#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
APPL1	26060	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	57283562	57283562	+	Silent	SNP	T	T	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr3:57283562T>A	ENST00000288266.3	+	11	1185	c.1038T>A	c.(1036-1038)tcT>tcA	p.S346S		NM_012096.2	NP_036228.1	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	346	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.|Required for RAB5A binding.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|insulin receptor signaling pathway (GO:0008286)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of glucose import (GO:0046324)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|protein kinase B binding (GO:0043422)	p.S346S(1)		breast(3)|endometrium(3)|kidney(3)|large_intestine(10)|liver(2)|lung(4)|prostate(2)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)		AGATCACCTCTTTCGATGGAA	0.368																																																	1	Substitution - coding silent(1)	kidney(1)											130.0	121.0	124.0					3																	57283562		2203	4300	6503	SO:0001819	synonymous_variant	26060			AB037849	CCDS2882.1	3p21.1-p14.3	2013-01-11			ENSG00000157500	ENSG00000157500		"""Pleckstrin homology (PH) domain containing"""	24035	protein-coding gene	gene with protein product		604299				10490823, 17030088	Standard	NM_012096		Approved	APPL	uc003dio.3	Q9UKG1	OTTHUMG00000133756	ENST00000288266.3:c.1038T>A	3.37:g.57283562T>A			Q9P2B9	Silent	SNP	ENST00000288266.3	37	CCDS2882.1																																																																																				0.368	APPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258196.2		NM_012096	
ARID3A	1820	hgsc.bcm.edu	37	19	971949	971950	+	In_Frame_Ins	INS	-	-	GCA	rs1051505|rs552779877	byFrequency	TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr19:971949_971950insGCA	ENST00000263620.3	+	9	1993_1994	c.1666_1667insGCA	c.(1666-1668)ggc>gGCAgc	p.559_560insS		NM_005224.2	NP_005215.1	Q99856	ARI3A_HUMAN	AT rich interactive domain 3A (BRIGHT-like)	559	Gly-rich.					cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	10		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)		cggcggcggcggcagcagcagc	0.653														147	0.029353	0.1059	0.0101	5008	,	,		8554	0.0		0.0	False		,,,				2504	0.0				Pancreas(29;54 1022 32760 50921)												0																																										SO:0001652	inframe_insertion	1820			U88047	CCDS12050.1	19p13.3	2013-02-07	2006-11-08	2004-01-30		ENSG00000116017		"""-"""	3031	protein-coding gene	gene with protein product		603265	"""dead ringer-like 1 (Drosophila)"", ""AT rich interactive domain 3A (BRIGHT- like)"""	DRIL1		9722953	Standard	NM_005224		Approved	BRIGHT	uc002lql.3	Q99856		ENST00000263620.3:c.1676_1678dupGCA	19.37:g.971956_971958dupGCA	ENSP00000263620:p.Ser559_Ser559dup		Q5I858|Q6P9C6|Q8IZA7|Q8N4Z3	In_Frame_Ins	INS	ENST00000263620.3	37	CCDS12050.1																																																																																				0.653	ARID3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458219.1		NM_005224	
ARSK	153642	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	94918640	94918640	+	Missense_Mutation	SNP	C	C	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr5:94918640C>A	ENST00000380009.4	+	4	642	c.437C>A	c.(436-438)aCa>aAa	p.T146K		NM_198150.2	NP_937793.1	Q6UWY0	ARSK_HUMAN	arylsulfatase family, member K	146					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.T146K(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(1)	16		all_cancers(142;3.38e-06)|all_epithelial(76;6.57e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)		all cancers(79;6.5e-16)		GAAGCGTGGACAAGAGATGTT	0.388																																																	1	Substitution - Missense(1)	kidney(1)											145.0	143.0	143.0					5																	94918640		2203	4300	6503	SO:0001583	missense	153642				CCDS4073.1	5q15	2013-02-14	2006-03-07		ENSG00000164291	ENSG00000164291		"""Arylsulfatase family"""	25239	protein-coding gene	gene with protein product		610011	"""arylsulfatase K"""			12975309, 16174644	Standard	NM_198150		Approved	DKFZp313G1735, TSULF	uc003kld.3	Q6UWY0	OTTHUMG00000121166	ENST00000380009.4:c.437C>A	5.37:g.94918640C>A	ENSP00000369346:p.Thr146Lys		A2BDE3|B4E1I4|Q3ZCW3|Q8N3Q8	Missense_Mutation	SNP	ENST00000380009.4	37	CCDS4073.1	.	.	.	.	.	.	.	.	.	.	C	33	5.211907	0.95069	.	.	ENSG00000164291	ENST00000380009;ENST00000537857	D	0.98602	-5.02	6.02	6.02	0.97574	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.98713	0.9568	M	0.76838	2.35	0.80722	D	1	D	0.57899	0.981	P	0.62885	0.908	D	0.98225	1.0480	10	0.19590	T	0.45	-22.2722	20.5373	0.99239	0.0:1.0:0.0:0.0	.	146	Q6UWY0	ARSK_HUMAN	K	146	ENSP00000369346:T146K	ENSP00000369346:T146K	T	+	2	0	ARSK	94944396	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.085000	0.76875	2.857000	0.98124	0.650000	0.86243	ACA		0.388	ARSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241652.2		NM_198150	
BRCA2	675	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	32945126	32945126	+	Missense_Mutation	SNP	T	T	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr13:32945126T>A	ENST00000380152.3	+	20	8754	c.8521T>A	c.(8521-8523)Ttt>Att	p.F2841I	BRCA2_ENST00000544455.1_Missense_Mutation_p.F2841I			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2841					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.F2841I(2)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		ATTATACATATTTCGCAATGA	0.358			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)		yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	2	Substitution - Missense(2)	kidney(2)											86.0	85.0	85.0					13																	32945126		2203	4300	6503	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.8521T>A	13.37:g.32945126T>A	ENSP00000369497:p.Phe2841Ile		O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.033832	0.93575	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	D;D	0.83163	-1.69;-1.69	5.1	5.1	0.69264	Nucleic acid-binding, OB-fold-like (1);Tower (1);	0.113563	0.64402	D	0.000011	D	0.90349	0.6980	M	0.74258	2.255	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	D	0.91018	0.4855	10	0.54805	T	0.06	.	14.8952	0.70639	0.0:0.0:0.0:1.0	.	2841	P51587	BRCA2_HUMAN	I	2841	ENSP00000369497:F2841I;ENSP00000439902:F2841I	ENSP00000369497:F2841I	F	+	1	0	BRCA2	31843126	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.907000	0.69908	1.923000	0.55706	0.397000	0.26171	TTT		0.358	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2		NM_000059	
IRF2BPL	64207	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	77492045	77492045	+	Silent	SNP	C	C	G			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr14:77492045C>G	ENST00000238647.3	-	1	2989	c.2091G>C	c.(2089-2091)gtG>gtC	p.V697V		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	697					development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.V697V(1)		endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						TTTGGGGGTGCACTTGGTCCA	0.637																																																	1	Substitution - coding silent(1)	kidney(1)											28.0	28.0	28.0					14																	77492045		2203	4300	6503	SO:0001819	synonymous_variant	0			AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"""enhanced at puberty 1"""	611720	"""chromosome 14 open reading frame 4"""	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.2091G>C	14.37:g.77492045C>G			Q8NDQ2|Q96JG2|Q9H3I7	Silent	SNP	ENST00000238647.3	37	CCDS9854.1																																																																																				0.637	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1		NM_024496	
