.1004G>T	3.37:g.101572374G>T	ENSP00000325663:p.Cys335Phe	Somatic	85	0		WXS	Illumina HiSeq	.	41	21	NM_031419	B3KNR2|D3DN54|Q8IUL4|Q8NAZ8	Missense_Mutation	SNP	ENST00000326172.5	37	CCDS2946.1	.	.	.	.	.	.	.	.	.	.	G	4.329	0.060496	0.08339	.	.	ENSG00000144802	ENST00000483180;ENST00000394054;ENST00000326172	T;T;T	0.54675	0.6;0.56;0.61	5.6	3.7	0.42460	.	0.359311	0.30419	N	0.009668	T	0.37785	0.1016	L	0.43923	1.385	0.38246	D	0.941456	B	0.16166	0.016	B	0.12156	0.007	T	0.19128	-1.0315	10	0.09338	T	0.73	-17.2492	8.1245	0.30990	0.0729:0.0:0.6557:0.2714	.	335	Q9BYH8	IKBZ_HUMAN	F	235;235;335	ENSP00000419800:C235F;ENSP00000377618:C235F;ENSP00000325663:C335F	ENSP00000325663:C335F	C	+	2	0	NFKBIZ	103055064	0.995000	0.38212	0.966000	0.40874	0.013000	0.08279	1.540000	0.36115	1.349000	0.45751	0.563000	0.77884	TGC	.		0.453	NFKBIZ-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353793.1	NM_031419	
ZSCAN1	284312	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	58549386	58549386	+	Missense_Mutation	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:58549386C>T	ENST00000282326.1	+	3	429	c.182C>T	c.(181-183)aCg>aTg	p.T61M	ZSCAN1_ENST00000601162.1_Missense_Mutation_p.T61M|ZSCAN1_ENST00000391700.1_Missense_Mutation_p.T61M	NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	61	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		CAGCTCTGGACGCTGTGCCGC	0.701																																					p.T61M		.											.	.	.	0			c.C182T						.						14.0	15.0	15.0					19																	58549386		2176	4268	6444	SO:0001583	missense	284312	exon3			TCTGGACGCTGTG	AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"""-"", ""Zinc fingers, C2H2-type"""	23712	protein-coding gene	gene with protein product			"""zinc finger with SCAN domain 1"""			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.182C>T	19.37:g.58549386C>T	ENSP00000282326:p.Thr61Met	Somatic	45	0		WXS	Illumina HiSeq	.	39	8	NM_182572	Q3B798|Q6WLH8|Q86WS8	Missense_Mutation	SNP	ENST00000282326.1	37	CCDS12969.1	.	.	.	.	.	.	.	.	.	.	C	9.015	0.983446	0.18889	.	.	ENSG00000152467	ENST00000391700;ENST00000282326	T;T	0.05717	3.4;3.4	2.09	-4.19	0.03835	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.01765	0.0056	N	0.03608	-0.345	0.09310	N	1	P;P	0.38745	0.513;0.645	B;B	0.26614	0.069;0.071	T	0.42224	-0.9464	9	0.45353	T	0.12	.	3.1285	0.06415	0.5591:0.2397:0.0:0.2011	.	61;61	Q8NBB4;Q8NBB4-2	ZSCA1_HUMAN;.	M	61	ENSP00000375581:T61M;ENSP00000282326:T61M	ENSP00000282326:T61M	T	+	2	0	ZSCAN1	63241198	0.008000	0.16893	0.013000	0.15412	0.063000	0.16089	-0.239000	0.08965	-0.937000	0.03719	0.407000	0.27541	ACG	.		0.701	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572	
CDH17	1015	hgsc.bcm.edu;broad.mit.edu	37	8	95186446	95186446	+	Missense_Mutation	SNP	G	G	A	rs376397791		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr8:95186446G>A	ENST00000027335.3	-	6	591	c.467C>T	c.(466-468)cCg>cTg	p.P156L	CDH17_ENST00000441892.2_Intron|CDH17_ENST00000450165.2_Missense_Mutation_p.P156L	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	156	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)	p.P156Q(1)		NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			GGGAGTGGCCGGATCATCCAG	0.413																																					p.P156L		.											CDH17,NS,carcinoma,0,2	CDH17	0	1	Substitution - Missense(1)	lung(1)	c.C467T						.	G	LEU/PRO,LEU/PRO	0,4406		0,0,2203	159.0	162.0	161.0		467,467	6.0	1.0	8		161	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CDH17	NM_001144663.1,NM_004063.3	98,98	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	156/833,156/833	95186446	1,13005	2203	4300	6503	SO:0001583	missense	1015	exon6			GTGGCCGGATCAT	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"""Cadherins / Major cadherins"""	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.467C>T	8.37:g.95186446G>A	ENSP00000027335:p.Pro156Leu	Somatic	65	1		WXS	Illumina HiSeq	.	75	5	NM_004063	Q15336|Q2M2E0	Missense_Mutation	SNP	ENST00000027335.3	37	CCDS6260.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.707740	0.89018	0.0	1.16E-4	ENSG00000079112	ENST00000027335;ENST00000450165	T;T	0.20069	2.1;2.1	5.96	5.96	0.96718	Cadherin (4);Cadherin-like (1);	0.000000	0.56097	D	0.000031	T	0.58047	0.2095	M	0.92507	3.315	0.80722	D	1	D	0.89917	1.0	D	0.69654	0.965	T	0.66885	-0.5810	10	0.87932	D	0	-14.1027	19.1934	0.93677	0.0:0.0:1.0:0.0	.	156	Q12864	CAD17_HUMAN	L	156	ENSP00000027335:P156L;ENSP00000401468:P156L	ENSP00000027335:P156L	P	-	2	0	CDH17	95255622	1.000000	0.71417	0.997000	0.53966	0.979000	0.70002	6.631000	0.74277	2.832000	0.97577	0.655000	0.94253	CCG	.		0.413	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063	
INADL	10207	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	62237282	62237282	+	Missense_Mutation	SNP	C	C	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr1:62237282C>A	ENST00000371158.2	+	6	818	c.704C>A	c.(703-705)aCa>aAa	p.T235K	INADL_ENST00000316485.6_Missense_Mutation_p.T235K	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	235					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						CTAAATGATACAACTCTGCCT	0.368																																					p.T235K		.											.	.	.	0			c.C704A						.						86.0	79.0	81.0					1																	62237282		2203	4300	6503	SO:0001583	missense	10207	exon6			ATGATACAACTCT	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.704C>A	1.37:g.62237282C>A	ENSP00000360200:p.Thr235Lys	Somatic	82	0		WXS	Illumina HiSeq	.	67	30	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	.	.	.	.	.	.	.	.	.	.	C	8.811	0.935183	0.18206	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.17054	2.3;2.3	4.6	1.48	0.22813	PDZ/DHR/GLGF (1);	0.706198	0.12419	N	0.470628	T	0.13628	0.0330	L	0.50333	1.59	0.09310	N	1	P;B;P	0.40834	0.554;0.361;0.73	B;B;B	0.36845	0.216;0.074;0.234	T	0.14615	-1.0466	10	0.37606	T	0.19	.	6.3462	0.21351	0.0:0.621:0.1381:0.2409	.	235;235;235	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	K	235	ENSP00000360200:T235K;ENSP00000326199:T235K	ENSP00000255202:T235K	T	+	2	0	INADL	62009870	0.000000	0.05858	0.009000	0.14445	0.113000	0.19764	0.059000	0.14322	0.931000	0.37242	0.460000	0.39030	ACA	.		0.368	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
ZYX	7791	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	143080207	143080207	+	Missense_Mutation	SNP	A	A	C			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr7:143080207A>C	ENST00000322764.5	+	5	1160	c.815A>C	c.(814-816)aAg>aCg	p.K272T	ZYX_ENST00000449423.2_Missense_Mutation_p.K185T|AC093673.5_ENST00000429630.1_RNA|ZYX_ENST00000477373.1_3'UTR|ZYX_ENST00000392910.2_Missense_Mutation_p.K115T	NM_001010972.1|NM_003461.4	NP_001010972.1|NP_003452.1	Q15942	ZYX_HUMAN	zyxin	272					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|integrin-mediated signaling pathway (GO:0007229)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)	17	Melanoma(164;0.205)					GTGACTCCTAAGTTTACTCCT	0.577																																					p.K272T		.											.	.	.	0			c.A815C						.						110.0	135.0	127.0					7																	143080207		2203	4300	6503	SO:0001583	missense	7791	exon5			CTCCTAAGTTTAC	X95735	CCDS5883.1	7q32	2010-02-26			ENSG00000159840	ENSG00000159840			13200	protein-coding gene	gene with protein product		602002				8917469, 8940160	Standard	XM_005250052		Approved		uc003wcx.3	Q15942	OTTHUMG00000023822	ENST00000322764.5:c.815A>C	7.37:g.143080207A>C	ENSP00000324422:p.Lys272Thr	Somatic	76	0		WXS	Illumina HiSeq	.	76	26	NM_003461	A4D2G6|Q6I9S4	Missense_Mutation	SNP	ENST00000322764.5	37	CCDS5883.1	.	.	.	.	.	.	.	.	.	.	A	12.24	1.879824	0.33162	.	.	ENSG00000159840	ENST00000322764;ENST00000354434;ENST00000449423;ENST00000392910	T;T;T;T	0.55234	0.62;0.54;0.53;0.54	4.25	1.81	0.25067	.	0.519308	0.16938	U	0.193383	T	0.58177	0.2104	M	0.63428	1.95	0.32754	N	0.506022	D;D	0.69078	0.991;0.997	P;P	0.57204	0.749;0.815	T	0.63906	-0.6531	10	0.44086	T	0.13	.	6.7723	0.23601	0.8032:0.0:0.1968:0.0	.	185;272	B4DQR8;Q15942	.;ZYX_HUMAN	T	272;240;185;115	ENSP00000324422:K272T;ENSP00000346417:K240T;ENSP00000394158:K185T;ENSP00000376642:K115T	ENSP00000324422:K272T	K	+	2	0	ZYX	142790329	0.840000	0.29493	0.986000	0.45419	0.207000	0.24258	0.691000	0.25467	0.514000	0.28300	0.533000	0.62120	AAG	.		0.577	ZYX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156296.2	NM_003461	
L1TD1	54596	hgsc.bcm.edu;broad.mit.edu	37	1	62672856	62672856	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr1:62672856G>T	ENST00000498273.1	+	3	851	c.556G>T	c.(556-558)Gga>Tga	p.G186*		NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	186										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						tgacagagatggaaatcgcaa	0.368																																					p.G186X		.											.	.	.	0			c.G556T						.						19.0	19.0	19.0					1																	62672856		2105	4111	6216	SO:0001587	stop_gained	54596	exon4			AGAGATGGAAATC	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.556G>T	1.37:g.62672856G>T	ENSP00000419901:p.Gly186*	Somatic	92	0		WXS	Illumina HiSeq	.	100	7	NM_001164835	Q8NDA1|Q9NUV8|Q9NV78	Nonsense_Mutation	SNP	ENST00000498273.1	37	CCDS619.1	.	.	.	.	.	.	.	.	.	.	g	17.74	3.464610	0.63513	.	.	ENSG00000240563	ENST00000498273	.	.	.	2.03	-4.06	0.03986	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	.	8.7621	0.34680	0.4427:0.0:0.5573:0.0	.	.	.	.	X	186	.	ENSP00000419901:G186X	G	+	1	0	L1TD1	62445444	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.944000	0.01538	-1.503000	0.01812	-1.740000	0.00687	GGA	.		0.368	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079	
SERPINE2	5270	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	224856592	224856592	+	Missense_Mutation	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr2:224856592G>A	ENST00000258405.4	-	4	855	c.613C>T	c.(613-615)Cgc>Tgc	p.R205C	SERPINE2_ENST00000409304.1_Missense_Mutation_p.R205C|SERPINE2_ENST00000409840.3_Missense_Mutation_p.R205C|SERPINE2_ENST00000447280.2_Missense_Mutation_p.R217C	NM_001136528.1|NM_006216.3	NP_001130000.1|NP_006207.1	P07093	GDN_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2	205					blood coagulation (GO:0007596)|cerebellar granular layer morphogenesis (GO:0021683)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|innervation (GO:0060384)|long-term synaptic potentiation (GO:0060291)|mating plug formation (GO:0042628)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein processing (GO:0010955)|negative regulation of proteolysis (GO:0045861)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of sodium ion transport (GO:0010766)|positive regulation of astrocyte differentiation (GO:0048711)|regulation of cell migration (GO:0030334)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of timing of cell differentiation (GO:0048505)|secretion by cell (GO:0032940)|secretory granule organization (GO:0033363)|seminal vesicle epithelium development (GO:0061108)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|neuromuscular junction (GO:0031594)|platelet alpha granule (GO:0031091)|vesicle (GO:0031982)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	17		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)		ACGAAAGTGCGTTTCTTTGTG	0.527																																					p.R217C		.											.	.	.	0			c.C649T						.						162.0	122.0	136.0					2																	224856592		2203	4300	6503	SO:0001583	missense	5270	exon4			AAGTGCGTTTCTT	M17783	CCDS2460.1, CCDS46525.1, CCDS46526.1	2q36.1	2014-02-18	2005-08-18		ENSG00000135919	ENSG00000135919		"""Serine (or cysteine) peptidase inhibitors"""	8951	protein-coding gene	gene with protein product	"""glial-derived nexin 1"""	177010	"""serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2"""	PI7		7665170, 24172014	Standard	NM_006216		Approved	PN1, GDN, PNI, nexin	uc002vnu.2	P07093	OTTHUMG00000133163	ENST00000258405.4:c.613C>T	2.37:g.224856592G>A	ENSP00000258405:p.Arg205Cys	Somatic	54	0		WXS	Illumina HiSeq	.	78	14	NM_001136530	B2R6A4|B4DIF2|Q53S15|Q5D0C4	Missense_Mutation	SNP	ENST00000258405.4	37	CCDS2460.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.835690	0.50951	.	.	ENSG00000135919	ENST00000409304;ENST00000258405;ENST00000409840;ENST00000447280;ENST00000432738	D;D;D;D;D	0.85171	-1.95;-1.95;-1.95;-1.95;-1.95	5.8	5.8	0.92144	Serpin domain (3);	0.000000	0.85682	D	0.000000	D	0.93167	0.7824	M	0.82823	2.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.74674	0.984;0.984	D	0.93119	0.6523	10	0.62326	D	0.03	.	20.0589	0.97667	0.0:0.0:1.0:0.0	.	217;205	B4DIF2;P07093	.;GDN_HUMAN	C	205;205;205;217;205	ENSP00000386412:R205C;ENSP00000258405:R205C;ENSP00000386969:R205C;ENSP00000415786:R217C;ENSP00000408452:R205C	ENSP00000258405:R205C	R	-	1	0	SERPINE2	224564836	1.000000	0.71417	0.248000	0.24265	0.171000	0.22731	3.936000	0.56568	2.732000	0.93576	0.650000	0.86243	CGC	.		0.527	SERPINE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256865.2	NM_006216	