C1orf110	339512	broad.mit.edu;ucsc.edu	37	1	162824983	162824983	+	Missense_Mutation	SNP	C	C	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr1:162824983C>T	ENST00000367910.1	-	4	601	c.481G>A	c.(481-483)Gat>Aat	p.D161N	C1orf110_ENST00000367911.2_Missense_Mutation_p.D156N|C1orf110_ENST00000367912.2_Missense_Mutation_p.D160N|C1orf110_ENST00000524691.1_Intron	NM_178550.4	NP_848645.3	Q86UF4	CA110_HUMAN	chromosome 1 open reading frame 110	161								p.D161N(1)		endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	12						TTCACAGAATCTTTCTCTTGG	0.468																																																	1	Substitution - Missense(1)	kidney(1)											263.0	252.0	256.0					1																	162824983		1905	4129	6034	SO:0001583	missense	339512			BC040018	CCDS44269.1	1q23.3	2012-06-26			ENSG00000185860	ENSG00000185860			28736	protein-coding gene	gene with protein product						12477932	Standard	NM_178550		Approved	MGC48998	uc001gck.2	Q86UF4	OTTHUMG00000034421	ENST00000367910.1:c.481G>A	1.37:g.162824983C>T	ENSP00000356886:p.Asp161Asn		Q5JSG1|Q6ZW57	Missense_Mutation	SNP	ENST00000367910.1	37	CCDS44269.1	.	.	.	.	.	.	.	.	.	.	C	14.60	2.583705	0.46006	.	.	ENSG00000185860	ENST00000367912;ENST00000367911;ENST00000367910	.	.	.	4.22	2.32	0.28847	.	1.170210	0.06261	N	0.693865	T	0.12220	0.0297	L	0.27053	0.805	0.26313	N	0.977794	P;P	0.41131	0.739;0.739	B;B	0.40602	0.334;0.334	T	0.15780	-1.0425	8	0.59425	D	0.04	-2.3888	4.67	0.12683	0.2176:0.6716:0.0:0.1108	.	160;161	Q86UF4-2;Q86UF4	.;CA110_HUMAN	N	160;156;161	.	ENSP00000356886:D161N	D	-	1	0	C1orf110	161091607	0.000000	0.05858	0.003000	0.11579	0.131000	0.20780	0.463000	0.21972	1.091000	0.41335	0.655000	0.94253	GAT		0.468	C1orf110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083211.2		NM_178550	
TMEM246	84302	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	104238212	104238212	+	Missense_Mutation	SNP	A	A	C			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr9:104238212A>C	ENST00000374851.1	-	4	2310	c.1163T>G	c.(1162-1164)aTc>aGc	p.I388S	TMEM246_ENST00000374847.1_Missense_Mutation_p.I388S|RP11-490D19.6_ENST00000431507.1_RNA|RP11-490D19.6_ENST00000425734.1_RNA|RP11-490D19.6_ENST00000450109.1_RNA|TMEM246_ENST00000374848.3_Missense_Mutation_p.I388S|RP11-490D19.6_ENST00000424154.1_RNA			Q9BRR3	TM246_HUMAN	transmembrane protein 246	388						integral component of membrane (GO:0016021)		p.I388S(1)									GAAGAGCCCGATGTGTTTCAC	0.522																																																	1	Substitution - Missense(1)	kidney(1)											103.0	100.0	101.0					9																	104238212		2203	4300	6503	SO:0001583	missense	0			BC006115	CCDS6757.1	9q31.1	2012-04-02	2012-04-02	2012-04-02	ENSG00000165152	ENSG00000165152			28180	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 125"""	C9orf125		12477932	Standard	NM_032342		Approved	MGC12992	uc004bbm.3	Q9BRR3	OTTHUMG00000020381	ENST00000374851.1:c.1163T>G	9.37:g.104238212A>C	ENSP00000363984:p.Ile388Ser		Q49AQ4	Missense_Mutation	SNP	ENST00000374851.1	37	CCDS6757.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.211872	0.79240	.	.	ENSG00000165152	ENST00000374848;ENST00000374847;ENST00000374851	.	.	.	5.68	5.68	0.88126	.	0.119765	0.56097	D	0.000026	T	0.64216	0.2578	M	0.64404	1.975	0.58432	D	0.999999	P	0.52061	0.95	P	0.49276	0.605	T	0.69202	-0.5207	9	0.87932	D	0	-8.0043	15.118	0.72419	1.0:0.0:0.0:0.0	.	388	Q9BRR3	CI125_HUMAN	S	388	.	ENSP00000363980:I388S	I	-	2	0	C9orf125	103278033	1.000000	0.71417	0.990000	0.47175	0.970000	0.65996	9.024000	0.93689	2.172000	0.68678	0.533000	0.62120	ATC		0.522	TMEM246-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053444.1		NM_032342	
CDK13	8621	broad.mit.edu;hgsc.bcm.edu	37	7	39991366	39991366	+	Missense_Mutation	SNP	T	T	C			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr7:39991366T>C	ENST00000181839.4	+	1	1731	c.1126T>C	c.(1126-1128)Tac>Cac	p.Y376H	CDK13_ENST00000340829.5_Missense_Mutation_p.Y376H|RP11-467D6.1_ENST00000569710.1_RNA	NM_003718.4|NM_031267.3	NP_003709.3|NP_112557.2	Q14004	CDK13_HUMAN	cyclin-dependent kinase 13	376					alternative mRNA splicing, via spliceosome (GO:0000380)|hemopoiesis (GO:0030097)|multicellular organismal development (GO:0007275)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|positive regulation of cell proliferation (GO:0008284)|regulation of mitosis (GO:0007088)|viral process (GO:0016032)	cyclin K-CDK13 complex (GO:0002945)|extracellular space (GO:0005615)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)	p.Y376H(1)		cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(2)|prostate(2)|skin(5)|stomach(2)|urinary_tract(1)	49						CCACAGCTCCTACGAGCGGGG	0.706																																																	1	Substitution - Missense(1)	kidney(1)											23.0	23.0	23.0					7																	39991366		1935	3863	5798	SO:0001583	missense	8621			M80629	CCDS5461.1, CCDS5462.1	7p14.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000065883	ENSG00000065883		"""Cyclin-dependent kinases"""	1733	protein-coding gene	gene with protein product	"""cholinesterase-related cell division controller"""	603309	"""cell division cycle 2-like 5 (cholinesterase-related cell division controller)"""	CDC2L5		1731328, 19884882	Standard	NM_003718		Approved	CHED, CDC2L, KIAA1791	uc003thh.4	Q14004	OTTHUMG00000023726	ENST00000181839.4:c.1126T>C	7.37:g.39991366T>C	ENSP00000181839:p.Tyr376His		Q53G78|Q6DKQ9|Q75MH4|Q75MH5|Q96JN4|Q9H4A0|Q9H4A1|Q9UDR4	Missense_Mutation	SNP	ENST00000181839.4	37	CCDS5461.1	.	.	.	.	.	.	.	.	.	.	T	14.81	2.645971	0.47258	.	.	ENSG00000065883	ENST00000181839;ENST00000340829	T;T	0.73152	-0.72;-0.72	4.15	4.15	0.48705	.	.	.	.	.	T	0.73860	0.3641	L	0.41492	1.28	0.41734	D	0.989577	D;D	0.69078	0.997;0.994	P;P	0.62184	0.899;0.796	T	0.73104	-0.4088	8	.	.	.	-3.3547	12.1053	0.53810	0.0:0.0:0.0:1.0	.	376;376	Q14004-2;Q14004	.;CDK13_HUMAN	H	376	ENSP00000181839:Y376H;ENSP00000340557:Y376H	.	Y	+	1	0	CDK13	39957891	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.942000	0.70203	1.626000	0.50381	0.374000	0.22700	TAC		0.706	CDK13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250726.2		NM_003718	
CXorf38	159013	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	40506319	40506319	+	Missense_Mutation	SNP	A	A	T	rs201677570		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chrX:40506319A>T	ENST00000327877.5	-	2	317	c.291T>A	c.(289-291)gaT>gaA	p.D97E	CXorf38_ENST00000378426.1_5'UTR|CXorf38_ENST00000440784.2_Intron|CXorf38_ENST00000378418.2_Missense_Mutation_p.D97E|CXorf38_ENST00000378421.1_5'UTR	NM_144970.2	NP_659407.1	Q8TB03	CX038_HUMAN	chromosome X open reading frame 38	97								p.D97E(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	12						CCCAGTGCACATCTCCATTTC	0.632																																																	1	Substitution - Missense(1)	kidney(1)											33.0	32.0	33.0					X																	40506319		2203	4300	6503	SO:0001583	missense	159013			AL832829	CCDS14253.1	Xp11	2008-02-05			ENSG00000185753	ENSG00000185753			28589	protein-coding gene	gene with protein product							Standard	NM_144970		Approved	MGC39350	uc004dew.3	Q8TB03	OTTHUMG00000024104	ENST00000327877.5:c.291T>A	X.37:g.40506319A>T	ENSP00000330488:p.Asp97Glu		B3KW28|D3DWB5|Q5JPF5|Q8N941	Missense_Mutation	SNP	ENST00000327877.5	37	CCDS14253.1	.	.	.	.	.	.	.	.	.	.	a	13.84	2.357441	0.41801	.	.	ENSG00000185753	ENST00000327877;ENST00000378418	T;T	0.40756	1.02;1.02	5.26	0.584	0.17422	.	0.199459	0.44097	D	0.000490	T	0.26122	0.0637	L	0.46157	1.445	0.21861	N	0.999502	B	0.27229	0.172	B	0.25291	0.059	T	0.11203	-1.0597	10	0.22706	T	0.39	-3.1586	1.6373	0.02745	0.4106:0.1317:0.3214:0.1362	.	97	Q8TB03	CX038_HUMAN	E	97	ENSP00000330488:D97E;ENSP00000367674:D97E	ENSP00000330488:D97E	D	-	3	2	CXorf38	40391263	0.680000	0.27605	0.984000	0.44739	0.882000	0.50991	-0.114000	0.10757	-0.115000	0.11915	-1.205000	0.01647	GAT		0.632	CXorf38-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060685.3		NM_144970	
DLG1	1739	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	196842954	196842954	+	Splice_Site	SNP	C	C	G			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr3:196842954C>G	ENST00000419354.1	-	14	1672	c.1386G>C	c.(1384-1386)agG>agC	p.R462S	DLG1_ENST00000450955.1_Splice_Site_p.R429S|DLG1_ENST00000392382.2_Splice_Site_p.R429S|DLG1_ENST00000448528.2_Splice_Site_p.R462S|DLG1_ENST00000357674.4_Splice_Site_p.R429S|DLG1_ENST00000346964.2_Splice_Site_p.R462S|DLG1_ENST00000452595.1_Splice_Site_p.R346S|DLG1_ENST00000314062.3_Splice_Site_p.R411S|DLG1_ENST00000422288.1_Splice_Site_p.R411S|DLG1_ENST00000443183.1_Splice_Site_p.R346S			Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	462					actin filament organization (GO:0007015)|activation of protein kinase activity (GO:0032147)|amyloid precursor protein metabolic process (GO:0042982)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|cortical actin cytoskeleton organization (GO:0030866)|dephosphorylation (GO:0016311)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell proliferation (GO:0001935)|establishment or maintenance of cell polarity (GO:0007163)|hard palate development (GO:0060022)|immunological synapse formation (GO:0001771)|lens development in camera-type eye (GO:0002088)|membrane raft organization (GO:0031579)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell proliferation (GO:0042130)|nucleotide phosphorylation (GO:0046939)|peristalsis (GO:0030432)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|protein localization to plasma membrane (GO:0072659)|regulation of membrane potential (GO:0042391)|regulation of myelination (GO:0031641)|regulation of sodium ion transmembrane transport (GO:1902305)|reproductive structure development (GO:0048608)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|synaptic transmission (GO:0007268)|T cell activation (GO:0042110)|T cell cytokine production (GO:0002369)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	basal lamina (GO:0005605)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell projection membrane (GO:0031253)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|immunological synapse (GO:0001772)|intercalated disc (GO:0014704)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|membrane raft (GO:0045121)|microtubule (GO:0005874)|MPP7-DLG1-LIN7 complex (GO:0097025)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|guanylate kinase activity (GO:0004385)|ion channel binding (GO:0044325)|L27 domain binding (GO:0097016)|mitogen-activated protein kinase kinase binding (GO:0031434)|phosphatase binding (GO:0019902)|phosphoprotein phosphatase activity (GO:0004721)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)	p.R462S(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		TTCTAGGTTCCCTAAAAATTA	0.318																																																	1	Substitution - Missense(1)	kidney(1)											59.0	64.0	62.0					3																	196842954		2202	4299	6501	SO:0001630	splice_region_variant	1739			U13897	CCDS3327.1, CCDS43194.1, CCDS56300.1, CCDS56301.1, CCDS75072.1	3q29	2008-12-15	2001-11-28		ENSG00000075711	ENSG00000075711			2900	protein-coding gene	gene with protein product	"""discs large homolog 1"", ""presynaptic protein SAP97"", ""synapse-associated protein 97"""	601014	"""discs, large (Drosophila) homolog 1"""			7937897, 8825652	Standard	NM_004087		Approved	SAP97, SAP-97, hdlg, DLGH1, dJ1061C18.1.1	uc003fxn.4	Q12959	OTTHUMG00000047972	ENST00000419354.1:c.1386-1G>C	3.37:g.196842954C>G			A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	Missense_Mutation	SNP	ENST00000419354.1	37	CCDS43194.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.343837	0.61073	.	.	ENSG00000075711	ENST00000346964;ENST00000359922;ENST00000357674;ENST00000381807;ENST00000314062;ENST00000419354;ENST00000452595;ENST00000422288;ENST00000448528;ENST00000443183;ENST00000392382;ENST00000450955;ENST00000447466	T;T;T;T;T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;2.26	5.2	4.33	0.51752	PDZ/DHR/GLGF (1);PDZ-associated domain of NMDA receptors (1);	0.000000	0.85682	D	0.000000	T	0.52240	0.1722	L	0.56769	1.78	0.80722	D	1	B;B;B;B;B;B;B	0.33477	0.138;0.413;0.29;0.29;0.138;0.267;0.055	B;B;B;B;B;P;B	0.45119	0.066;0.292;0.305;0.305;0.121;0.47;0.084	T	0.46005	-0.9222	10	0.21540	T	0.41	.	13.0043	0.58694	0.0:0.922:0.0:0.078	.	429;346;346;346;429;462;462	Q12959-4;E9PG21;E7EWL7;B4DGU1;Q12959-3;Q12959;Q12959-2	.;.;.;.;.;DLG1_HUMAN;.	S	462;462;429;462;411;462;346;411;462;346;429;429;271	ENSP00000345731:R462S;ENSP00000350303:R429S;ENSP00000321087:R411S;ENSP00000407531:R462S;ENSP00000398939:R346S;ENSP00000413238:R411S;ENSP00000391732:R462S;ENSP00000396658:R346S;ENSP00000376187:R429S;ENSP00000411278:R429S;ENSP00000398702:R271S	ENSP00000321087:R411S	R	-	3	2	DLG1	198327351	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.989000	0.40707	1.343000	0.45638	0.591000	0.81541	AGG		0.318	DLG1-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258170.2		NM_004087	Missense_Mutation