VPS26A	9559	hgsc.bcm.edu;bcgsc.ca	37	10	70928304	70928304	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr10:70928304G>T	ENST00000373382.1	+	9	1440	c.787G>T	c.(787-789)Gat>Tat	p.D263Y	VPS26A_ENST00000541711.1_Missense_Mutation_p.D152Y|VPS26A_ENST00000546041.1_Missense_Mutation_p.D246Y|VPS26A_ENST00000395098.1_Intron|VPS26A_ENST00000489794.1_Intron|VPS26A_ENST00000490696.1_3'UTR|VPS26A_ENST00000263559.6_Missense_Mutation_p.D263Y			O75436	VP26A_HUMAN	vacuolar protein sorting 26 homolog A (S. pombe)	263					retrograde transport, endosome to Golgi (GO:0042147)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|vesicle (GO:0031982)	protein transporter activity (GO:0008565)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)	8						AACAATGAGAGATGTGAACAA	0.363																																					p.D263Y	Colon(90;545 1358 4729 6702 16773)	.											.	.	.	0			c.G787T						.						95.0	100.0	98.0					10																	70928304		2203	4300	6503	SO:0001583	missense	9559	exon8			ATGAGAGATGTGA	AF054179	CCDS7286.1, CCDS41536.1	10q21.1	2007-01-12	2007-01-12	2005-10-11	ENSG00000122958	ENSG00000122958			12711	protein-coding gene	gene with protein product		605506	"""vacuolar protein sorting 26 (yeast homolog)"", ""vacuolar protein sorting 26 (yeast)"", ""vacuolar protein sorting 26 homolog A (yeast)"""	VPS26		1638986, 9653160	Standard	NM_004896		Approved	Hbeta58, PEP8A	uc001jpb.3	O75436	OTTHUMG00000018376	ENST00000373382.1:c.787G>T	10.37:g.70928304G>T	ENSP00000362480:p.Asp263Tyr	Somatic	55	0		WXS	Illumina HiSeq	.	53	4	NM_004896	A8MZ56|B2RDD3|Q8TBH4|Q9H982	Missense_Mutation	SNP	ENST00000373382.1	37	CCDS7286.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.810837	0.90707	.	.	ENSG00000122958	ENST00000373382;ENST00000263559;ENST00000546041;ENST00000541711	.	.	.	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.85022	0.5602	M	0.89414	3.03	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.993	D	0.88034	0.2777	9	0.72032	D	0.01	-11.9614	18.4875	0.90835	0.0:0.0:1.0:0.0	.	246;263	F5H4L7;O75436	.;VP26A_HUMAN	Y	263;263;246;152	.	ENSP00000263559:D263Y	D	+	1	0	VPS26A	70598310	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.864000	0.99589	2.453000	0.82957	0.563000	0.77884	GAT	.		0.363	VPS26A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048403.1	NM_004896	
QRFPR	84109	hgsc.bcm.edu	37	4	122301568	122301568	+	Missense_Mutation	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr4:122301568C>T	ENST00000394427.2	-	1	646	c.235G>A	c.(235-237)Gtc>Atc	p.V79I	QRFPR_ENST00000334383.5_Missense_Mutation_p.V79I	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	79					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)	p.V79I(1)		endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						ATGTTGGTGACGGTGCGCATG	0.582																																					p.V79I		.											QRFPR,colon,carcinoma,0,1	QRFPR	0	1	Substitution - Missense(1)	large_intestine(1)	c.G235A						.						115.0	89.0	98.0					4																	122301568		2203	4300	6503	SO:0001583	missense	84109	exon1			TGGTGACGGTGCG	AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"""GPCR / Class A : RF amide peptide receptors"""	15565	protein-coding gene	gene with protein product		606925	"""G protein-coupled receptor 103"""	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.235G>A	4.37:g.122301568C>T	ENSP00000377948:p.Val79Ile	Somatic	42	0		WXS	Illumina HiSeq	.	21	2	NM_198179		Missense_Mutation	SNP	ENST00000394427.2	37	CCDS3719.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.993200	0.93167	.	.	ENSG00000186867	ENST00000394427;ENST00000334383	T;T	0.38722	1.12;1.12	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.053025	0.85682	D	0.000000	T	0.44644	0.1303	L	0.47016	1.485	0.58432	D	0.999999	P;P;D	0.53462	0.882;0.934;0.96	B;P;B	0.45310	0.257;0.476;0.345	T	0.46992	-0.9151	10	0.56958	D	0.05	.	18.2778	0.90088	0.0:1.0:0.0:0.0	.	79;79;79	F2Z3L3;Q96P65;G4XH69	.;QRFPR_HUMAN;.	I	79	ENSP00000377948:V79I;ENSP00000335610:V79I	ENSP00000335610:V79I	V	-	1	0	QRFPR	122521018	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.525000	0.81892	2.383000	0.81215	0.467000	0.42956	GTC	.		0.582	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179	
STK11IP	114790	hgsc.bcm.edu	37	2	220473349	220473349	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr2:220473349G>T	ENST00000456909.1	+	15	1738	c.1648G>T	c.(1648-1650)Gag>Tag	p.E550*	STK11IP_ENST00000295641.10_Nonsense_Mutation_p.E561*			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	561	Glu-rich.				protein localization (GO:0008104)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)	protein kinase binding (GO:0019901)			breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	23		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGAGGGGCCTGAGGGCGTACG	0.607																																					p.E561X		.											STK11IP_ENST00000295641,NS,carcinoma,0,3	STK11IP_ENST00000295641	0	0			c.G1681T						.						50.0	55.0	53.0					2																	220473349		1986	4143	6129	SO:0001587	stop_gained	114790	exon15			GGGCCTGAGGGCG	AF450267	CCDS46521.1	2q35	2008-06-03			ENSG00000144589	ENSG00000144589			19184	protein-coding gene	gene with protein product	"""LKB1 interacting protein"""	607172				11741830	Standard	NM_052902		Approved	LIP1, KIAA1898, LKB1IP, STK11IP1	uc002vml.3	Q8N1F8	OTTHUMG00000059239	ENST00000456909.1:c.1648G>T	2.37:g.220473349G>T	ENSP00000389383:p.Glu550*	Somatic	37	0		WXS	Illumina HiSeq	.	34	2	NM_052902	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Nonsense_Mutation	SNP	ENST00000456909.1	37		.	.	.	.	.	.	.	.	.	.	G	25.7	4.664537	0.88251	.	.	ENSG00000144589	ENST00000456909;ENST00000426736;ENST00000295641	.	.	.	4.5	1.56	0.23342	.	0.842078	0.10336	N	0.686940	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	-0.6098	7.1985	0.25866	0.0925:0.3295:0.578:0.0	.	.	.	.	X	550;529;561	.	ENSP00000295641:E561X	E	+	1	0	STK11IP	220181593	0.005000	0.15991	0.000000	0.03702	0.296000	0.27459	0.676000	0.25247	0.115000	0.18071	0.561000	0.74099	GAG	.		0.607	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902	
HHIPL2	79802	hgsc.bcm.edu	37	1	222715437	222715437	+	Silent	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr1:222715437G>T	ENST00000343410.6	-	3	1093	c.1035C>A	c.(1033-1035)ggC>ggA	p.G345G		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	345					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)			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)		AGCCATCCAGGCCAAAAAGAA	0.483																																					p.G345G		.											.	.	.	0			c.C1035A						.						72.0	67.0	69.0					1																	222715437		2203	4300	6503	SO:0001819	synonymous_variant	79802	exon3			ATCCAGGCCAAAA	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.1035C>A	1.37:g.222715437G>T		Somatic	57	0		WXS	Illumina HiSeq	.	69	4	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Silent	SNP	ENST00000343410.6	37	CCDS1530.2																																																																																			.		0.483	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746	
MUC16	94025	hgsc.bcm.edu	37	19	9083333	9083333	+	Missense_Mutation	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:9083333C>T	ENST00000397910.4	-	1	8685	c.8482G>A	c.(8482-8484)Gcc>Acc	p.A2828T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2828	Ser-rich.|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)				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						TCAGACATGGCTGTAACCTCA	0.502																																					p.A2828T		.											MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16_ENST00000397910	0	0			c.G8482A						.						113.0	109.0	110.0					19																	9083333		2023	4179	6202	SO:0001583	missense	94025	exon1			ACATGGCTGTAAC	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.8482G>A	19.37:g.9083333C>T	ENSP00000381008:p.Ala2828Thr	Somatic	47	0		WXS	Illumina HiSeq	.	47	2	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	10.90	1.482153	0.26598	.	.	ENSG00000181143	ENST00000397910	T	0.02709	4.19	0.869	0.869	0.19096	.	.	.	.	.	T	0.03695	0.0105	N	0.08118	0	.	.	.	D	0.60575	0.988	P	0.62885	0.908	T	0.44267	-0.9339	8	0.87932	D	0	.	5.0445	0.14477	0.0:1.0:0.0:0.0	.	2828	B5ME49	.	T	2828	ENSP00000381008:A2828T	ENSP00000381008:A2828T	A	-	1	0	MUC16	8944333	0.001000	0.12720	0.054000	0.19295	0.874000	0.50279	0.091000	0.15046	0.740000	0.32651	0.313000	0.20887	GCC	.		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZBTB49	166793	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	4304317	4304317	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr4:4304317G>T	ENST00000337872.4	+	3	875	c.754G>T	c.(754-756)Gta>Tta	p.V252L	ZBTB49_ENST00000538529.1_5'UTR|ZBTB49_ENST00000355834.3_Missense_Mutation_p.V252L	NM_145291.3	NP_660334.3	Q6ZSB9	ZBT49_HUMAN	zinc finger and BTB domain containing 49	252					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	28						CCTTACCACGGTAGAGAGCCA	0.522																																					p.V252L		.											.	.	.	0			c.G754T						.						113.0	108.0	110.0					4																	4304317		2203	4300	6503	SO:0001583	missense	166793	exon3			ACCACGGTAGAGA	AK095878	CCDS3375.1	4p16.2	2013-01-08	2010-01-26	2010-01-26	ENSG00000168826	ENSG00000168826		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	19883	protein-coding gene	gene with protein product			"""zinc finger protein 509"""	ZNF509		12477932	Standard	NM_145291		Approved	FLJ38559	uc003ghu.3	Q6ZSB9	OTTHUMG00000090325	ENST00000337872.4:c.754G>T	4.37:g.4304317G>T	ENSP00000338807:p.Val252Leu	Somatic	17	0		WXS	Illumina HiSeq	.	32	5	NM_145291	Q59FJ4|Q5EBN0|Q8TB80	Missense_Mutation	SNP	ENST00000337872.4	37	CCDS3375.1	.	.	.	.	.	.	.	.	.	.	G	9.325	1.059153	0.19987	.	.	ENSG00000168826	ENST00000355834;ENST00000337872	T;T	0.14144	2.53;2.83	4.96	4.12	0.48240	.	0.686881	0.13154	N	0.409593	T	0.10508	0.0257	L	0.44542	1.39	0.20074	N	0.999933	B	0.16603	0.018	B	0.18871	0.023	T	0.39663	-0.9603	10	0.11182	T	0.66	.	5.976	0.19379	0.157:0.0:0.6897:0.1534	.	252	Q6ZSB9	ZBT49_HUMAN	L	252	ENSP00000348091:V252L;ENSP00000338807:V252L	ENSP00000338807:V252L	V	+	1	0	ZBTB49	4355218	0.000000	0.05858	0.001000	0.08648	0.082000	0.17680	0.506000	0.22658	1.240000	0.43803	0.591000	0.81541	GTA	.		0.522	ZBTB49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206688.3	NM_145291	
ZFYVE26	23503	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	68275965	68275965	+	Silent	SNP	A	A	G			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr14:68275965A>G	ENST00000347230.4	-	4	453	c.315T>C	c.(313-315)ctT>ctC	p.L105L	ZFYVE26_ENST00000555452.1_Silent_p.L105L	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	105					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		CTGACAATAAAAGAAACTCAA	0.413																																					p.L105L		.											.	.	.	0			c.T315C						.						102.0	103.0	102.0					14																	68275965		2203	4300	6503	SO:0001819	synonymous_variant	23503	exon4			CAATAAAAGAAAC	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"""Zinc fingers, FYVE domain containing"""	20761	protein-coding gene	gene with protein product	"""spastizin"", ""FYVE-CENT"""	612012	"""spastic paraplegia 15 (complicated, autosomal recessive)"""	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.315T>C	14.37:g.68275965A>G		Somatic	77	0		WXS	Illumina HiSeq	.	44	36	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Silent	SNP	ENST00000347230.4	37	CCDS9788.1																																																																																			.		0.413	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346	