EBF2	64641	broad.mit.edu	37	8	25899690	25899690	+	Missense_Mutation	SNP	A	A	G			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr8:25899690A>G	ENST00000520164.1	-	2	746	c.209T>C	c.(208-210)gTc>gCc	p.V70A	EBF2_ENST00000408929.3_5'Flank	NM_022659.3	NP_073150.2	Q9HAK2	COE2_HUMAN	early B-cell factor 2	70					adipose tissue development (GO:0060612)|brown fat cell differentiation (GO:0050873)|cell fate determination (GO:0001709)|positive regulation of chromatin binding (GO:0035563)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V70A(2)		endometrium(3)|kidney(2)|large_intestine(3)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)		GAGCGCCAGGACGAAGTGAAA	0.582																																					Esophageal Squamous(166;1018 1046 3854 8328 13429 13634 14071 26624 32918)												2	Substitution - Missense(2)	kidney(2)											70.0	79.0	76.0					8																	25899690		2182	4296	6478	SO:0001583	missense	64641			AK021562, AK001144	CCDS43726.1	8p21.1	2007-07-26			ENSG00000221818	ENSG00000221818			19090	protein-coding gene	gene with protein product		609934				9151732	Standard	NM_022659		Approved	FLJ11500, COE2	uc003xes.2	Q9HAK2	OTTHUMG00000163838	ENST00000520164.1:c.209T>C	8.37:g.25899690A>G	ENSP00000430241:p.Val70Ala		A0PJM4|A6NMF7|F5H645|Q66VZ3|Q6DK36|Q6IS86|Q6ISA4	Missense_Mutation	SNP	ENST00000520164.1	37	CCDS43726.1	.	.	.	.	.	.	.	.	.	.	A	33	5.286967	0.95517	.	.	ENSG00000221818	ENST00000520164	T	0.58940	0.3	5.02	5.02	0.67125	.	0.000000	0.64402	U	0.000003	T	0.75895	0.3912	M	0.86178	2.8	0.80722	D	1	D	0.69078	0.997	P	0.61592	0.891	T	0.81127	-0.1074	10	0.87932	D	0	-10.4056	14.9071	0.70727	1.0:0.0:0.0:0.0	.	70	Q9HAK2	COE2_HUMAN	A	70	ENSP00000430241:V70A	ENSP00000430241:V70A	V	-	2	0	EBF2	25955607	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.139000	0.94554	2.128000	0.65567	0.459000	0.35465	GTC		0.582	EBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375886.2		NM_022659	
EEF1G	1937	broad.mit.edu	37	11	62339115	62339115	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr11:62339115G>A	ENST00000329251.4	-	4	405	c.275C>T	c.(274-276)gCa>gTa	p.A92V	MIR3654_ENST00000496634.2_3'UTR|EEF1G_ENST00000532986.1_5'UTR|EEF1G_ENST00000378019.3_Missense_Mutation_p.A142V	NM_001404.4	NP_001395.1	P26641	EF1G_HUMAN	eukaryotic translation elongation factor 1 gamma	92	GST C-terminal.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to virus (GO:0009615)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	translation elongation factor activity (GO:0003746)	p.A92V(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						CACCTGGGCTGCTGCCTCTGG	0.577																																																	1	Substitution - Missense(1)	kidney(1)											21.0	21.0	21.0					11																	62339115		1935	4133	6068	SO:0001583	missense	1937			X63526	CCDS44626.1	11q12.3	2008-02-05			ENSG00000254772	ENSG00000254772			3213	protein-coding gene	gene with protein product		130593				1598220, 1461723	Standard	NM_001404		Approved	EF1G	uc001ntm.1	P26641	OTTHUMG00000167567	ENST00000329251.4:c.275C>T	11.37:g.62339115G>A	ENSP00000331901:p.Ala92Val		B4DTG2|Q6PJ62|Q6PK31|Q96CU2|Q9P196	Missense_Mutation	SNP	ENST00000329251.4	37	CCDS44626.1	.	.	.	.	.	.	.	.	.	.	G	17.38	3.374740	0.61735	.	.	ENSG00000254772	ENST00000329251;ENST00000378019	T;T	0.17691	2.26;2.26	5.25	5.25	0.73442	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);	0.402443	0.25823	N	0.028072	T	0.29389	0.0732	M	0.89785	3.06	0.40417	D	0.979809	P;B	0.39940	0.696;0.116	B;B	0.36766	0.232;0.091	T	0.31668	-0.9935	10	0.30854	T	0.27	.	16.7037	0.85366	0.0:0.0:1.0:0.0	.	142;92	B4DTG2;P26641	.;EF1G_HUMAN	V	92;142	ENSP00000331901:A92V;ENSP00000367258:A142V	ENSP00000331901:A92V	A	-	2	0	EEF1G	62095691	0.999000	0.42202	0.908000	0.35775	0.985000	0.73830	4.696000	0.61774	2.620000	0.88729	0.563000	0.77884	GCA		0.577	EEF1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395047.1		NM_001404	
EXOSC10	5394	hgsc.bcm.edu;ucsc.edu	37	1	11147603	11147603	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr1:11147603delT	ENST00000376936.4	-	9	1040	c.991delA	c.(991-993)attfs	p.I331fs	EXOSC10_ENST00000304457.7_Frame_Shift_Del_p.I331fs|EXOSC10_ENST00000544779.1_Frame_Shift_Del_p.I331fs	NM_001001998.1	NP_001001998.1	Q01780	EXOSX_HUMAN	exosome component 10	331					CUT catabolic process (GO:0071034)|dosage compensation by inactivation of X chromosome (GO:0009048)|histone mRNA catabolic process (GO:0071044)|maturation of 5.8S rRNA (GO:0000460)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear retention of unspliced pre-mRNA at the site of transcription (GO:0071048)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5' exonuclease activity (GO:0008408)|exoribonuclease activity (GO:0004532)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|stomach(3)|upper_aerodigestive_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)		CGAGTAGAAATTTGCATCAGG	0.468																																					Colon(179;105 1987 14326 27364 29542)												0													173.0	176.0	175.0					1																	11147603		2203	4300	6503	SO:0001589	frameshift_variant	5394			BC073788	CCDS126.1, CCDS30584.1	1p36.22	2008-02-05	2004-06-16	2004-06-18	ENSG00000171824	ENSG00000171824			9138	protein-coding gene	gene with protein product	"""polymyositis/scleroderma autoantigen 2 (100kD)"""	605960	"""polymyositis/scleroderma autoantigen 2, 100kDa"""	PMSCL2		1383382, 1644924	Standard	NM_001001998		Approved	PM-Scl, PM/Scl-100, Rrp6p, RRP6, p2, p3, p4	uc001asa.3	Q01780	OTTHUMG00000002123	ENST00000376936.4:c.991delA	1.37:g.11147603delT	ENSP00000366135:p.Ile331fs		B1AKQ0|B1AKQ1|Q15158	Frame_Shift_Del	DEL	ENST00000376936.4	37	CCDS30584.1																																																																																				0.468	EXOSC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006078.1		NM_001001998	
FBL	2091	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	40330954	40330954	+	Nonsense_Mutation	SNP	A	A	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr19:40330954A>T	ENST00000221801.3	-	4	410	c.297T>A	c.(295-297)tgT>tgA	p.C99*	FBL_ENST00000593503.1_5'Flank	NM_001436.3	NP_001427.2	P22087	FBRL_HUMAN	fibrillarin	99					histone glutamine methylation (GO:1990258)|osteoblast differentiation (GO:0001649)|rRNA processing (GO:0006364)|snoRNA metabolic process (GO:0016074)|tRNA processing (GO:0008033)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|extracellular vesicular exosome (GO:0070062)|granular component (GO:0001652)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone-glutamine methyltransferase activity (GO:1990259)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.C99*(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)	9	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)	Renal(1328;0.000518)|Hepatocellular(1079;0.0893)	Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)	GBM - Glioblastoma multiforme(1328;0.000826)|STAD - Stomach adenocarcinoma(1328;0.138)		CCTTTCCTCGACAAATGAAGA	0.587																																																	1	Substitution - Nonsense(1)	kidney(1)											106.0	99.0	101.0					19																	40330954		2203	4300	6503	SO:0001587	stop_gained	2091			AC005393	CCDS12545.1	19q13.1	2010-02-17			ENSG00000105202	ENSG00000105202			3599	protein-coding gene	gene with protein product		134795				1846968, 2026646	Standard	NM_001436		Approved	RNU3IP1, FLRN, FIB	uc002omn.3	P22087		ENST00000221801.3:c.297T>A	19.37:g.40330954A>T	ENSP00000221801:p.Cys99*		B5BUE8|O75259|Q6IAT5|Q9UPI6	Nonsense_Mutation	SNP	ENST00000221801.3	37	CCDS12545.1	.	.	.	.	.	.	.	.	.	.	A	36	5.905567	0.97087	.	.	ENSG00000105202	ENST00000221801	.	.	.	5.08	1.55	0.23275	.	0.044204	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	-13.0983	7.9414	0.29961	0.6531:0.0:0.3469:0.0	.	.	.	.	X	99	.	ENSP00000221801:C99X	C	-	3	2	FBL	45022794	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	1.382000	0.34374	-0.008000	0.14320	0.418000	0.28097	TGT		0.587	FBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462509.4		NM_001436	
FAM71E1	112703	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	50979507	50979507	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr19:50979507G>A	ENST00000600100.1	-	1	503	c.139C>T	c.(139-141)Cgc>Tgc	p.R47C	FAM71E1_ENST00000595790.1_Missense_Mutation_p.R47C|EMC10_ENST00000598585.1_5'Flank|EMC10_ENST00000334976.6_5'Flank|EMC10_ENST00000376918.3_5'Flank			Q6IPT2	F71E1_HUMAN	family with sequence similarity 71, member E1	47								p.R47C(1)		breast(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.0077)|GBM - Glioblastoma multiforme(134;0.026)		GGGAGAAAGCGAGGGGGCGGG	0.652																																																	1	Substitution - Missense(1)	kidney(1)											51.0	54.0	53.0					19																	50979507		2197	4288	6485	SO:0001583	missense	112703				CCDS33081.1	19q13.33	2007-11-20				ENSG00000142530			25107	protein-coding gene	gene with protein product							Standard	XM_005258472		Approved		uc002psg.3	Q6IPT2		ENST00000600100.1:c.139C>T	19.37:g.50979507G>A	ENSP00000472421:p.Arg47Cys		Q96EJ5|Q9BSM9	Missense_Mutation	SNP	ENST00000600100.1	37		.	.	.	.	.	.	.	.	.	.	G	14.67	2.604358	0.46423	.	.	ENSG00000142530	ENST00000391816;ENST00000270620	T;T	0.13196	2.63;2.61	3.86	-4.81	0.03180	.	2.694200	0.01573	N	0.020680	T	0.08403	0.0209	N	0.22421	0.69	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.34104	-0.9842	10	0.87932	D	0	.	1.7781	0.03025	0.2005:0.3331:0.326:0.1403	.	47;47	Q6IPT2;Q6IPT2-2	F71E1_HUMAN;.	C	47	ENSP00000375692:R47C;ENSP00000270620:R47C	ENSP00000270620:R47C	R	-	1	0	FAM71E1	55671319	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.034000	0.01424	-0.741000	0.04797	0.467000	0.42956	CGC		0.652	FAM71E1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464754.2			
FBLN1	2192	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	45931087	45931087	+	Silent	SNP	C	C	T	rs144704783		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr22:45931087C>T	ENST00000327858.6	+	8	887	c.792C>T	c.(790-792)gaC>gaT	p.D264D	FBLN1_ENST00000442170.2_Silent_p.D264D|FBLN1_ENST00000348697.2_Silent_p.D264D|FBLN1_ENST00000402984.3_Silent_p.D302D|FBLN1_ENST00000262722.7_Silent_p.D264D|FBLN1_ENST00000340923.5_Silent_p.D264D	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1	264	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504)	p.D264D(3)		biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	30		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		CAGATATTGACGAGTGTGAGA	0.418																																																	3	Substitution - coding silent(3)	kidney(3)							,,,	1,4405	2.1+/-5.4	0,1,2202	144.0	131.0	136.0		792,792,792,792	4.4	1.0	22	dbSNP_134	136	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FBLN1	NM_001996.3,NM_006485.3,NM_006486.2,NM_006487.2	,,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,	264/684,264/602,264/704,264/567	45931087	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2192				CCDS14067.1, CCDS14068.1, CCDS14069.1, CCDS43028.1	22q13.31	2010-06-15			ENSG00000077942	ENSG00000077942		"""Fibulins"""	3600	protein-coding gene	gene with protein product		135820				2269669, 1400330	Standard	NM_006485		Approved	FBLN	uc003bgj.1	P23142	OTTHUMG00000151340	ENST00000327858.6:c.792C>T	22.37:g.45931087C>T			B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Silent	SNP	ENST00000327858.6	37	CCDS14067.1																																																																																				0.418	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1		NM_006486	
FBXL13	222235	hgsc.bcm.edu;ucsc.edu	37	7	102665597	102665597	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr7:102665597delA	ENST00000313221.4	-	6	834	c.408delT	c.(406-408)tttfs	p.F136fs	FBXL13_ENST00000393772.2_Frame_Shift_Del_p.F136fs|FBXL13_ENST00000379308.3_Frame_Shift_Del_p.F136fs|FBXL13_ENST00000379305.3_Frame_Shift_Del_p.F136fs|FBXL13_ENST00000379306.3_Frame_Shift_Del_p.F136fs|FBXL13_ENST00000455112.2_Frame_Shift_Del_p.F136fs|FBXL13_ENST00000456695.1_Frame_Shift_Del_p.F136fs|FBXL13_ENST00000436908.1_Frame_Shift_Del_p.F136fs|FBXL13_ENST00000471074.1_5'UTR	NM_145032.3	NP_659469.3	Q8NEE6	FXL13_HUMAN	F-box and leucine-rich repeat protein 13	136										NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|skin(3)|stomach(1)	27						TTCGTTCAGGAAAATTGGATT	0.303																																																	0													56.0	54.0	55.0					7																	102665597		2201	4298	6499	SO:0001589	frameshift_variant	222235			BC031285	CCDS5726.1, CCDS47678.1, CCDS75649.1	7q22.1	2014-07-18			ENSG00000161040	ENSG00000161040		"""F-boxes / Leucine-rich repeats"""	21658	protein-coding gene	gene with protein product		609080					Standard	NM_145032		Approved	MGC21636, Fbl13	uc003vaq.2	Q8NEE6	OTTHUMG00000157224	ENST00000313221.4:c.408delT	7.37:g.102665597delA	ENSP00000321927:p.Phe136fs		C9J565|C9J566|Q6UVW7|Q6UVW8|Q75MN5|Q86UJ5|Q8N7Y4|Q8TCL2|Q8WUF9|Q8WUG0	Frame_Shift_Del	DEL	ENST00000313221.4	37	CCDS5726.1																																																																																				0.303	FBXL13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348001.1		NM_145032	
HMBOX1	79618	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	28906483	28906483	+	Missense_Mutation	SNP	T	T	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr8:28906483T>A	ENST00000397358.3	+	10	1747	c.1043T>A	c.(1042-1044)cTg>cAg	p.L348Q	HMBOX1_ENST00000524238.1_Missense_Mutation_p.L347Q|HMBOX1_ENST00000444075.1_Missense_Mutation_p.L347Q|HMBOX1_ENST00000517386.1_3'UTR|HMBOX1_ENST00000558662.1_Missense_Mutation_p.L347Q|HMBOX1_ENST00000355231.5_Missense_Mutation_p.L347Q|HMBOX1_ENST00000519047.1_Missense_Mutation_p.L347Q|HMBOX1_ENST00000523613.1_Missense_Mutation_p.L348Q|RNA5SP260_ENST00000363849.1_RNA|HMBOX1_ENST00000287701.10_Missense_Mutation_p.L348Q	NM_024567.3	NP_078843.2	Q6NT76	HMBX1_HUMAN	homeobox containing 1	348					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.L348Q(1)		cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	11		Ovarian(32;0.0192)		KIRC - Kidney renal clear cell carcinoma(542;0.135)|Kidney(114;0.161)		GCAGCAATCCTGGAGAGTCAT	0.448																																																	1	Substitution - Missense(1)	kidney(1)											162.0	158.0	159.0					8																	28906483		2203	4300	6503	SO:0001583	missense	79618			AY522342	CCDS6071.1	8p12	2013-05-23			ENSG00000147421	ENSG00000147421		"""Homeoboxes / HNF class"""	26137	protein-coding gene	gene with protein product	"""homeobox telomere-binding protein 1"""					16825764	Standard	NM_024567		Approved	HNF1LA, PBHNF, FLJ21616, HOT1	uc003xhd.4	Q6NT76	OTTHUMG00000172138	ENST00000397358.3:c.1043T>A	8.37:g.28906483T>A	ENSP00000380516:p.Leu348Gln		A4K385|A8K3R8|B4DHY5|D3DSU0|Q3Y6P1|Q96GS5|Q9H701	Missense_Mutation	SNP	ENST00000397358.3	37	CCDS6071.1	.	.	.	.	.	.	.	.	.	.	T	19.92	3.916607	0.73098	.	.	ENSG00000147421	ENST00000287701;ENST00000444075;ENST00000519047;ENST00000397358;ENST00000524238;ENST00000517340;ENST00000355231	D;D;D;D;D	0.99894	-7.58;-7.5;-7.47;-7.58;-7.5	5.32	5.32	0.75619	Homeodomain-like (1);	0.082734	0.51477	D	0.000093	D	0.99691	0.9883	L	0.29908	0.895	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.998;0.995;0.999	D;D;D;D;D;D	0.80764	0.994;0.986;0.984;0.974;0.979;0.963	D	0.97346	0.9960	10	0.35671	T	0.21	-3.9125	15.2709	0.73699	0.0:0.0:0.0:1.0	.	347;348;347;346;348;347	Q6NT76-5;D3DSU2;Q6NT76-2;Q6NT76-3;Q6NT76;E5RGZ2	.;.;.;.;HMBX1_HUMAN;.	Q	348;347;347;348;347;346;347	ENSP00000287701:L348Q;ENSP00000401769:L347Q;ENSP00000430059:L347Q;ENSP00000380516:L348Q;ENSP00000430110:L347Q	ENSP00000287701:L348Q	L	+	2	0	HMBOX1	28962402	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.371000	0.79600	1.999000	0.58509	0.533000	0.62120	CTG		0.448	HMBOX1-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255267.4		NM_024567	