CAMK2D	817	hgsc.bcm.edu	37	4	114680566	114680566	+	Missense_Mutation	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr4:114680566C>T	ENST00000342666.5	-	2	69	c.70G>A	c.(70-72)Gca>Aca	p.A24T	CAMK2D_ENST00000514328.1_Missense_Mutation_p.A24T|CAMK2D_ENST00000454265.2_Missense_Mutation_p.A24T|CAMK2D_ENST00000394522.3_Missense_Mutation_p.A24T|CAMK2D_ENST00000509907.1_5'UTR|CAMK2D_ENST00000296402.5_Missense_Mutation_p.A24T|CAMK2D_ENST00000394524.3_Missense_Mutation_p.A24T|CAMK2D_ENST00000418639.2_Missense_Mutation_p.A24T|CAMK2D_ENST00000429180.1_Missense_Mutation_p.A24T|CAMK2D_ENST00000511664.1_Missense_Mutation_p.A24T|CAMK2D_ENST00000508738.1_Missense_Mutation_p.A24T|CAMK2D_ENST00000379773.2_Missense_Mutation_p.A24T|CAMK2D_ENST00000515496.1_Missense_Mutation_p.A24T|CAMK2D_ENST00000394526.2_Missense_Mutation_p.A24T|CAMK2D_ENST00000505990.1_Missense_Mutation_p.A24T			Q13557	KCC2D_HUMAN	calcium/calmodulin-dependent protein kinase II delta	24	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				calcium ion transport (GO:0006816)|cardiac muscle cell contraction (GO:0086003)|cellular response to calcium ion (GO:0071277)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle cell action potential (GO:0098901)|regulation of cardiac muscle cell action potential involved in regulation of contraction (GO:0098909)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of cell growth (GO:0001558)|regulation of cellular localization (GO:0060341)|regulation of generation of L-type calcium current (GO:1902514)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of histone deacetylase activity (GO:1901725)|regulation of membrane depolarization (GO:0003254)|regulation of relaxation of cardiac muscle (GO:1901897)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of the force of heart contraction (GO:0002026)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|relaxation of cardiac muscle (GO:0055119)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|calcium channel complex (GO:0034704)|calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intercalated disc (GO:0014704)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|ion channel binding (GO:0044325)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|sodium channel inhibitor activity (GO:0019871)|titin binding (GO:0031432)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	13		Ovarian(17;0.00369)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000271)		ACTGAGAATGCCCCCCTGGAA	0.323																																					p.A24T		.											.	.	.	0			c.G70A						.						84.0	85.0	85.0					4																	114680566		2203	4300	6503	SO:0001583	missense	817	exon2			AGAATGCCCCCCT	U50361	CCDS3703.1, CCDS3704.1, CCDS43263.1, CCDS47127.1, CCDS54797.1	4q26	2008-10-30	2008-10-30		ENSG00000145349	ENSG00000145349			1462	protein-coding gene	gene with protein product		607708	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II delta"""	CAMKD			Standard	NM_001221		Approved		uc003ibi.3	Q13557	OTTHUMG00000132910	ENST00000342666.5:c.70G>A	4.37:g.114680566C>T	ENSP00000339740:p.Ala24Thr	Somatic	178	0		WXS	Illumina HiSeq	.	95	2	NM_172128	A8MVS8|Q52PK4|Q59G21|Q8N553|Q9UGH6|Q9UQE9	Missense_Mutation	SNP	ENST00000342666.5	37	CCDS3703.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.489880	0.84962	.	.	ENSG00000145349	ENST00000394524;ENST00000454265;ENST00000429180;ENST00000418639;ENST00000394526;ENST00000296402;ENST00000511664;ENST00000342666;ENST00000515496;ENST00000514328;ENST00000394522;ENST00000505990;ENST00000379773;ENST00000508738	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.25579	1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79	5.71	5.71	0.89125	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	U	0.000006	T	0.23846	0.0577	N	0.11756	0.17	0.80722	D	1	P;P;P;P;P	0.43826	0.818;0.782;0.782;0.657;0.706	P;B;B;B;B	0.45829	0.494;0.288;0.288;0.288;0.412	T	0.05989	-1.0852	10	0.72032	D	0.01	.	19.4741	0.94979	0.0:1.0:0.0:0.0	.	24;24;24;24;24	E9PF82;Q13557-3;Q13557-6;Q13557-12;Q13557	.;.;.;.;KCC2D_HUMAN	T	24	ENSP00000378032:A24T;ENSP00000415248:A24T;ENSP00000415707:A24T;ENSP00000406131:A24T;ENSP00000378034:A24T;ENSP00000296402:A24T;ENSP00000425824:A24T;ENSP00000339740:A24T;ENSP00000423482:A24T;ENSP00000423677:A24T;ENSP00000378030:A24T;ENSP00000424245:A24T;ENSP00000369098:A24T;ENSP00000422566:A24T	ENSP00000296402:A24T	A	-	1	0	CAMK2D	114900015	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	7.381000	0.79718	2.705000	0.92388	0.467000	0.42956	GCA	.		0.323	CAMK2D-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256420.2		
RBM42	79171	hgsc.bcm.edu;bcgsc.ca	37	19	36123879	36123879	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:36123879G>T	ENST00000262633.4	+	5	589	c.484G>T	c.(484-486)Gtc>Ttc	p.V162F	RBM42_ENST00000588161.1_Intron|RBM42_ENST00000589871.1_Intron|RBM42_ENST00000592202.1_Intron|RBM42_ENST00000586618.1_Intron|RBM42_ENST00000360475.4_Intron|RBM42_ENST00000589559.1_Intron	NM_024321.3	NP_077297.2	Q9BTD8	RBM42_HUMAN	RNA binding motif protein 42	162						cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(7)|lung(9)|prostate(1)	21	all_lung(56;1.58e-07)|Lung NSC(56;2.43e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			TCCAGCCTTCGTCCCCCACGT	0.637																																					p.V162F		.											.	.	.	0			c.G484T						.						113.0	122.0	119.0					19																	36123879		2203	4300	6503	SO:0001583	missense	79171	exon5			GCCTTCGTCCCCC	BC004204	CCDS12468.1	19q13.12	2013-02-12				ENSG00000126254		"""RNA binding motif (RRM) containing"""	28117	protein-coding gene	gene with protein product		613232				12477932	Standard	NM_024321		Approved	MGC10433	uc002oan.3	Q9BTD8		ENST00000262633.4:c.484G>T	19.37:g.36123879G>T	ENSP00000262633:p.Val162Phe	Somatic	42	0		WXS	Illumina HiSeq	.	56	4	NM_024321	O00320|Q8N5R7|Q9BU66	Missense_Mutation	SNP	ENST00000262633.4	37	CCDS12468.1	.	.	.	.	.	.	.	.	.	.	G	17.75	3.466150	0.63625	.	.	ENSG00000126254	ENST00000262633	T	0.10099	2.91	5.18	0.704	0.18121	.	0.199899	0.43416	D	0.000571	T	0.07234	0.0183	L	0.34521	1.04	0.80722	D	1	B	0.34290	0.447	B	0.30572	0.117	T	0.29366	-1.0014	10	0.59425	D	0.04	-5.7983	7.7043	0.28640	0.421:0.0:0.579:0.0	.	162	Q9BTD8	RBM42_HUMAN	F	162	ENSP00000262633:V162F	ENSP00000262633:V162F	V	+	1	0	RBM42	40815719	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	0.836000	0.27545	0.087000	0.17167	-0.812000	0.03155	GTC	.		0.637	RBM42-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459057.2	NM_024321	
PVRL3	25945	hgsc.bcm.edu;bcgsc.ca	37	3	110852607	110852607	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr3:110852607G>T	ENST00000485303.1	+	6	1470	c.1195G>T	c.(1195-1197)Gat>Tat	p.D399Y	PVRL3_ENST00000493615.1_Intron|PVRL3_ENST00000319792.3_3'UTR	NM_001243286.1|NM_015480.2	NP_001230215.1|NP_056295.1	Q9NQS3	PVRL3_HUMAN	poliovirus receptor-related 3	399					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|fertilization (GO:0009566)|homophilic cell adhesion (GO:0007156)|lens morphogenesis in camera-type eye (GO:0002089)|retina morphogenesis in camera-type eye (GO:0060042)|single organismal cell-cell adhesion (GO:0016337)	apical junction complex (GO:0043296)|cell-cell adherens junction (GO:0005913)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	cell adhesion molecule binding (GO:0050839)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(3)	19						AACAATTAAGGATGACACAAT	0.443																																					p.D399Y		.											.	.	.	0			c.G1195T						.						164.0	160.0	162.0					3																	110852607		2203	4300	6503	SO:0001583	missense	25945	exon6			ATTAAGGATGACA	AF282874	CCDS2957.1, CCDS58842.1, CCDS58843.1	3q13	2013-01-29			ENSG00000177707	ENSG00000177707		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17664	protein-coding gene	gene with protein product		607147				11024295	Standard	NM_015480		Approved	nectin-3, PPR3, PVRR3, DKFZP566B0846, CDw113, CD113	uc003dxt.2	Q9NQS3	OTTHUMG00000159239	ENST00000485303.1:c.1195G>T	3.37:g.110852607G>T	ENSP00000418070:p.Asp399Tyr	Somatic	88	0		WXS	Illumina HiSeq	.	62	4	NM_015480	E9PFR0|Q6NVZ3|Q8NC05|Q8WVU4|Q9BVA9|Q9Y412	Missense_Mutation	SNP	ENST00000485303.1	37	CCDS2957.1	.	.	.	.	.	.	.	.	.	.	G	12.40	1.926679	0.34002	.	.	ENSG00000177707	ENST00000485303	T	0.16324	2.35	5.62	4.73	0.59995	.	0.290655	0.42053	D	0.000766	T	0.21962	0.0529	L	0.46157	1.445	0.80722	D	1	P	0.42785	0.79	P	0.44732	0.459	T	0.01192	-1.1423	10	0.56958	D	0.05	.	14.3042	0.66375	0.0:0.1498:0.8502:0.0	.	399	Q9NQS3	PVRL3_HUMAN	Y	399	ENSP00000418070:D399Y	ENSP00000418070:D399Y	D	+	1	0	PVRL3	112335297	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.706000	0.74649	1.351000	0.45789	0.467000	0.42956	GAT	.		0.443	PVRL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354045.1	NM_015480	
NOTCH2NL	388677	broad.mit.edu;bcgsc.ca	37	1	145290447	145290447	+	Missense_Mutation	SNP	C	C	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr1:145290447C>A	ENST00000344859.3	+	5	1015	c.653C>A	c.(652-654)cCt>cAt	p.P218H	RP11-458D21.5_ENST00000468030.1_Intron|NBPF10_ENST00000369339.3_5'UTR|NBPF10_ENST00000342960.5_5'Flank|NOTCH2NL_ENST00000479995.2_3'UTR|NBPF10_ENST00000369338.1_5'Flank			Q7Z3S9	NT2NL_HUMAN	notch 2 N-terminal like	0	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|Notch signaling pathway (GO:0007219)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	27						CCAATCTTTCCTAAGCTGCTC	0.378																																					.													.	.	.	0			.						.						360.0	362.0	361.0					1																	145290447		876	1989	2865	SO:0001583	missense	388677	.			TCTTTCCTAAGCT		CCDS72880.1	1q21.2	2010-06-24	2010-06-24		ENSG00000213240	ENSG00000213240			31862	protein-coding gene	gene with protein product			"""Notch homolog 2 (Drosophila) N-terminal like"""			14673143	Standard	NM_203458		Approved	N2N	uc001emn.4	Q7Z3S9	OTTHUMG00000013754	ENST00000344859.3:c.653C>A	1.37:g.145290447C>A	ENSP00000344557:p.Pro218His	Somatic	325	0		WXS	Illumina GAIIx	Phase_I	467	10	.	Q5BKT8|Q5VTG9|Q5XG84|Q6P192|Q8NC23|Q8WUQ9|Q96FY1	Missense_Mutation	SNP	ENST00000344859.3	37		.	.	.	.	.	.	.	.	.	.	.	6.611	0.481123	0.12581	.	.	ENSG00000213240	ENST00000344859	D	0.85484	-1.99	0.566	0.566	0.17317	.	.	.	.	.	T	0.62048	0.2396	.	.	.	0.09310	N	0.999998	B	0.09022	0.002	B	0.01281	0.0	T	0.59700	-0.7405	7	0.87932	D	0	.	.	.	.	.	218	Q7Z3S9-2	.	H	218	ENSP00000344557:P218H	ENSP00000344557:P218H	P	+	2	0	NOTCH2NL	144001804	0.001000	0.12720	0.018000	0.16275	0.140000	0.21249	0.767000	0.26575	0.571000	0.29365	0.184000	0.17185	CCT	.		0.378	NOTCH2NL-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000038544.1	NM_203458	
UHMK1	127933	broad.mit.edu	37	1	162468011	162468011	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr1:162468011G>T	ENST00000489294.1	+	1	379	c.221G>T	c.(220-222)cGc>cTc	p.R74L	UHMK1_ENST00000282169.8_3'UTR|UHMK1_ENST00000538489.1_Missense_Mutation_p.R74L|UHMK1_ENST00000545294.1_Intron	NM_175866.4	NP_787062.1	Q8TAS1	UHMK1_HUMAN	U2AF homology motif (UHM) kinase 1	74	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				cell cycle arrest (GO:0007050)|neuron projection development (GO:0031175)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of translational initiation (GO:0045948)|protein autophosphorylation (GO:0046777)|regulation of protein export from nucleus (GO:0046825)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|neuronal ribonucleoprotein granule (GO:0071598)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)|transferase activity (GO:0016740)			endometrium(1)|large_intestine(2)|lung(6)|prostate(2)	11	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			TATGGTTTCCGCAAAGAGAGG	0.642																																					p.R74L													.	UHMK1	65	0			c.G221T						.						21.0	22.0	22.0					1																	162468011		2202	4300	6502	SO:0001583	missense	127933	exon1			GTTTCCGCAAAGA	BC026046	CCDS1239.1, CCDS53423.1, CCDS53424.1	1q23.1	2013-02-12			ENSG00000152332	ENSG00000152332		"""RNA binding motif (RRM) containing"""	19683	protein-coding gene	gene with protein product		608849				12093740, 12782393	Standard	NM_175866		Approved	KIS, Kist	uc001gcc.2	Q8TAS1	OTTHUMG00000031373	ENST00000489294.1:c.221G>T	1.37:g.162468011G>T	ENSP00000420270:p.Arg74Leu	Somatic	32	0		WXS	Illumina GAIIx	Phase_I	52	3	NM_144624	A8K8K4|G3V1M1|Q96C22	Missense_Mutation	SNP	ENST00000489294.1	37	CCDS1239.1	.	.	.	.	.	.	.	.	.	.	G	13.03	2.114409	0.37339	.	.	ENSG00000152332	ENST00000538489;ENST00000489294	T;T	0.17691	2.26;2.26	4.94	4.94	0.65067	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.235404	0.44902	D	0.000402	T	0.03348	0.0097	N	0.03115	-0.41	.	.	.	B;B	0.06786	0.001;0.001	B;B	0.08055	0.002;0.003	T	0.34750	-0.9816	9	0.25106	T	0.35	-8.2846	15.3696	0.74551	0.0:0.0:1.0:0.0	.	74;74	Q8TAS1-2;Q8TAS1	.;UHMK1_HUMAN	L	74	ENSP00000446416:R74L;ENSP00000420270:R74L	ENSP00000420270:R74L	R	+	2	0	UHMK1	160734635	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.493000	0.53266	2.715000	0.92844	0.655000	0.94253	CGC	.		0.642	UHMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076788.1	NM_175866	
PRG4	10216	broad.mit.edu	37	1	186276029	186276029	+	Missense_Mutation	SNP	C	C	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr1:186276029C>A	ENST00000445192.2	+	7	1223	c.1178C>A	c.(1177-1179)cCc>cAc	p.P393H	PRG4_ENST00000367484.3_Missense_Mutation_p.P352H|PRG4_ENST00000367485.4_Missense_Mutation_p.P300H|PRG4_ENST00000367483.4_Missense_Mutation_p.P352H|PRG4_ENST00000367486.3_Missense_Mutation_p.P350H	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	393	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CCCACCACTCCCAAGGAGCCT	0.637																																					p.P393H													.	PRG4	259	0			c.C1178A						.						100.0	97.0	98.0					1																	186276029		2203	4294	6497	SO:0001583	missense	10216	exon7			CCACTCCCAAGGA	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1178C>A	1.37:g.186276029C>A	ENSP00000399679:p.Pro393His	Somatic	145	0		WXS	Illumina GAIIx	Phase_I	197	5	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	-	6.150	0.395938	0.11638	.	.	ENSG00000116690	ENST00000367486;ENST00000367484;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T;T	0.06687	3.32;3.27;3.46;3.36;3.47	2.98	1.91	0.25777	.	.	.	.	.	T	0.12732	0.0309	L	0.32530	0.975	0.09310	N	1	D;D;P;D	0.61697	0.99;0.972;0.953;0.972	P;P;P;P	0.57548	0.823;0.726;0.536;0.726	T	0.20273	-1.0280	8	.	.	.	.	9.1688	0.37067	0.0:0.7737:0.2263:0.0	.	259;300;393;352	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	H	350;352;259;352;300;393	ENSP00000356456:P350H;ENSP00000356454:P352H;ENSP00000356453:P352H;ENSP00000356455:P300H;ENSP00000399679:P393H	.	P	+	2	0	PRG4	184542652	0.000000	0.05858	0.070000	0.20053	0.015000	0.08874	0.964000	0.29306	1.393000	0.46605	0.478000	0.44815	CCC	.		0.637	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