GPR124	25960	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	37696506	37696506	+	Silent	SNP	C	C	T	rs147055217		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr8:37696506C>T	ENST00000412232.2	+	15	2305	c.2292C>T	c.(2290-2292)ggC>ggT	p.G764G	GPR124_ENST00000315215.7_Silent_p.G547G	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	764					central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.G757G(1)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			AGGTGGGGGGCGCCGGGGCAG	0.662													C|||	1	0.000199681	0.0	0.0014	5008	,	,		17926	0.0		0.0	False		,,,				2504	0.0																1	Substitution - coding silent(1)	kidney(1)						C		0,4406		0,0,2203	33.0	35.0	34.0		2292	3.5	0.8	8	dbSNP_134	34	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	GPR124	NM_032777.9		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		764/1339	37696506	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	25960			AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17849	protein-coding gene	gene with protein product	"""tumor endothelial marker 5"""	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.2292C>T	8.37:g.37696506C>T			A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Silent	SNP	ENST00000412232.2	37	CCDS6097.2																																																																																				0.662	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2			
HMSD	284293	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	61627535	61627535	+	Silent	SNP	C	C	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr18:61627535C>T	ENST00000408945.3	+	4	568	c.366C>T	c.(364-366)ttC>ttT	p.F122F	HMSD_ENST00000481726.1_Intron	NM_001123366.1	NP_001116838.1	A8MTL9	HMSD_HUMAN	histocompatibility (minor) serpin domain containing	122						extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.F122F(1)		kidney(1)|large_intestine(2)|lung(2)|stomach(1)	6						TATTCTATTTCGATAATATTT	0.299																																																	1	Substitution - coding silent(1)	kidney(1)																																								SO:0001819	synonymous_variant	284293			AC009802	CCDS42441.1	18q21.33	2008-02-04			ENSG00000221887	ENSG00000221887			23037	protein-coding gene	gene with protein product		612086		C18orf53		17409267	Standard	NM_001123366		Approved	ACC-6	uc010dqj.3	A8MTL9	OTTHUMG00000060593	ENST00000408945.3:c.366C>T	18.37:g.61627535C>T				Silent	SNP	ENST00000408945.3	37	CCDS42441.1																																																																																				0.299	HMSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134010.2		XM_209104	
HSPG2	3339	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	22178652	22178652	+	Missense_Mutation	SNP	C	C	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr1:22178652C>T	ENST00000374695.3	-	53	6878	c.6799G>A	c.(6799-6801)Gtg>Atg	p.V2267M	HSPG2_ENST00000430507.1_3'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2267	Ig-like C2-type 8.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)	p.V2267M(1)		breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CCTGCCACCACGCAGCTCAGA	0.657																																																	1	Substitution - Missense(1)	kidney(1)											48.0	47.0	47.0					1																	22178652		2203	4300	6503	SO:0001583	missense	3339			M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.6799G>A	1.37:g.22178652C>T	ENSP00000363827:p.Val2267Met		Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	C	16.46	3.128665	0.56721	.	.	ENSG00000142798	ENST00000374695	T	0.67171	-0.25	5.48	3.49	0.39957	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.230767	0.21879	N	0.067762	T	0.62660	0.2446	L	0.33710	1.025	0.30047	N	0.812067	P;P	0.50710	0.938;0.904	P;B	0.49421	0.61;0.354	T	0.63355	-0.6656	10	0.44086	T	0.13	.	13.4744	0.61299	0.0:0.7001:0.2999:0.0	.	207;2267	Q59EG0;P98160	.;PGBM_HUMAN	M	2267	ENSP00000363827:V2267M	ENSP00000363827:V2267M	V	-	1	0	HSPG2	22051239	0.000000	0.05858	0.994000	0.49952	0.977000	0.68977	-0.380000	0.07427	1.311000	0.45024	0.561000	0.74099	GTG		0.657	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1		NM_005529	
ITGAX	3687	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	31373943	31373943	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr16:31373943G>A	ENST00000268296.4	+	12	1349	c.1228G>A	c.(1228-1230)Gag>Aag	p.E410K	ITGAX_ENST00000562522.1_Missense_Mutation_p.E410K	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	410					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)	p.E410K(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						TTACTCCACCGAGCTGGCCCT	0.677																																																	1	Substitution - Missense(1)	kidney(1)																																								SO:0001583	missense	3687			BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"""CD molecules"", ""Complement system"", ""Integrins"""	6152	protein-coding gene	gene with protein product		151510	"""integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"""	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.1228G>A	16.37:g.31373943G>A	ENSP00000268296:p.Glu410Lys		Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	37	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	g	9.382	1.073145	0.20147	.	.	ENSG00000140678	ENST00000268296	T	0.21543	2.0	3.91	1.84	0.25277	.	.	.	.	.	T	0.23249	0.0562	M	0.86178	2.8	0.09310	N	1	D	0.53885	0.963	B	0.31337	0.128	T	0.24297	-1.0164	9	0.33940	T	0.23	.	13.3997	0.60876	0.0:0.4526:0.5474:0.0	.	410	P20702	ITAX_HUMAN	K	410	ENSP00000268296:E410K	ENSP00000268296:E410K	E	+	1	0	ITGAX	31281444	0.988000	0.35896	0.036000	0.18154	0.253000	0.25986	2.284000	0.43478	0.238000	0.21222	-0.521000	0.04368	GAG		0.677	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2		NM_000887	