MUC2	4583	broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	1096456	1096456	+	Missense_Mutation	SNP	G	G	A	rs569670287		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr11:1096456G>A	ENST00000441003.2	+	34	6508	c.6481G>A	c.(6481-6483)Gac>Aac	p.D2161N	MUC2_ENST00000361558.6_Missense_Mutation_p.D299N	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4523					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	AGTTTACATCGACAACTACCA	0.572													G|||	1	0.000199681	0.0	0.0	5008	,	,		20705	0.0		0.0	False		,,,				2504	0.001				p.D2157N													MUC2_ENST00000441003,NS,carcinoma,0,1	MUC2	614	0			c.G6469A						.						113.0	125.0	121.0					11																	1096456		2176	4264	6440	SO:0001583	missense	4583	exon35			TACATCGACAACT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.6481G>A	11.37:g.1096456G>A	ENSP00000415183:p.Asp2161Asn	Somatic	22	0		WXS	Illumina GAIIx	Phase_I	26	4	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	g	14.32	2.500650	0.44455	.	.	ENSG00000198788	ENST00000441003;ENST00000361558	T;T	0.59772	0.24;0.24	3.95	0.963	0.19649	.	.	.	.	.	T	0.43523	0.1251	L	0.52011	1.625	0.26564	N	0.973688	P	0.38504	0.634	B	0.29942	0.109	T	0.19679	-1.0298	9	0.40728	T	0.16	.	7.1852	0.25795	0.1612:0.1395:0.6993:0.0	.	2161	E7EUV1	.	N	2161;299	ENSP00000415183:D2161N;ENSP00000354885:D299N	ENSP00000354885:D299N	D	+	1	0	MUC2	1086456	1.000000	0.71417	0.147000	0.22382	0.126000	0.20510	5.245000	0.65405	0.016000	0.14998	0.479000	0.44913	GAC	.		0.572	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OVCH2	341277	broad.mit.edu	37	11	7716913	7716913	+	RNA	SNP	T	T	A	rs372744251		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr11:7716913T>A	ENST00000533663.1	-	0	0				OVCH2_ENST00000534193.2_RNA|OVCH2_ENST00000454689.1_RNA			Q7RTZ1	OVCH2_HUMAN	ovochymase 2 (gene/pseudogene)							extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			cervix(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(2)	15				Epithelial(150;7.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.197)		TAAGAATGGATGAggccgggc	0.517																																					.													.	OVCH2	47	0			.						.						31.0	27.0	28.0					11																	7716913		1795	4050	5845			341277	.			AATGGATGAGGCC	BN000120	CCDS73251.1	11p15.4	2012-10-02	2010-06-08		ENSG00000183378	ENSG00000183378			29970	protein-coding gene	gene with protein product			"""ovochymase 2"""			12838346	Standard	XM_006718221		Approved	OVTN	uc031pyw.1	Q7RTZ1	OTTHUMG00000165418		11.37:g.7716913T>A		Somatic	36	1		WXS	Illumina GAIIx	Phase_I	26	2	.		RNA	SNP	ENST00000533663.1	37		.	.	.	.	.	.	.	.	.	.	T	9.209	1.030505	0.19512	.	.	ENSG00000183378	ENST00000454689	.	.	.	2.99	2.99	0.34606	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.7424	0.28849	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	OVCH2	7673489	1.000000	0.71417	0.173000	0.22940	0.020000	0.10135	0.290000	0.18975	1.313000	0.45069	0.000000	0.15137	.	.		0.517	OVCH2-002	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000383928.1	NM_198185	
HERC2P3	283755	broad.mit.edu	37	15	20613810	20613810	+	RNA	SNP	A	A	G			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr15:20613810A>G	ENST00000428453.1	-	0	4041							Q9BVR0	HRC23_HUMAN	hect domain and RLD 2 pseudogene 3								metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(1)|lung(14)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	35						gctggtgagaagcagagctga	0.393																																					.													.	HERC2P3	53	0			.						.																																					0	.			GTGAGAAGCAGAG	AF041081		15q11.2	2010-08-02			ENSG00000180229	ENSG00000180229			4871	pseudogene	pseudogene						9730612	Standard	NR_036432		Approved	D15F37S4, LOC283755	uc001ytg.3	Q9BVR0	OTTHUMG00000157175		15.37:g.20613810A>G		Somatic	45	0		WXS	Illumina GAIIx	Phase_I	35	3	.		RNA	SNP	ENST00000428453.1	37																																																																																				.		0.393	HERC2P3-014	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000347772.2	NG_008269	
HERC2P3	283755	broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	20643872	20643872	+	RNA	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr15:20643872G>A	ENST00000428453.1	-	0	3587							Q9BVR0	HRC23_HUMAN	hect domain and RLD 2 pseudogene 3								metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(1)|lung(14)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	35						ATGGGCAAACGTGACACGTCC	0.483																																					.													.	HERC2P3	53	0			.						.						95.0	79.0	84.0					15																	20643872		2188	4269	6457			0	.			GCAAACGTGACAC	AF041081		15q11.2	2010-08-02			ENSG00000180229	ENSG00000180229			4871	pseudogene	pseudogene						9730612	Standard	NR_036432		Approved	D15F37S4, LOC283755	uc001ytg.3	Q9BVR0	OTTHUMG00000157175		15.37:g.20643872G>A		Somatic	205	0		WXS	Illumina GAIIx	Phase_I	179	46	.		RNA	SNP	ENST00000428453.1	37																																																																																				.		0.483	HERC2P3-014	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000347772.2	NG_008269	
MVP	9961	broad.mit.edu	37	16	29855899	29855899	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr16:29855899G>T	ENST00000357402.5	+	11	1858	c.1720G>T	c.(1720-1722)Gcc>Tcc	p.A574S	MVP_ENST00000395353.1_Missense_Mutation_p.A574S	NM_005115.4|NM_017458.3	NP_005106.2|NP_059447.2	Q14764	MVP_HUMAN	major vault protein	574					cell proliferation (GO:0008283)|ERBB signaling pathway (GO:0038127)|mRNA transport (GO:0051028)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of signaling (GO:0023057)|protein activation cascade (GO:0072376)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(7)|ovary(2)|skin(3)|soft_tissue(1)|stomach(1)	27						TGCCTGCAAAGCCATCGCATC	0.552																																					p.A574S													.	MVP	80	0			c.G1720T						.						88.0	83.0	84.0					16																	29855899		2197	4300	6497	SO:0001583	missense	9961	exon11			TGCAAAGCCATCG	X79882	CCDS10656.1	16p11.2	2012-04-25			ENSG00000013364	ENSG00000013364			7531	protein-coding gene	gene with protein product	"""lung resistance-related protein"""	605088				7585126	Standard	NM_005115		Approved	LRP, VAULT1	uc002dui.3	Q14764	OTTHUMG00000048227	ENST00000357402.5:c.1720G>T	16.37:g.29855899G>T	ENSP00000349977:p.Ala574Ser	Somatic	33	0		WXS	Illumina GAIIx	Phase_I	31	3	NM_017458	Q96BG4|Q9BPW6|Q9BQT1|Q9UBD1	Missense_Mutation	SNP	ENST00000357402.5	37	CCDS10656.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.790368	0.90367	.	.	ENSG00000013364	ENST00000357402;ENST00000395353	T;T	0.44881	0.91;0.91	5.91	4.96	0.65561	Shoulder domain (1);	0.000000	0.85682	D	0.000000	T	0.53753	0.1816	M	0.61703	1.905	0.80722	D	1	D	0.58620	0.983	P	0.58077	0.832	T	0.50524	-0.8818	10	0.23891	T	0.37	-28.863	12.9861	0.58592	0.078:0.0:0.922:0.0	.	574	Q14764	MVP_HUMAN	S	574	ENSP00000349977:A574S;ENSP00000378760:A574S	ENSP00000349977:A574S	A	+	1	0	MVP	29763400	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.354000	0.73036	1.515000	0.48885	0.655000	0.94253	GCC	.		0.552	MVP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109711.3	NM_005115	
ANKRD36C	400986	broad.mit.edu	37	2	96643871	96643871	+	Splice_Site	SNP	T	T	C	rs201215924		TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr2:96643871T>C	ENST00000456556.1	-	6	882	c.798A>G	c.(796-798)ccA>ccG	p.P266P				Q5JPF3	AN36C_HUMAN	ankyrin repeat domain 36C	266							ion channel inhibitor activity (GO:0008200)	p.P266P(2)		breast(1)|endometrium(8)|kidney(5)|lung(4)	18						AAATCTTACCTGGATTGCTAT	0.239																																					.													ENSG00000174501,NS,carcinoma,0,2	.	.	2	Substitution - coding silent(2)	endometrium(1)|kidney(1)	.						.																																			SO:0001630	splice_region_variant	400986	.			CTTACCTGGATTG	AL832836		2q11.1	2013-01-10			ENSG00000174501	ENSG00000174501		"""Ankyrin repeat domain containing"""	32946	protein-coding gene	gene with protein product	"""protein immuno-reactive with anti-PTH polyclonal antibodies"""						Standard	XR_251121		Approved	DKFZp667P0924	uc002suz.1	Q5JPF3	OTTHUMG00000155211	ENST00000456556.1:c.799+1A>G	2.37:g.96643871T>C		Somatic	39	1		WXS	Illumina GAIIx	Phase_I	149	8	.	C9JZ08|Q15694|Q53S06|Q658V2	Splice_Site	SNP	ENST00000456556.1	37																																																																																				.		0.239	ANKRD36C-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000338799.2	NM_001010914	Silent
TPTE	7179	broad.mit.edu	37	21	10944697	10944697	+	Frame_Shift_Del	DEL	A	A	-			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr21:10944697delA	ENST00000361285.4	-	11	866	c.537delT	c.(535-537)tttfs	p.F179fs	TPTE_ENST00000342420.5_Frame_Shift_Del_p.F141fs|TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000298232.7_Frame_Shift_Del_p.F161fs	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	179					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ACTTAATGTCAAAAAAAATGT	0.299																																					p.F179fs													.	TPTE	513	0			c.537delT						.						157.0	168.0	164.0					21																	10944697		2203	4300	6503	SO:0001589	frameshift_variant	7179	exon11			AATGTCAAAAAAA	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.537delT	21.37:g.10944697delA	ENSP00000355208:p.Phe179fs	Somatic	128	0		WXS	Illumina GAIIx	Phase_I	217	7	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Frame_Shift_Del	DEL	ENST00000361285.4	37	CCDS13560.2																																																																																			.		0.299	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1		
CYP2D6	1565	broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	42526688	42526688	+	Missense_Mutation	SNP	C	C	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr22:42526688C>A	ENST00000360608.5	-	1	220	c.106G>T	c.(106-108)Ggc>Tgc	p.G36C	CYP2D6_ENST00000389970.3_Missense_Mutation_p.G36C|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000359033.4_Missense_Mutation_p.G36C|NDUFA6-AS1_ENST00000608491.1_RNA|NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000608288.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	36					alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GGCAGGGGGCCTGGTGGGTAG	0.657																																					p.G36C													.	CYP2D6	104	0			c.G106T						.						45.0	36.0	39.0					22																	42526688		2195	4298	6493	SO:0001583	missense	1565	exon1			GGGGGCCTGGTGG	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"""Cytochrome P450s"""	2625	protein-coding gene	gene with protein product		124030	"""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6"", ""cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2"", ""cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2"", ""cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2"", ""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"""	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.106G>T	22.37:g.42526688C>A	ENSP00000353820:p.Gly36Cys	Somatic	60	0		WXS	Illumina GAIIx	Phase_I	66	12	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	.	.	.	.	.	.	.	.	.	.	c	14.36	2.512772	0.44660	.	.	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000359033;ENST00000542856	D;D;T	0.85484	-1.99;-1.99;4.45	3.46	3.46	0.39613	.	0.000000	0.64402	D	0.000008	D	0.92456	0.7605	M	0.90977	3.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92603	0.6093	10	0.87932	D	0	.	8.6425	0.33985	0.0:0.8879:0.0:0.1121	.	36;36	Q6NXU8;Q6NWU0	.;.	C	36	ENSP00000353820:G36C;ENSP00000374620:G36C;ENSP00000351927:G36C	ENSP00000351927:G36C	G	-	1	0	CYP2D6	40856632	0.993000	0.37304	0.813000	0.32504	0.125000	0.20455	3.174000	0.50847	2.218000	0.71995	0.484000	0.47621	GGC	.		0.657	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
HMGB1P5	10354	broad.mit.edu	37	3	22424366	22424366	+	RNA	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr3:22424366G>T	ENST00000451497.1	+	0	931									high mobility group box 1 pseudogene 5																		CTGTTTTGTTGACATTCTGAA	0.333																																					.													.	.	.	0			.						.																																					0	.			TTTGTTGACATTC	AF076677		3p24	2011-09-21	2011-04-05	2010-10-15	ENSG00000132967	ENSG00000132967		"""High mobility group / HMG-box pseudogenes"""	4997	pseudogene	pseudogene			"""high-mobility group (nonhistone chromosomal) protein 1-like 5"", ""high-mobility group (nonhistone chromosomal) protein 1-like 5 pseudogene"", ""high-mobility group box 1-like 5 pseudogene"", ""high-mobility group box 1-like 15"", ""high-mobility group box 1 pseudogene 2"", ""high-mobility group box 1-like 5"", ""high-mobility group box 1 pseudogene 5"""	HMG1L5, HMGB1L15, HMGB1P2, HMGB1L5		9925949	Standard	NG_000897		Approved				OTTHUMG00000155591		3.37:g.22424366G>T		Somatic	34	0		WXS	Illumina GAIIx	Phase_I	41	7	.		RNA	SNP	ENST00000451497.1	37																																																																																				.		0.333	HMGB1P5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000340803.1	NG_000897	
CAMK2D	817	broad.mit.edu	37	4	114435036	114435036	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr4:114435036G>T	ENST00000342666.5	-	11	852	c.853C>A	c.(853-855)Cag>Aag	p.Q285K	CAMK2D_ENST00000514328.1_Missense_Mutation_p.Q285K|CAMK2D_ENST00000454265.2_Missense_Mutation_p.Q285K|CAMK2D_ENST00000394522.3_Missense_Mutation_p.Q285K|CAMK2D_ENST00000296402.5_Missense_Mutation_p.Q285K|CAMK2D_ENST00000394524.3_Missense_Mutation_p.Q285K|CAMK2D_ENST00000418639.2_Missense_Mutation_p.Q285K|CAMK2D_ENST00000429180.1_Missense_Mutation_p.Q285K|CAMK2D_ENST00000511664.1_Missense_Mutation_p.Q285K|CAMK2D_ENST00000508738.1_Missense_Mutation_p.Q285K|CAMK2D_ENST00000379773.2_Missense_Mutation_p.Q285K|CAMK2D_ENST00000515496.1_Missense_Mutation_p.Q285K|CAMK2D_ENST00000394526.2_Missense_Mutation_p.Q285K|CAMK2D_ENST00000505990.1_Missense_Mutation_p.Q285K			Q13557	KCC2D_HUMAN	calcium/calmodulin-dependent protein kinase II delta	285	Autoinhibitory domain. {ECO:0000250}.				calcium ion transport (GO:0006816)|cardiac muscle cell contraction (GO:0086003)|cellular response to calcium ion (GO:0071277)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle cell action potential (GO:0098901)|regulation of cardiac muscle cell action potential involved in regulation of contraction (GO:0098909)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of cell growth (GO:0001558)|regulation of cellular localization (GO:0060341)|regulation of generation of L-type calcium current (GO:1902514)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of histone deacetylase activity (GO:1901725)|regulation of membrane depolarization (GO:0003254)|regulation of relaxation of cardiac muscle (GO:1901897)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of the force of heart contraction (GO:0002026)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|relaxation of cardiac muscle (GO:0055119)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|calcium channel complex (GO:0034704)|calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intercalated disc (GO:0014704)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|ion channel binding (GO:0044325)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|sodium channel inhibitor activity (GO:0019871)|titin binding (GO:0031432)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	13		Ovarian(17;0.00369)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000271)		ACAGTCTCCTGTCTGTGCATC	0.333																																					p.Q285K													.	CAMK2D	55	0			c.C853A						.						45.0	44.0	45.0					4																	114435036		2203	4300	6503	SO:0001583	missense	817	exon11			TCTCCTGTCTGTG	U50361	CCDS3703.1, CCDS3704.1, CCDS43263.1, CCDS47127.1, CCDS54797.1	4q26	2008-10-30	2008-10-30		ENSG00000145349	ENSG00000145349			1462	protein-coding gene	gene with protein product		607708	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II delta"""	CAMKD			Standard	NM_001221		Approved		uc003ibi.3	Q13557	OTTHUMG00000132910	ENST00000342666.5:c.853C>A	4.37:g.114435036G>T	ENSP00000339740:p.Gln285Lys	Somatic	98	0		WXS	Illumina GAIIx	Phase_I	48	3	NM_172128	A8MVS8|Q52PK4|Q59G21|Q8N553|Q9UGH6|Q9UQE9	Missense_Mutation	SNP	ENST00000342666.5	37	CCDS3703.1	.	.	.	.	.	.	.	.	.	.	G	19.29	3.799608	0.70567	.	.	ENSG00000145349	ENST00000394524;ENST00000454265;ENST00000429180;ENST00000418639;ENST00000394526;ENST00000296402;ENST00000511664;ENST00000342666;ENST00000515496;ENST00000514328;ENST00000394522;ENST00000505990;ENST00000379773;ENST00000508738;ENST00000509594	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.68181	-0.29;-0.28;-0.28;-0.24;-0.23;-0.29;-0.31;-0.3;-0.23;-0.3;-0.31;-0.29;-0.29;1.86;1.67	5.11	5.11	0.69529	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.74741	0.3756	M	0.89658	3.05	0.80722	D	1	B;B;B;B;B	0.27380	0.111;0.177;0.177;0.104;0.111	B;B;B;B;B	0.24848	0.052;0.056;0.056;0.038;0.017	T	0.77897	-0.2416	10	0.87932	D	0	.	18.5125	0.90921	0.0:0.0:1.0:0.0	.	285;285;285;285;285	E9PF82;Q13557-3;Q13557-6;Q13557-12;Q13557	.;.;.;.;KCC2D_HUMAN	K	285;285;285;285;285;285;285;285;285;285;285;285;285;285;80	ENSP00000378032:Q285K;ENSP00000415248:Q285K;ENSP00000415707:Q285K;ENSP00000406131:Q285K;ENSP00000378034:Q285K;ENSP00000296402:Q285K;ENSP00000425824:Q285K;ENSP00000339740:Q285K;ENSP00000423482:Q285K;ENSP00000423677:Q285K;ENSP00000378030:Q285K;ENSP00000424245:Q285K;ENSP00000369098:Q285K;ENSP00000422566:Q285K;ENSP00000423753:Q80K	ENSP00000296402:Q285K	Q	-	1	0	CAMK2D	114654485	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.772000	0.98984	2.352000	0.79861	0.462000	0.41574	CAG	.		0.333	CAMK2D-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256420.2		
CTD-2066L21.3	0	broad.mit.edu	37	5	33162972	33162972	+	lincRNA	SNP	C	C	A	rs7447930	byFrequency	TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr5:33162972C>A	ENST00000510327.1	-	0	346																											TCCCCCCCCCCCAAAAAAAAG	0.353													C|||	405	0.0808706	0.1589	0.0476	5008	,	,		16133	0.0645		0.0517	False		,,,				2504	0.046				.													.	.	.	0			.						.																																					0	.			CCCCCCCCAAAAA																													5.37:g.33162972C>A		Somatic	52	5		WXS	Illumina GAIIx	Phase_I	52	13	.		RNA	SNP	ENST00000510327.1	37																																																																																				.		0.353	CTD-2066L21.3-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000366718.1		
CATSPER3	347732	broad.mit.edu;bcgsc.ca	37	5	134305631	134305631	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr5:134305631G>T	ENST00000282611.6	+	2	187	c.101G>T	c.(100-102)aGg>aTg	p.R34M	CATSPER3_ENST00000511235.1_3'UTR	NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	34					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|endoplasmic reticulum (GO:0005783)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TTTGACAGGAGGAACGATGAT	0.393																																					p.R34M													.	CATSPER3	38	0			c.G101T						.						154.0	144.0	148.0					5																	134305631		2203	4300	6503	SO:0001583	missense	347732	exon2			ACAGGAGGAACGA	AF432876	CCDS4181.1	5q31.2	2011-07-05			ENSG00000152705	ENSG00000152705		"""Voltage-gated ion channels / Cation channels, sperm associated"""	20819	protein-coding gene	gene with protein product		609120				12646162, 12932298, 17227845, 16382101	Standard	NM_178019		Approved	CACRC	uc003lag.3	Q86XQ3	OTTHUMG00000129137	ENST00000282611.6:c.101G>T	5.37:g.134305631G>T	ENSP00000282611:p.Arg34Met	Somatic	66	0		WXS	Illumina GAIIx	Phase_I	68	4	NM_178019	Q86XS6	Missense_Mutation	SNP	ENST00000282611.6	37	CCDS4181.1	.	.	.	.	.	.	.	.	.	.	G	16.64	3.180452	0.57800	.	.	ENSG00000152705	ENST00000282611	D	0.97505	-4.41	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000008	D	0.97164	0.9073	L	0.29908	0.895	0.38927	D	0.957856	D	0.89917	1.0	D	0.85130	0.997	D	0.98593	1.0655	10	0.87932	D	0	-32.8901	16.8675	0.86033	0.0:0.0:1.0:0.0	.	34	Q86XQ3	CTSR3_HUMAN	M	34	ENSP00000282611:R34M	ENSP00000282611:R34M	R	+	2	0	CATSPER3	134333530	1.000000	0.71417	0.999000	0.59377	0.183000	0.23260	3.415000	0.52700	2.804000	0.96469	0.650000	0.86243	AGG	.		0.393	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019	
RUFY1	80230	broad.mit.edu	37	5	178977642	178977642	+	Frame_Shift_Del	DEL	G	G	-			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr5:178977642delG	ENST00000319449.4	+	1	84	c.72delG	c.(70-72)ccgfs	p.P24fs	RUFY1_ENST00000377001.2_Frame_Shift_Del_p.P24fs	NM_025158.4	NP_079434.3	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1	24					endocytosis (GO:0006897)|regulation of endocytosis (GO:0030100)	cytoplasm (GO:0005737)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	lipid binding (GO:0008289)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			agccggggccggggcCCGGGT	0.746										HNSCC(44;0.11)																											p.P24fs													.	RUFY1	101	0			c.72delG						.						3.0	4.0	4.0					5																	178977642		1521	3608	5129	SO:0001589	frameshift_variant	80230	exon1			GGGGCCGGGGCCC	AF361055	CCDS4445.2, CCDS34312.1	5q35.3	2008-02-05			ENSG00000176783	ENSG00000176783		"""Zinc fingers, FYVE domain containing"""	19760	protein-coding gene	gene with protein product		610327				11877430	Standard	NM_001040451		Approved	FLJ22251, ZFYVE12, RABIP4	uc003mka.2	Q96T51	OTTHUMG00000130913	ENST00000319449.4:c.72delG	5.37:g.178977642delG	ENSP00000325594:p.Pro24fs	Somatic	4	0		WXS	Illumina GAIIx	Phase_I	6	1	NM_025158	Q59FF3|Q71S93|Q9H6I3	Frame_Shift_Del	DEL	ENST00000319449.4	37	CCDS4445.2																																																																																			.		0.746	RUFY1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253505.2	NM_001040451	
PGBD1	84547	broad.mit.edu	37	6	28251597	28251597	+	Missense_Mutation	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr6:28251597G>A	ENST00000405948.2	+	2	427	c.7G>A	c.(7-9)Gaa>Aaa	p.E3K	PGBD1_ENST00000259883.3_Missense_Mutation_p.E3K	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	3						membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						CAACATGTATGAAGCTTTGCC	0.458																																					p.E3K													.	PGBD1	106	0			c.G7A						.						81.0	87.0	85.0					6																	28251597		2203	4300	6503	SO:0001583	missense	84547	exon2			ATGTATGAAGCTT	D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"""-"""	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.7G>A	6.37:g.28251597G>A	ENSP00000385213:p.Glu3Lys	Somatic	31	0		WXS	Illumina GAIIx	Phase_I	31	3	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Missense_Mutation	SNP	ENST00000405948.2	37	CCDS4648.1	.	.	.	.	.	.	.	.	.	.	G	16.56	3.156985	0.57259	.	.	ENSG00000137338	ENST00000405948;ENST00000259883	T;T	0.01455	4.87;4.87	4.39	4.39	0.52855	Speract/scavenger receptor (1);	.	.	.	.	T	0.01870	0.0059	L	0.27053	0.805	0.28448	N	0.916487	D	0.76494	0.999	D	0.78314	0.991	T	0.54262	-0.8320	9	0.39692	T	0.17	8.2187	8.464	0.32944	0.102:0.0:0.898:0.0	.	3	Q96JS3	PGBD1_HUMAN	K	3	ENSP00000385213:E3K;ENSP00000259883:E3K	ENSP00000259883:E3K	E	+	1	0	PGBD1	28359576	1.000000	0.71417	0.994000	0.49952	0.725000	0.41563	2.414000	0.44627	2.704000	0.92352	0.655000	0.94253	GAA	.		0.458	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2		
COL26A1	136227	broad.mit.edu	37	7	101071948	101071949	+	RNA	DEL	GT	GT	-			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr7:101071948_101071949delGT	ENST00000397927.3	+	0	494				COL26A1_ENST00000528707.1_RNA|COL26A1_ENST00000313669.7_RNA	NM_001278563.1	NP_001265492.1	Q96A83	COQA1_HUMAN	collagen, type XXVI, alpha 1						collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)											ttttgtggtCgtgtgtgtgtgt	0.48																																					.													.	.	.	0			.						.																																					136227	.			GTGGTCGTGTGTG	AJ416091	CCDS64739.1	7q22.1	2013-01-16	2013-01-16	2013-01-16	ENSG00000160963	ENSG00000160963		"""Collagens"", ""EMI domain containing"""	18038	protein-coding gene	gene with protein product	"""Emu2 gene"""	608927	"""EMI domain containing 2"""	EMID2		12221002, 12145293	Standard	NM_001278563		Approved	Emu2, EMI6	uc003uyo.1	Q96A83	OTTHUMG00000150033		7.37:g.101071958_101071959delGT		Somatic	5	0		WXS	Illumina GAIIx	Phase_I	6	1	.	Q32M90	RNA	DEL	ENST00000397927.3	37																																																																																				.		0.480	COL26A1-002	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000315898.2	NM_133457	
DPY19L2P2	349152	broad.mit.edu	37	7	102898132	102898132	+	RNA	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr7:102898132C>T	ENST00000312132.4	-	0	2440							Q6ZN68	D19P2_HUMAN	DPY19L2 pseudogene 2							integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)										AATAAATTCACTATTCCCATG	0.333																																					.													.	.	.	0			.						.																																					0	.			AATTCACTATTCC	AL834175		7q22.1	2013-09-12	2013-09-12		ENSG00000170629	ENSG00000170629			21764	pseudogene	pseudogene			"""dpy-19-like 2 pseudogene 2 (C. elegans)"""				Standard	NR_027768		Approved	DKFZp434E092, FLJ36166	uc003vbh.4	Q6ZN68	OTTHUMG00000157200		7.37:g.102898132C>T		Somatic	151	0		WXS	Illumina GAIIx	Phase_I	154	7	.	Q8N9V4|Q8ND62	RNA	SNP	ENST00000312132.4	37																																																																																				.		0.333	DPY19L2P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000347877.1	NM_182634	