IRX5	10265	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	54967655	54967655	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr16:54967655G>T	ENST00000394636.4	+	3	1659	c.1322G>T	c.(1321-1323)gGa>gTa	p.G441V	IRX5_ENST00000560154.1_Missense_Mutation_p.G221V|CTD-3032H12.2_ENST00000560487.1_lincRNA|IRX5_ENST00000320990.5_Missense_Mutation_p.G440V|IRX5_ENST00000558597.1_Missense_Mutation_p.G375V			P78411	IRX5_HUMAN	iroquois homeobox 5	441					embryonic cranial skeleton morphogenesis (GO:0048701)|gonad development (GO:0008406)|neuron maturation (GO:0042551)|regulation of heart rate (GO:0002027)|regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|vitamin D binding (GO:0005499)	p.G441V(1)		kidney(3)|large_intestine(6)|lung(4)|prostate(1)	14						CATTTCAATGGATTAAACCAG	0.572																																																	1	Substitution - Missense(1)	kidney(1)											38.0	45.0	43.0					16																	54967655		2195	4300	6495	SO:0001583	missense	10265			U90309	CCDS10751.1, CCDS58462.1	16q12.2	2011-06-20	2007-07-13		ENSG00000176842	ENSG00000176842		"""Homeoboxes / TALE class"""	14361	protein-coding gene	gene with protein product		606195					Standard	NM_005853		Approved	IRX-2a	uc002ehv.3	P78411	OTTHUMG00000133201	ENST00000394636.4:c.1322G>T	16.37:g.54967655G>T	ENSP00000378132:p.Gly441Val		H0YMS7|P78416|Q7Z2E1	Missense_Mutation	SNP	ENST00000394636.4	37	CCDS10751.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.193592	0.58017	.	.	ENSG00000176842	ENST00000394636;ENST00000320990	T;T	0.50813	0.73;0.73	4.77	4.77	0.60923	.	0.278614	0.36893	N	0.002351	T	0.61664	0.2365	L	0.40543	1.245	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.63752	-0.6566	10	0.56958	D	0.05	-2.8799	17.9725	0.89117	0.0:0.0:1.0:0.0	.	441	P78411	IRX5_HUMAN	V	441;440	ENSP00000378132:G441V;ENSP00000316250:G440V	ENSP00000316250:G440V	G	+	2	0	IRX5	53525156	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.912000	0.92726	2.455000	0.83008	0.650000	0.86243	GGA		0.572	IRX5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256911.2			
SPIDR	23514	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	48353095	48353095	+	Missense_Mutation	SNP	T	T	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr8:48353095T>A	ENST00000297423.4	+	8	1472	c.1088T>A	c.(1087-1089)tTc>tAc	p.F363Y	SPIDR_ENST00000518074.1_Missense_Mutation_p.F303Y|SPIDR_ENST00000521214.1_3'UTR|SPIDR_ENST00000541342.1_Missense_Mutation_p.F293Y	NM_001080394.2|NM_001282916.1	NP_001073863.1|NP_001269845.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	363	Necessary for interaction with RAD51.				cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of protein complex assembly (GO:0031334)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of establishment of protein localization to chromosome (GO:0070202)	nuclear chromosome (GO:0000228)		p.F363Y(1)									GTCCGGATCTTCCCTCCCTGG	0.517																																																	1	Substitution - Missense(1)	kidney(1)											43.0	45.0	45.0					8																	48353095		1950	4149	6099	SO:0001583	missense	23514			AK055680	CCDS43737.1, CCDS64890.1, CCDS64891.1	8q11.21	2013-07-02	2013-07-02	2013-07-02	ENSG00000164808	ENSG00000164808			28971	protein-coding gene	gene with protein product		615384	"""KIAA0146"""	KIAA0146		8590280, 23509288	Standard	XM_005251189		Approved		uc003xqd.3	Q14159	OTTHUMG00000164176	ENST00000297423.4:c.1088T>A	8.37:g.48353095T>A	ENSP00000297423:p.Phe363Tyr		B4DFV2|B4E0Y6|Q96BI5	Missense_Mutation	SNP	ENST00000297423.4	37	CCDS43737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	6.141|6.141	0.394271|0.394271	0.11638|0.11638	.|.	.|.	ENSG00000164808|ENSG00000164808	ENST00000297423;ENST00000518074;ENST00000541342;ENST00000524006|ENST00000519401	.|.	.|.	.|.	5.54|5.54	3.08|3.08	0.35506|0.35506	.|.	0.217327|.	0.40144|.	N|.	0.001168|.	T|T	0.17023|0.17023	0.0409|0.0409	N|N	0.04162|0.04162	-0.26|-0.26	0.29384|0.29384	N|N	0.863111|0.863111	B;B;B;B|.	0.11235|.	0.004;0.001;0.001;0.001|.	B;B;B;B|.	0.10450|.	0.005;0.004;0.003;0.004|.	T|T	0.24621|0.24621	-1.0155|-1.0155	9|5	0.05721|.	T|.	0.95|.	.|.	9.3269|9.3269	0.37999|0.37999	0.5814:0.0:0.0:0.4186|0.5814:0.0:0.0:0.4186	.|.	303;293;363;363|.	B4E0Y6;B4DFV2;B4DEV5;Q14159|.	.;.;.;K0146_HUMAN|.	Y|T	363;303;293;52|45	.|.	ENSP00000297423:F363Y|.	F|S	+|+	2|1	0|0	KIAA0146|KIAA0146	48515648|48515648	1.000000|1.000000	0.71417|0.71417	0.981000|0.981000	0.43875|0.43875	0.817000|0.817000	0.46193|0.46193	3.031000|3.031000	0.49728|0.49728	0.354000|0.354000	0.24105|0.24105	0.533000|0.533000	0.62120|0.62120	TTC|TCC		0.517	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1		NM_001080394	
MPP6	51678	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	24720095	24720095	+	Missense_Mutation	SNP	C	C	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr7:24720095C>T	ENST00000222644.5	+	11	1652	c.1402C>T	c.(1402-1404)Cac>Tac	p.H468Y	MPP6_ENST00000409761.1_Missense_Mutation_p.H356Y|MPP6_ENST00000396475.2_Missense_Mutation_p.H468Y			Q99547	MPH6_HUMAN	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	0					maturation of 5.8S rRNA (GO:0000460)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)	p.H468Y(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|skin(2)	20						ACGTGCCATGCACAAGGCTGT	0.433																																																	1	Substitution - Missense(1)	kidney(1)											164.0	145.0	151.0					7																	24720095		2203	4300	6503	SO:0001583	missense	51678			AF162130	CCDS5388.1	7p15	2007-08-01			ENSG00000105926	ENSG00000105926			18167	protein-coding gene	gene with protein product		606959				10753959, 11311936	Standard	NM_016447		Approved	PALS2, VAM-1, p55T	uc003swx.3	Q9NZW5	OTTHUMG00000023507	ENST00000222644.5:c.1402C>T	7.37:g.24720095C>T	ENSP00000222644:p.His468Tyr		B2RAF0	Missense_Mutation	SNP	ENST00000222644.5	37	CCDS5388.1	.	.	.	.	.	.	.	.	.	.	C	15.93	2.977567	0.53720	.	.	ENSG00000105926	ENST00000222644;ENST00000409761;ENST00000396475	T;T;T	0.16457	2.34;2.34;2.34	5.43	5.43	0.79202	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2);	0.000000	0.56097	D	0.000031	T	0.14570	0.0352	N	0.16266	0.395	0.80722	D	1	B	0.19331	0.035	B	0.28305	0.088	T	0.12142	-1.0559	10	0.26408	T	0.33	.	19.2417	0.93887	0.0:1.0:0.0:0.0	.	468	Q9NZW5	MPP6_HUMAN	Y	468;356;468	ENSP00000222644:H468Y;ENSP00000386262:H356Y;ENSP00000379737:H468Y	ENSP00000222644:H468Y	H	+	1	0	MPP6	24686620	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.818000	0.86416	2.541000	0.85698	0.561000	0.74099	CAC		0.433	MPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250272.4			