FOXP2	93986	broad.mit.edu	37	7	114269938	114269949	+	In_Frame_Del	DEL	CAGCAGCAACAA	CAGCAGCAACAA	-	rs62640396	byFrequency	TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr7:114269938_114269949delCAGCAGCAACAA	ENST00000393494.2	+	5	754_765	c.475_486delCAGCAGCAACAA	c.(475-486)cagcagcaacaadel	p.QQQQ187del	AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000393489.3_In_Frame_Del_p.QQQQ95del|FOXP2_ENST00000403559.4_In_Frame_Del_p.QQQQ204del|FOXP2_ENST00000408937.3_In_Frame_Del_p.QQQQ212del|FOXP2_ENST00000393498.2_In_Frame_Del_p.QQQQ167del|FOXP2_ENST00000393500.3_In_Frame_Del_p.QQQQ112del|FOXP2_ENST00000390668.3_In_Frame_Del_p.QQQQ211del|FOXP2_ENST00000393491.3_In_Frame_Del_p.QQQQ95del|FOXP2_ENST00000350908.4_In_Frame_Del_p.QQQQ187del|FOXP2_ENST00000378237.3_In_Frame_Del_p.QQQQ187del|FOXP2_ENST00000360232.4_In_Frame_Del_p.QQQQ187del			O15409	FOXP2_HUMAN	forkhead box P2	187	Gln-rich.				camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|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)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						gcaacagcagcagcagcaacaacagcagcaac	0.472																																					p.184_187del													FOXP2,NS,carcinoma,0,1	FOXP2	133	0			c.550_561del						.																																			SO:0001651	inframe_deletion	93986	exon5			CAGCAGCAGCAGC	U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"""Forkhead boxes"""	13875	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 10"", ""forkhead/winged-helix transcription factor"", ""speech and language disorder 1"", ""CAG repeat protein 44"""	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.475_486delCAGCAGCAACAA	7.37:g.114269938_114269949delCAGCAGCAACAA	ENSP00000377132:p.Gln187_Gln190del	Somatic	53	0		WXS	Illumina GAIIx	Phase_I	51	4	NM_001172767	A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	In_Frame_Del	DEL	ENST00000393494.2	37	CCDS5760.1																																																																																			.		0.472	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491	
PMS2P3	5387	broad.mit.edu	37	7	75141201	75141202	+	RNA	DEL	TA	TA	-	rs372497718|rs587694460	byFrequency	TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr7:75141201_75141202delTA	ENST00000418756.1	-	0	1191				Y_RNA_ENST00000364004.1_RNA	NR_028059.1		Q13401	PM2P3_HUMAN	postmeiotic segregation increased 2 pseudogene 3						mismatch repair (GO:0006298)|regulation of transcription, DNA-templated (GO:0006355)	mismatch repair complex (GO:0032300)	nucleic acid binding (GO:0003676)			lung(1)	1						catatatgtgtatatatatata	0.213														1141	0.227835	0.3684	0.183	5008	,	,		10689	0.0585		0.1889	False		,,,				2504	0.2843				.	NSCLC(70;602 1339 5301 18528 38453)												.	PMS2P3	7	0			.						.																																					0	.			TATGTGTATATAT	D38437		7q11.23	2010-10-26	2010-10-26	2010-10-26	ENSG00000127957	ENSG00000127957			9128	pseudogene	pseudogene			"""postmeiotic segregation increased 2-like 3"", ""postmeiotic segregation increased 2-like 3, pseudogene"""	PMS2L9, PMS2L3		8586419	Standard	NR_028059		Approved	PMS5, PMSR3	uc022agi.1	Q13401	OTTHUMG00000156049		7.37:g.75141211_75141212delTA		Somatic	4	0		WXS	Illumina GAIIx	Phase_I	6	1	.	A6NG70|Q3MJ29	RNA	DEL	ENST00000418756.1	37																																																																																				.		0.213	PMS2P3-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000342862.2	NR_028059	
GRM3	2913	broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	86416121	86416121	+	Missense_Mutation	SNP	A	A	G			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr7:86416121A>G	ENST00000361669.2	+	3	2112	c.1013A>G	c.(1012-1014)cAg>cGg	p.Q338R	GRM3_ENST00000439827.1_Missense_Mutation_p.Q338R|AC005009.2_ENST00000452471.1_RNA|GRM3_ENST00000394720.2_Missense_Mutation_p.Q336R|AC005009.2_ENST00000418031.1_RNA|GRM3_ENST00000536043.1_Missense_Mutation_p.Q210R|GRM3_ENST00000546348.1_Intron	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	338					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					CGCTACTTCCAGAGCCTCAAC	0.617																																					p.Q338R	GBM(52;969 1098 3139 52280)												.	GRM3	237	0			c.A1013G						.						41.0	41.0	41.0					7																	86416121		2203	4300	6503	SO:0001583	missense	0	exon3			ACTTCCAGAGCCT		CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.1013A>G	7.37:g.86416121A>G	ENSP00000355316:p.Gln338Arg	Somatic	26	0		WXS	Illumina GAIIx	Phase_I	43	4	NM_000840	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Missense_Mutation	SNP	ENST00000361669.2	37	CCDS5600.1	.	.	.	.	.	.	.	.	.	.	A	8.549	0.875098	0.17395	.	.	ENSG00000198822	ENST00000361669;ENST00000536043;ENST00000439827;ENST00000394720	D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62	5.93	4.78	0.61160	Extracellular ligand-binding receptor (1);	0.118514	0.64402	N	0.000019	T	0.67850	0.2937	N	0.19112	0.55	0.50813	D	0.999899	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.002	T	0.58808	-0.7571	10	0.07482	T	0.82	.	11.0614	0.47950	0.9281:0.0:0.0719:0.0	.	210;338;338	F5GYZ2;G5E9K2;Q14832	.;.;GRM3_HUMAN	R	338;210;338;336	ENSP00000355316:Q338R;ENSP00000441407:Q210R;ENSP00000398767:Q338R;ENSP00000378209:Q336R	ENSP00000355316:Q338R	Q	+	2	0	GRM3	86254057	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.455000	0.52993	1.075000	0.40932	0.533000	0.62120	CAG	.		0.617	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2		
TRBV30	28557	broad.mit.edu;ucsc.edu	37	7	142511015	142511015	+	RNA	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr7:142511015G>A	ENST00000417977.2	-	0	69									T cell receptor beta variable 30 (gene/pseudogene)																		GGGGACAGACGCCTCCTCTTC	0.592																																					.													.	.	.	0			.						.						29.0	37.0	35.0					7																	142511015		1995	4173	6168			0	.			ACAGACGCCTCCT	L36092		7q34	2012-02-07	2008-09-12		ENSG00000237254	ENSG00000237254		"""T cell receptors / TRB locus"""	12214	other	T cell receptor gene			"""T cell receptor beta variable 30"""			8650574	Standard	NG_001333		Approved	TCRBV20S1A1N2, TCRBV30S1			OTTHUMG00000158907		7.37:g.142511015G>A		Somatic	30	0		WXS	Illumina GAIIx	Phase_I	32	17	.		RNA	SNP	ENST00000417977.2	37																																																																																				.		0.592	TRBV30-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TR_V_gene	OTTHUMT00000352519.1	NG_001333	
ZNF467	168544	broad.mit.edu	37	7	149462038	149462038	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr7:149462038G>T	ENST00000302017.3	-	5	1966	c.1553C>A	c.(1552-1554)gCc>gAc	p.A518D	ZNF467_ENST00000484747.1_Intron	NM_207336.1	NP_997219.1	Q7Z7K2	ZN467_HUMAN	zinc finger protein 467	518					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|liver(1)|lung(7)|urinary_tract(1)	13	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GGCGCAGACGGCGCAGGCGTG	0.706																																					p.A518D													.	ZNF467	50	0			c.C1553A						.						24.0	30.0	28.0					7																	149462038		2194	4291	6485	SO:0001583	missense	168544	exon5			CAGACGGCGCAGG	BC029296	CCDS5899.1	7q36.1	2013-01-08			ENSG00000181444	ENSG00000181444		"""Zinc fingers, C2H2-type"""	23154	protein-coding gene	gene with protein product		614040				12426389	Standard	NM_207336		Approved	EZI, Zfp467	uc003wgd.2	Q7Z7K2	OTTHUMG00000157883	ENST00000302017.3:c.1553C>A	7.37:g.149462038G>T	ENSP00000304769:p.Ala518Asp	Somatic	40	0		WXS	Illumina GAIIx	Phase_I	43	3	NM_207336		Missense_Mutation	SNP	ENST00000302017.3	37	CCDS5899.1	.	.	.	.	.	.	.	.	.	.	G	13.61	2.288919	0.40494	.	.	ENSG00000181444	ENST00000302017	T	0.13901	2.55	3.82	3.82	0.43975	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.568464	0.13166	U	0.408676	T	0.06962	0.0177	N	0.01761	-0.735	0.34958	D	0.751888	P	0.37176	0.586	B	0.40165	0.321	T	0.43734	-0.9373	10	0.17369	T	0.5	-11.6448	15.504	0.75722	0.0:0.0:1.0:0.0	.	518	Q7Z7K2	ZN467_HUMAN	D	518	ENSP00000304769:A518D	ENSP00000304769:A518D	A	-	2	0	ZNF467	149092971	0.004000	0.15560	1.000000	0.80357	0.995000	0.86356	0.726000	0.25984	1.989000	0.58080	0.462000	0.41574	GCC	.		0.706	ZNF467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349833.1	NM_207336	
MT-CO2	4513	broad.mit.edu	37	M	7820	7820	+	Missense_Mutation	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chrM:7820C>T	ENST00000361739.1	+	1	235	c.235C>T	c.(235-237)Cca>Tca	p.P79S	MT-ND3_ENST00000361227.2_5'Flank|MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TK_ENST00000387421.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-TD_ENST00000387419.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-TS1_ENST00000387416.2_RNA|MT-TW_ENST00000387382.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-ATP6_ENST00000361899.2_5'Flank			P00403	COX2_HUMAN	mitochondrially encoded cytochrome c oxidase II	79					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|respiratory chain complex IV (GO:0045277)	copper ion binding (GO:0005507)|cytochrome-c oxidase activity (GO:0004129)			endometrium(5)|kidney(8)|lung(2)|pancreas(3)|prostate(1)	19						TCATCGCCCTCCCATCCCTAC	0.478																																					p.P79S													.	.	.	0			c.C235T						.																																			SO:0001583	missense	4513	exon1			GCCCTCCCATCCC			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198712	ENSG00000198712		"""Mitochondrial respiratory chain complex / Complex IV"""	7421	protein-coding gene	gene with protein product		516040	"""cytochrome c oxidase II"""	MTCO2		1712754, 1989603	Standard			Approved	COX2, CO2		P00403		ENST00000361739.1:c.235C>T	M.37:g.7820C>T	ENSP00000354876:p.Pro79Ser	Somatic	1282	0		WXS	Illumina GAIIx	Phase_I	1592	12	ENST00000361739	Q37526	Missense_Mutation	SNP	ENST00000361739.1	37																																																																																				.		0.478	MT-CO2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024029	
TMEM200B	399474	ucsc.edu	37	1	29447458	29447458	+	Missense_Mutation	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr1:29447458C>T	ENST00000420504.2	-	2	1040	c.883G>A	c.(883-885)Gcc>Acc	p.A295T	TMEM200B_ENST00000521452.1_Missense_Mutation_p.A295T	NM_001171868.1	NP_001165339.1	Q69YZ2	T200B_HUMAN	transmembrane protein 200B	295						integral component of membrane (GO:0016021)				ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.00765)|Lung NSC(340;0.0153)|all_lung(284;0.0173)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;7.32e-08)|COAD - Colon adenocarcinoma(152;4.92e-06)|STAD - Stomach adenocarcinoma(196;0.00618)|BRCA - Breast invasive adenocarcinoma(304;0.0501)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.126)		CCCAATTTGGCATAGCCCCCA	0.642																																					p.A295T													.	TMEM200B	9	0			c.G883A						.						17.0	19.0	18.0					1																	29447458		2202	4300	6502	SO:0001583	missense	399474	exon2			ATTTGGCATAGCC		CCDS30658.1	1p35	2007-12-18			ENSG00000253304	ENSG00000253304			33785	protein-coding gene	gene with protein product						15722956	Standard	NM_001003682		Approved	TTMB	uc001brn.2	Q69YZ2	OTTHUMG00000003658	ENST00000420504.2:c.883G>A	1.37:g.29447458C>T	ENSP00000428544:p.Ala295Thr	Somatic	73	0		WXS	Illumina HiSeq		34	4	NM_001171868	Q6P2G8|Q6P2Q5	Missense_Mutation	SNP	ENST00000420504.2	37	CCDS30658.1	.	.	.	.	.	.	.	.	.	.	C	14.83	2.651612	0.47362	.	.	ENSG00000253304	ENST00000521452;ENST00000420504	.	.	.	4.26	3.34	0.38264	.	0.175913	0.26955	U	0.021643	T	0.20740	0.0499	N	0.04508	-0.205	0.29908	N	0.823784	B	0.20550	0.046	B	0.12156	0.007	T	0.11665	-1.0578	9	0.39692	T	0.17	.	11.9599	0.53003	0.0:0.9102:0.0:0.0898	.	295	Q69YZ2	T200B_HUMAN	T	295	.	ENSP00000428544:A295T	A	-	1	0	TMEM200B	29320045	0.999000	0.42202	1.000000	0.80357	0.960000	0.62799	0.558000	0.23469	2.348000	0.79779	0.655000	0.94253	GCC	.		0.642	TMEM200B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010377.2	NM_001003682	
HDGF	3068	ucsc.edu;bcgsc.ca	37	1	156714048	156714048	+	Silent	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr1:156714048G>A	ENST00000357325.5	-	4	710	c.396C>T	c.(394-396)agC>agT	p.S132S	HDGF_ENST00000416666.2_Silent_p.S100S|HDGF_ENST00000537739.1_Silent_p.S132S|HDGF_ENST00000368209.5_Silent_p.S125S|HDGF_ENST00000465180.1_5'UTR|HDGF_ENST00000368206.5_Silent_p.S148S	NM_004494.2	NP_004485.1	P51858	HDGF_HUMAN	hepatoma-derived growth factor	132	Glu-rich.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription corepressor binding (GO:0001222)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9	all_hematologic(923;0.088)|Hepatocellular(266;0.158)	Breast(1374;0.198)		Colorectal(1306;0.018)		CCTCGTCGCTGCTGCCCTCTG	0.562																																					p.S148S													.	HDGF	60	0			c.C444T						.						442.0	379.0	401.0					1																	156714048		2203	4300	6503	SO:0001819	synonymous_variant	3068	exon4			GTCGCTGCTGCCC	D16431	CCDS1156.1, CCDS44247.1, CCDS44248.1	1q23.1	2013-10-14	2010-03-19		ENSG00000143321	ENSG00000143321			4856	protein-coding gene	gene with protein product	"""high-mobility group protein 1-like"""	600339	"""hepatoma-derived growth factor (high-mobility group protein 1-like)"""			8833162	Standard	NM_004494		Approved	HMG1L2	uc001fpy.4	P51858	OTTHUMG00000041295	ENST00000357325.5:c.396C>T	1.37:g.156714048G>A		Somatic	32	0		WXS	Illumina HiSeq		35	4	NM_001126050	B3KU21|D3DVC9|Q5SZ07|Q5SZ08|Q5SZ09	Silent	SNP	ENST00000357325.5	37	CCDS1156.1																																																																																			.		0.562	HDGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098946.1	NM_004494	
Unknown	0	bcgsc.ca	37	3	48162464	48162464	+	IGR	SNP	T	T	C			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr3:48162464T>C								RN7SL664P (25869 upstream) : CDC25A (36171 downstream)																							GGGACACCAATTTTGTGTCCA	0.433																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			CACCAATTTTGTG																													3.37:g.48162464T>C		Somatic	43	0		WXS	Illumina HiSeq	Phase_1	30	9	.		RNA	SNP		37																																																																																				.	0	0.433								
PSMD6	9861	bcgsc.ca	37	3	64008458	64008458	+	Intron	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr3:64008458C>T	ENST00000295901.4	-	2	286				PSMD6_ENST00000394431.2_Intron|PSMD6_ENST00000492933.1_Silent_p.R55R|PSMD6_ENST00000482510.1_Intron|RP11-245J9.6_ENST00000605919.1_RNA	NM_014814.1	NP_055629.1	Q15008	PSMD6_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 6						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATPase activity (GO:0016887)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(1)|skin(1)	13		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000805)|Kidney(15;0.00188)|KIRC - Kidney renal clear cell carcinoma(15;0.00212)		TTTGCTCTTGCCGGATTCTGT	0.468																																					p.R55R													.	PSMD6	30	0			c.G165A						.																																			SO:0001627	intron_variant	9861	exon2			CTCTTGCCGGATT	AF215935	CCDS2901.1, CCDS63677.1, CCDS63678.1, CCDS63679.1	3p14.1	2008-05-22			ENSG00000163636	ENSG00000163636		"""Proteasome (prosome, macropain) subunits"""	9564	protein-coding gene	gene with protein product						10723133	Standard	NM_001271779		Approved	S10, p44S10, KIAA0107, Rpn7	uc003dmb.2	Q15008	OTTHUMG00000158765	ENST00000295901.4:c.146-259G>A	3.37:g.64008458C>T		Somatic	34	0		WXS	Illumina HiSeq	Phase_1	22	3	NM_001271779	A8K2E0|E9PHI9|Q6UV22	Silent	SNP	ENST00000295901.4	37	CCDS2901.1																																																																																			.		0.468	PSMD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352082.1	NM_014814	
HSP90AB2P	391634	bcgsc.ca	37	4	13339615	13339615	+	RNA	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr4:13339615G>T	ENST00000602906.1	+	0	966							Q58FF8	H90B2_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 2, pseudogene						protein folding (GO:0006457)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			kidney(3)|lung(1)	4						AAGTATGGAAGCGGGACTCCA	0.488																																					.													.	.	.	0			.						.																																					391634	.			ATGGAAGCGGGAC	AY956763		4p15.33	2012-04-18	2011-04-15		ENSG00000205940	ENSG00000205940			32537	pseudogene	pseudogene			"""heat shock protein 90kDa alpha (cytosolic), class B member 2 (pseudogene)"""			16269234	Standard	NG_032979		Approved	HSP90BB		Q58FF8			4.37:g.13339615G>T		Somatic	87	0		WXS	Illumina HiSeq	Phase_1	72	4	.		RNA	SNP	ENST00000602906.1	37																																																																																				.		0.488	HSP90AB2P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000359156.2		
Unknown	0	bcgsc.ca	37	4	49490648	49490648	+	IGR	SNP	T	T	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr4:49490648T>A								AC118282.4 (279183 upstream) : AC119751.5 (94393 downstream)																							TAATTGTTTTTTATATTGTGC	0.274																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			TGTTTTTTATATT																													4.37:g.49490648T>A		Somatic	85	0		WXS	Illumina HiSeq	Phase_1	206	68	.		RNA	SNP		37																																																																																				.	0	0.274								
TPD52L1	7164	bcgsc.ca	37	6	125584047	125584047	+	Missense_Mutation	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr6:125584047C>T	ENST00000534000.1	+	7	850	c.554C>T	c.(553-555)gCc>gTc	p.A185V	TPD52L1_ENST00000392482.2_3'UTR|HDDC2_ENST00000608456.1_Intron|TPD52L1_ENST00000530868.1_3'UTR|TPD52L1_ENST00000527711.1_Missense_Mutation_p.A172V|TPD52L1_ENST00000532429.1_Missense_Mutation_p.A156V|TPD52L1_ENST00000524679.1_3'UTR|TPD52L1_ENST00000368388.2_3'UTR|TPD52L1_ENST00000534199.1_3'UTR|TPD52L1_ENST00000368402.5_3'UTR|TPD52L1_ENST00000304877.13_Missense_Mutation_p.A190V|TPD52L1_ENST00000528193.1_3'UTR	NM_003287.2	NP_003278.1	Q16890	TPD53_HUMAN	tumor protein D52-like 1	185					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(2)|prostate(1)	5			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0265)		ACGGCCCATGCCAGTGCCCAG	0.582																																					p.A185V													.	TPD52L1	14	0			c.C554T						.						52.0	48.0	50.0					6																	125584047		2203	4300	6503	SO:0001583	missense	7164	exon7			CCCATGCCAGTGC	U44427	CCDS5130.1, CCDS34527.1, CCDS34528.1, CCDS43502.1, CCDS75513.1, CCDS75514.1	6q22-q23	2008-07-29			ENSG00000111907	ENSG00000111907			12006	protein-coding gene	gene with protein product		604069				8812487, 16112108	Standard	NM_003287		Approved	D53, hD53	uc003pzu.1	Q16890	OTTHUMG00000015505	ENST00000534000.1:c.554C>T	6.37:g.125584047C>T	ENSP00000434142:p.Ala185Val	Somatic	28	0		WXS	Illumina HiSeq	Phase_1	20	3	NM_003287	A8K757|A8K772|A8MUD2|A8MUJ7|A8MW70|F6V707|O43397|Q5TC99|Q5TDQ0|Q9BUQ6|Q9C054	Missense_Mutation	SNP	ENST00000534000.1	37	CCDS5130.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.047195	0.93740	.	.	ENSG00000111907	ENST00000304877;ENST00000534000;ENST00000527711;ENST00000532429;ENST00000392484	T;T;T;T	0.25579	1.79;1.79;1.79;1.79	5.53	5.53	0.82687	.	0.103836	0.64402	D	0.000004	T	0.45276	0.1334	M	0.73962	2.25	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.44251	-0.9340	10	0.72032	D	0.01	-3.0898	16.3926	0.83545	0.0:1.0:0.0:0.0	.	185	Q16890	TPD53_HUMAN	V	190;185;172;156;185	ENSP00000306285:A190V;ENSP00000434142:A185V;ENSP00000436953:A172V;ENSP00000435447:A156V	ENSP00000306285:A190V	A	+	2	0	TPD52L1	125625746	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	4.802000	0.62539	2.603000	0.88011	0.650000	0.86243	GCC	.		0.582	TPD52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042065.2		
TTYH3	80727	bcgsc.ca	37	7	2685484	2685484	+	Intron	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr7:2685484G>T	ENST00000258796.7	+	2	328				TTYH3_ENST00000403167.1_5'Flank|TTYH3_ENST00000407643.1_Intron	NM_025250.2	NP_079526.1	Q9C0H2	TTYH3_HUMAN	tweety family member 3						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|intracellular calcium activated chloride channel activity (GO:0005229)			kidney(1)|large_intestine(3)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	17		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)		AAAACCTCAGGACTACAGCTG	0.607																																					.													.	TTYH3	36	0			.						.																																			SO:0001627	intron_variant	80727	.			CCTCAGGACTACA		CCDS34588.1	7p22	2013-09-02	2013-09-02		ENSG00000136295	ENSG00000136295			22222	protein-coding gene	gene with protein product		608919	"""tweety homolog 3 (Drosophila)"""				Standard	NM_025250		Approved	KIAA1691	uc003smp.3	Q9C0H2	OTTHUMG00000152050	ENST00000258796.7:c.124-1003G>T	7.37:g.2685484G>T		Somatic	52	0		WXS	Illumina HiSeq	Phase_1	42	4	.	A4D201|B7WP98|Q6L749|Q6ZVG3|Q8TEG6	Missense_Mutation	SNP	ENST00000258796.7	37	CCDS34588.1	.	.	.	.	.	.	.	.	.	.	G	0.034	-1.317249	0.01331	.	.	ENSG00000136295	ENST00000400376	T	0.42900	0.96	1.56	0.646	0.17789	.	.	.	.	.	T	0.18882	0.0453	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.26677	-1.0096	6	0.10377	T	0.69	.	5.6951	0.17851	0.0:0.6465:0.3535:0.0	.	.	.	.	S	36	ENSP00000383227:R36S	ENSP00000383227:R36S	R	+	3	2	TTYH3	2652010	0.001000	0.12720	0.054000	0.19295	0.019000	0.09904	-0.095000	0.11077	0.220000	0.20860	-0.306000	0.09157	AGG	.		0.607	TTYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325082.2	XM_166523	
GDI2P1	2667	bcgsc.ca	37	7	48942831	48942831	+	IGR	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr7:48942831G>A								AC004899.1 (51610 upstream) : AC010971.1 (326901 downstream)																							ATGGACTTTTGACGTATCTTG	0.388																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	2667	.			ACTTTTGACGTAT																													7.37:g.48942831G>A		Somatic	42	0		WXS	Illumina HiSeq	Phase_1	54	25	.		RNA	SNP		37																																																																																				.	0	0.388								
SFMBT2	57713	bcgsc.ca	37	10	7212892	7212892	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr10:7212892G>T	ENST00000361972.4	-	20	2632	c.2542C>A	c.(2542-2544)Cag>Aag	p.Q848K	SFMBT2_ENST00000397167.1_Missense_Mutation_p.Q848K	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	848	SAM.				negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						CACCGTACCTGCTCCTGAAAT	0.557																																					p.Q848K													.	SFMBT2	209	0			c.C2542A						.						221.0	173.0	189.0					10																	7212892		2203	4300	6503	SO:0001583	missense	57713	exon20			GTACCTGCTCCTG	AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"""Sterile alpha motif (SAM) domain containing"""	20256	protein-coding gene	gene with protein product		615392	"""Scm-related gene containing four mbt domains 2"""			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.2542C>A	10.37:g.7212892G>T	ENSP00000355109:p.Gln848Lys	Somatic	63	0		WXS	Illumina HiSeq	Phase_1	42	4	NM_001029880	A7MD09|Q9HCF5	Missense_Mutation	SNP	ENST00000361972.4	37	CCDS31138.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.024782	0.93518	.	.	ENSG00000198879	ENST00000361972;ENST00000397167	T;T	0.49720	0.77;0.77	5.1	5.1	0.69264	Sterile alpha motif domain (1);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	1.296800	0.05029	N	0.474227	T	0.75443	0.3850	M	0.80508	2.5	0.80722	D	1	D	0.60160	0.987	D	0.69654	0.965	T	0.64803	-0.6321	10	0.62326	D	0.03	.	18.8831	0.92364	0.0:0.0:1.0:0.0	.	848	Q5VUG0	SMBT2_HUMAN	K	848	ENSP00000355109:Q848K;ENSP00000380353:Q848K	ENSP00000355109:Q848K	Q	-	1	0	SFMBT2	7252898	1.000000	0.71417	0.999000	0.59377	0.934000	0.57294	9.641000	0.98458	2.537000	0.85549	0.561000	0.74099	CAG	.		0.557	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880	
OR5D2P	8595	bcgsc.ca	37	11	55483081	55483081	+	IGR	SNP	T	T	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr11:55483081T>A								RP11-674C21.9 (29445 upstream) : OR5D13 (57832 downstream)																							CAAGGTGGCCTCTGTCTTTTA	0.458																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	8595	.			GTGGCCTCTGTCT																													11.37:g.55483081T>A		Somatic	72	0		WXS	Illumina HiSeq	Phase_1	41	14	.		RNA	SNP		37																																																																																				.	0	0.458								
Unknown	0	bcgsc.ca	37	11	79700531	79700531	+	IGR	SNP	T	T	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr11:79700531T>A								AP000478.1 (296958 upstream) : CTD-2555I5.1 (332132 downstream)																							AAAAAATGGATGCAAATTCTA	0.353																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			AATGGATGCAAAT																													11.37:g.79700531T>A		Somatic	27	0		WXS	Illumina HiSeq	Phase_1	15	8	.		RNA	SNP		37																																																																																				.	0	0.353								
SLC25A1P1	100131457	bcgsc.ca	37	11	85646289	85646289	+	IGR	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr11:85646289C>T								RP11-90K17.2 (11564 upstream) : PICALM (22437 downstream)																							GAAGATTGTGCGGGAACAAGG	0.562																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	100131457	.			ATTGTGCGGGAAC																													11.37:g.85646289C>T		Somatic	26	0		WXS	Illumina HiSeq	Phase_1	23	7	.		RNA	SNP		37																																																																																				.	0	0.562								
RP11-597A11.1	0	bcgsc.ca	37	14	20137327	20137327	+	RNA	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr14:20137327G>A	ENST00000548261.1	+	0	391																											ATGGGATGCCGGGAGGCCGAG	0.597																																					.													.	.	.	0			.						.																																					0	.			GATGCCGGGAGGC																													14.37:g.20137327G>A		Somatic	244	0		WXS	Illumina HiSeq	Phase_1	165	22	.		RNA	SNP	ENST00000548261.1	37																																																																																				.		0.597	RP11-597A11.1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000409571.1		
PIEZO1	9780	bcgsc.ca	37	16	88808499	88808499	+	Silent	SNP	G	G	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr16:88808499G>A	ENST00000301015.9	-	4	534	c.288C>T	c.(286-288)agC>agT	p.S96S	RP5-1142A6.2_ENST00000567968.1_RNA|RP5-1142A6.8_ENST00000333666.1_RNA|RP5-1142A6.7_ENST00000566114.1_RNA|RP5-1142A6.8_ENST00000567588.1_RNA|RP5-1142A6.2_ENST00000440406.2_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	96					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						TCTCCCAGCGGCTGCCTGCAG	0.632																																					p.S96S													.	PIEZO1	79	0			c.C288T						.						31.0	35.0	34.0					16																	88808499		692	1590	2282	SO:0001819	synonymous_variant	9780	exon4			CCAGCGGCTGCCT	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776	ENST00000301015.9:c.288C>T	16.37:g.88808499G>A		Somatic	220	1		WXS	Illumina HiSeq	Phase_1	167	6	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1	.	.	.	.	.	.	.	.	.	.	G	9.014	0.983207	0.18889	.	.	ENSG00000103335	ENST00000451779	.	.	.	4.61	3.63	0.41609	.	.	.	.	.	T	0.61211	0.2329	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59198	-0.7499	4	.	.	.	.	11.2285	0.48899	0.0981:0.0:0.9019:0.0	.	.	.	.	S	42	.	.	P	-	1	0	FAM38A	87336000	1.000000	0.71417	0.881000	0.34555	0.221000	0.24807	4.592000	0.61027	2.267000	0.75376	0.561000	0.74099	CCG	.		0.632	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
XAB2	56949	bcgsc.ca	37	19	7690922	7690922	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:7690922G>T	ENST00000358368.4	-	6	703	c.666C>A	c.(664-666)caC>caA	p.H222Q	XAB2_ENST00000534844.1_Missense_Mutation_p.H219Q	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	222					blastocyst development (GO:0001824)|DNA repair (GO:0006281)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	26						CGCACAGCTCGTGCCACAGCT	0.672								Direct reversal of damage;Nucleotide excision repair (NER)																													p.H222Q													XAB2,rectum,carcinoma,0,1	XAB2	69	0			c.C666A						.						55.0	53.0	54.0					19																	7690922		2203	4300	6503	SO:0001583	missense	56949	exon6			CAGCTCGTGCCAC	AB026111	CCDS32892.1	19p13.3	2013-08-21				ENSG00000076924			14089	protein-coding gene	gene with protein product	"""SYF1 homolog, RNA splicing factor (S. cerevisiae)"", ""SYF1 pre-mRNA-splicing factor"""	610850				10944529	Standard	NM_020196		Approved	HCNP, HCRN, SYF1, NTC90	uc002mgx.3	Q9HCS7		ENST00000358368.4:c.666C>A	19.37:g.7690922G>T	ENSP00000351137:p.His222Gln	Somatic	33	0		WXS	Illumina HiSeq	Phase_1	43	4	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Missense_Mutation	SNP	ENST00000358368.4	37	CCDS32892.1	.	.	.	.	.	.	.	.	.	.	G	10.26	1.301505	0.23736	.	.	ENSG00000076924	ENST00000358368;ENST00000534844	T;T	0.62498	0.02;0.02	4.61	-1.35	0.09114	.	0.065141	0.64402	D	0.000012	T	0.30324	0.0761	N	0.03608	-0.345	0.44956	D	0.997971	B	0.09022	0.002	B	0.09377	0.004	T	0.02202	-1.1196	10	0.25751	T	0.34	-45.9916	7.5803	0.27961	0.6209:0.0:0.3791:0.0	.	222	Q9HCS7	SYF1_HUMAN	Q	222;219	ENSP00000351137:H222Q;ENSP00000438225:H219Q	ENSP00000351137:H222Q	H	-	3	2	XAB2	7596922	0.177000	0.23109	0.997000	0.53966	0.968000	0.65278	-0.545000	0.06069	-0.024000	0.13941	-0.266000	0.10368	CAC	.		0.672	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196	
COMP	1311	bcgsc.ca	37	19	18901408	18901408	+	Silent	SNP	C	C	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:18901408C>T	ENST00000222271.2	-	3	224	c.180G>A	c.(178-180)acG>acA	p.T60T	COMP_ENST00000542601.2_Silent_p.T27T|COMP_ENST00000425807.1_Silent_p.T60T	NM_000095.2	NP_000086.2	P49747	COMP_HUMAN	cartilage oligomeric matrix protein	60	COMP N-terminal.				apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|limb development (GO:0060173)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|protease binding (GO:0002020)			breast(6)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						TTTTCAGGAACGTGATCTCCC	0.622																																					p.T60T													.	COMP	62	0			c.G180A						.						186.0	195.0	192.0					19																	18901408		2203	4300	6503	SO:0001819	synonymous_variant	1311	exon3			CAGGAACGTGATC	L32137	CCDS12385.1	19p13.1	2008-02-05				ENSG00000105664			2227	protein-coding gene	gene with protein product	"""thrombospondin-5"""	600310	"""cartilage oligomeric matrix protein (pseudoachondroplasia, epiphyseal dysplasia 1, multiple)"""	PSACH, EDM1, EPD1		7713493, 8307576	Standard	NM_000095		Approved	MED, THBS5	uc002nke.3	P49747	OTTHUMG00000169318	ENST00000222271.2:c.180G>A	19.37:g.18901408C>T		Somatic	51	0		WXS	Illumina HiSeq	Phase_1	51	4	NM_000095	B4DKJ3|O14592|Q16388|Q16389|Q2NL86|Q8N4T2	Silent	SNP	ENST00000222271.2	37	CCDS12385.1																																																																																			.		0.622	COMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403457.1	NM_000095	
Unknown	0	bcgsc.ca	37	X	100794005	100794005	+	IGR	SNP	C	C	A			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chrX:100794005C>A								ARMCX4 (43211 upstream) : ARMCX1 (11508 downstream)																							GTAAAGGCTTCTTCTAACTCC	0.448																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			AGGCTTCTTCTAA																													X.37:g.100794005C>A		Somatic	19	0		WXS	Illumina HiSeq	Phase_1	20	4	.		RNA	SNP		37																																																																																				.	0	0.448								
TCP11X3P	106481605	bcgsc.ca	37	X	101428159	101428159	+	IGR	SNP	T	T	C			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chrX:101428159T>C								BEX5 (17130 upstream) : TCP11X3P (9128 downstream)																							CTGACTTCACTTGTGCTCTTG	0.438													T|||	1	0.000264901	0.0	0.0	3775	,	,		14027	0.0		0.0	False		,,,				2504	0.001				.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			CTTCACTTGTGCT																													X.37:g.101428159T>C		Somatic	172	0		WXS	Illumina HiSeq	Phase_1	147	5	.		RNA	SNP		37																																																																																				.	0	0.438								
COL21A1	81578	hgsc.bcm.edu	37	6	56141605	56141606	+	Intron	DNP	GT	GT	TG	rs200830355|rs367712707|rs386701433|rs201667407	byFrequency	TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr6:56141605_56141606GT>TG	ENST00000370819.1	-	2	124							Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1						extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			tgttttttttgttttttttgtt	0.446																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	100873774	.			TTTTTGTTTTTTT	AF330693	CCDS55025.1	6p12.3-p11.2	2013-01-16			ENSG00000124749	ENSG00000124749		"""Collagens"""	17025	protein-coding gene	gene with protein product		610002				11566190	Standard	XR_241922		Approved		uc003pcs.3	Q96P44	OTTHUMG00000014907	ENST00000370819.1:c.1_1delinsTG	6.37:g.56141605_56141606delinsTG		Somatic	21	0		WXS	Illumina HiSeq	.	27	6	.	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	RNA	DNP	ENST00000370819.1	37																																																																																				.		0.446	COL21A1-002	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041005.1		
CHEK2	11200	broad.mit.edu	37	22	29091840	29091841	+	Missense_Mutation	DNP	TG	TG	CA	rs142470496|rs146546850	byFrequency	TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	TG	TG						Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr22:29091840_29091841TG>CA	ENST00000405598.1	-	12	1307_1308	c.1116_1117CA>TG	c.(1114-1119)tcCAag>tcTGag	p.K373E	CHEK2_ENST00000544772.1_Missense_Mutation_p.K152E|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000464581.1_5'Flank|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E			O96017	CHK2_HUMAN	checkpoint kinase 2	373	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.K373E(9)|p.S372S(8)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCCAAAATCTTGGAGTGCCCAA	0.416			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																													p.K416E			yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	CHEK2,bladder,carcinoma,0,38	CHEK2	438	17	Substitution - Missense(9)|Substitution - coding silent(8)	kidney(8)|prostate(4)|endometrium(2)|central_nervous_system(2)|stomach(1)	c.C1245T						.																																			SO:0001583	missense	11200	exon12			AATCTTGGAGTGC	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1116_1117delinsCA	22.37:g.29091840_29091841delinsCA	ENSP00000386087:p.Lys373Glu	Somatic	86	2		WXS	Illumina GAIIx	Phase_I	84	4	NM_001005735	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	DNP	ENST00000405598.1	37	CCDS13843.1																																																																																			.		0.416	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735	
PCDH15	65217	hgsc.bcm.edu	37	10	55566478	55566478	+	Missense_Mutation	SNP	G	G	T			TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr10:55566478G>T	ENST00000373965.2	-	36	5310	c.4916C>A	c.(4915-4917)aCa>aAa	p.T1639K	PCDH15_ENST00000414778.1_Missense_Mutation_p.T1636K	NM_001142771.1|NM_001142772.1	NP_001136243.1|NP_001136244.1	Q96QU1	PCD15_HUMAN	protocadherin-related 15	0					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				CTGTTCAACTGTGCTTTTCAG	0.463										HNSCC(58;0.16)																											.		.											PCDH15_ENST00000414778,NS,carcinoma,0,1	PCDH15_ENST00000414778	0	0			.						.						356.0	301.0	318.0					10																	55566478		1568	3582	5150	SO:0001583	missense	65217	p.T1639K			TCAACTGTGCTTT	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000373965.2:c.4916C>A	10.37:g.55566478G>T	ENSP00000363076:p.Thr1639Lys	Somatic	51	0		WXS	Illumina HiSeq	Phase_I	30	2	.	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000373965.2	37		.	.	.	.	.	.	.	.	.	.	G	15.46	2.839715	0.51057	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746	T;T	0.58358	0.34;0.39	6.02	4.12	0.48240	.	.	.	.	.	T	0.48804	0.1520	L	0.54323	1.7	0.80722	D	1	B;B	0.12630	0.006;0.003	B;B	0.06405	0.002;0.002	T	0.46707	-0.9172	9	0.87932	D	0	.	12.981	0.58564	0.0:0.1243:0.7463:0.1294	.	1630;1636	C6ZEF7;C9J4F3	.;.	K	1639;1636;1632	ENSP00000363076:T1639K;ENSP00000410304:T1636K	ENSP00000363076:T1639K	T	-	2	0	PCDH15	55236484	1.000000	0.71417	0.948000	0.38648	0.995000	0.86356	7.429000	0.80309	0.821000	0.34540	0.655000	0.94253	ACA	.		0.463	PCDH15-008	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000291336.1	NM_033056	
UHRF1	29128	hgsc.bcm.edu	37	19	4954679	4954679	+	RNA	SNP	G	G	C	rs397767650|rs55946225	byFrequency	TCGA-ZH-A8Y4-01A-11D-A417-09	TCGA-ZH-A8Y4-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	7c0d8315-be09-4965-8cf6-0659b15116af	88264350-4923-47c7-a831-5715420c907f	g.chr19:4954679G>C	ENST00000592666.1	+	0	2551							Q96T88	UHRF1_HUMAN	ubiquitin-like with PHD and ring finger domains 1						cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|histone monoubiquitination (GO:0010390)|histone ubiquitination (GO:0016574)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity (GO:2000373)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autoubiquitination (GO:0051865)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|replication fork (GO:0005657)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|hemi-methylated DNA-binding (GO:0044729)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|upper_aerodigestive_tract(2)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0276)		CCCGAGCAGGGCGGGTCCCCG	0.682																																					.		.											.,12	.	56	0			.						.						8.0	10.0	9.0					19																	4954679		1801	4029	5830			29128	p.A672P			AGCAGGGCGGGTC	AF129507	CCDS74262.1, CCDS74263.1	19p13.3	2012-04-20	2008-08-14		ENSG00000034063	ENSG00000276043		"""RING-type (C3HC4) zinc fingers"""	12556	protein-coding gene	gene with protein product		607990				10646863	Standard	NM_001048201		Approved	ICBP90, Np95, FLJ21925, RNF106	uc002mbo.3	Q96T88			19.37:g.4954679G>C		Somatic	39	0		WXS	Illumina HiSeq	Phase_I	38	1	.	A0JBR2|A8K024|B2RBA9|Q2HIX7|Q8J022|Q9H6S6|Q9P115|Q9P1U7	Missense_Mutation	SNP	ENST00000592666.1	37		.	.	.	.	.	.	.	.	.	.	G	11.88	1.771659	0.31320	.	.	ENSG00000034063	ENST00000262952;ENST00000396708;ENST00000455180;ENST00000543616;ENST00000398240	.	.	.	4.45	-6.05	0.02172	.	.	.	.	.	T	0.21509	0.0518	L	0.29908	0.895	.	.	.	.	.	.	.	.	.	T	0.35748	-0.9776	5	0.35671	T	0.21	-7.3513	3.4755	0.07583	0.0793:0.2334:0.3323:0.355	.	.	.	.	P	659;274;659;659;672	.	ENSP00000262952:A659P	A	+	1	0	UHRF1	4905679	0.241000	0.23857	0.000000	0.03702	0.082000	0.17680	1.208000	0.32345	-0.475000	0.06852	0.462000	0.41574	GCG	.		0.682	UHRF1-006	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000450444.1	NM_001048201	