NDUFS3	4722	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	47602127	47602127	+	Nonsense_Mutation	SNP	G	G	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr11:47602127G>T	ENST00000263774.4	+	3	266	c.184G>T	c.(184-186)Gga>Tga	p.G62*	NDUFS3_ENST00000534208.1_Nonsense_Mutation_p.G62*|KBTBD4_ENST00000395288.2_5'Flank|NDUFS3_ENST00000528192.1_Nonsense_Mutation_p.G62*|NDUFS3_ENST00000533507.1_3'UTR|KBTBD4_ENST00000525720.1_5'Flank|KBTBD4_ENST00000430070.2_5'Flank|NDUFS3_ENST00000534716.2_Nonsense_Mutation_p.G62*|KBTBD4_ENST00000526005.1_5'Flank|KBTBD4_ENST00000533290.1_5'Flank	NM_004551.2	NP_004542.1	O75489	NDUS3_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase)	62					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)	p.G62*(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)	9					Doxorubicin(DB00997)	CTCAGCTTTTGGAGAGTATGT	0.438																																					Pancreas(15;551 601 22438 23457 52512)												1	Substitution - Nonsense(1)	kidney(1)											96.0	89.0	91.0					11																	47602127		2201	4298	6499	SO:0001587	stop_gained	4722			AF067139	CCDS7941.1	11p11.11	2011-08-03	2002-08-29		ENSG00000213619	ENSG00000213619	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7710	protein-coding gene	gene with protein product	"""complex I 30kDa subunit"", ""NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial"""	603846	"""NADH dehydrogenase (ubiquinone) Fe-S protein 3 (30kD) (NADH-coenzyme Q reductase)"""			9763677	Standard	NM_004551		Approved	CI-30	uc001nga.2	O75489	OTTHUMG00000166893	ENST00000263774.4:c.184G>T	11.37:g.47602127G>T	ENSP00000263774:p.Gly62*		B2R9J1|B4DFM8|Q9UNQ8	Nonsense_Mutation	SNP	ENST00000263774.4	37	CCDS7941.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.087111	0.76642	.	.	ENSG00000213619	ENST00000263774;ENST00000528192;ENST00000530295;ENST00000534208;ENST00000534716	.	.	.	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-15.1086	18.8963	0.92424	0.0:0.0:1.0:0.0	.	.	.	.	X	62;62;40;62;62	.	ENSP00000263774:G62X	G	+	1	0	NDUFS3	47558703	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.411000	0.97342	2.452000	0.82932	0.563000	0.77884	GGA		0.438	NDUFS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391749.1		NM_004551	
NOTCH2	4853	broad.mit.edu	37	1	120612003	120612004	+	Frame_Shift_Del	DEL	GG	GG	-	rs372504208		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr1:120612003_120612004delGG	ENST00000256646.2	-	1	236_237	c.17_18delCC	c.(16-18)cccfs	p.P6fs		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	6					apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)	p.P6fs*27(2)		breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACAGCAGAGCGGGGCGCAGGGC	0.762			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome																															Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	2	Deletion - Frameshift(2)	haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)																																								SO:0001589	frameshift_variant	4853	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.17_18delCC	1.37:g.120612005_120612006delGG	ENSP00000256646:p.Pro6fs		Q5T3X7|Q99734|Q9H240	Frame_Shift_Del	DEL	ENST00000256646.2	37	CCDS908.1																																																																																				0.762	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1		NM_024408	
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52598158	52598158	+	Nonsense_Mutation	SNP	G	G	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr3:52598158G>T	ENST00000296302.7	-	23	3784	c.3783C>A	c.(3781-3783)taC>taA	p.Y1261*	PBRM1_ENST00000409767.1_Nonsense_Mutation_p.Y1276*|PBRM1_ENST00000337303.4_Nonsense_Mutation_p.Y1261*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.Y1276*|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.Y1236*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.Y1261*|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.Y1229*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.Y1236*			Q86U86	PB1_HUMAN	polybromo 1	1261	BAH 2. {ECO:0000255|PROSITE- ProRule:PRU00370}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.Y1261*(2)|p.Y1229*(1)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		CGCTCTCATTGTAGCGGCTCT	0.418			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	3	Substitution - Nonsense(3)	kidney(3)											109.0	107.0	108.0					3																	52598158		2203	4300	6503	SO:0001587	stop_gained	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.3783C>A	3.37:g.52598158G>T	ENSP00000296302:p.Tyr1261*		A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	G	40	8.478808	0.98829	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351	.	.	.	5.05	1.17	0.20885	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.0515	9.2637	0.37627	0.372:0.0:0.628:0.0	.	.	.	.	X	1229;1236;1261;1261;1261;1236;1276;1276;1260	.	ENSP00000296302:Y1261X	Y	-	3	2	PBRM1	52573198	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.255000	0.32909	0.524000	0.28502	0.655000	0.94253	TAC		0.418	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PHF20	51230	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	34457385	34457385	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr20:34457385G>T	ENST00000374012.3	+	7	963	c.834G>T	c.(832-834)ttG>ttT	p.L278F	PHF20_ENST00000481202.1_3'UTR|PHF20_ENST00000439301.1_Missense_Mutation_p.A257S			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	278					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.L278F(1)		breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					CTCAAACTTTGCAACCAATAA	0.318																																																	1	Substitution - Missense(1)	kidney(1)											100.0	99.0	99.0					20																	34457385		2203	4300	6503	SO:0001583	missense	51230			AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	16098	protein-coding gene	gene with protein product	"""tudor domain containing 20A"""	610335	"""chromosome 20 open reading frame 104"""	C20orf104			Standard	NM_016436		Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.834G>T	20.37:g.34457385G>T	ENSP00000363124:p.Leu278Phe		A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Missense_Mutation	SNP	ENST00000374012.3	37	CCDS13268.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.83|15.83	2.948265|2.948265	0.53186|0.53186	.|.	.|.	ENSG00000025293|ENSG00000025293	ENST00000439301|ENST00000374012;ENST00000339089;ENST00000374000	T|T;T;T	0.49432|0.54866	0.78|1.22;0.55;0.56	5.35|5.35	3.41|3.41	0.39046|0.39046	.|.	.|0.367965	.|0.25543	.|N	.|0.029960	T|T	0.54224|0.54224	0.1845|0.1845	L|L	0.29908|0.29908	0.895|0.895	0.28022|0.28022	N|N	0.934469|0.934469	.|D;D;D	.|0.89917	.|1.0;0.999;1.0	.|D;D;D	.|0.91635	.|0.999;0.999;0.999	T|T	0.46638|0.46638	-0.9177|-0.9177	7|10	0.32370|0.12103	T|T	0.25|0.63	.|.	9.8207|9.8207	0.40880|0.40880	0.2212:0.0:0.7788:0.0|0.2212:0.0:0.7788:0.0	.|.	.|278;278;278	.|Q566Q2;Q9BVI0;Q66K49	.|.;PHF20_HUMAN;.	S|F	257|278	ENSP00000410373:A257S|ENSP00000363124:L278F;ENSP00000341900:L278F;ENSP00000363112:L278F	ENSP00000410373:A257S|ENSP00000341900:L278F	A|L	+|+	1|3	0|2	PHF20|PHF20	33920799|33920799	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.968000|0.968000	0.65278|0.65278	1.793000|1.793000	0.38764|0.38764	0.645000|0.645000	0.30675|0.30675	-0.237000|-0.237000	0.12165|0.12165	GCA|TTG		0.318	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2		NM_016436	
PNPLA3	80339	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	44322959	44322959	+	Missense_Mutation	SNP	C	C	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr22:44322959C>A	ENST00000216180.3	+	2	505	c.332C>A	c.(331-333)tCc>tAc	p.S111Y	PNPLA3_ENST00000478713.1_3'UTR|PNPLA3_ENST00000423180.2_Missense_Mutation_p.S107Y	NM_025225.2	NP_079501.2	Q9NST1	PLPL3_HUMAN	patatin-like phospholipase domain containing 3	111	Patatin.				acylglycerol acyl-chain remodeling (GO:0036155)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	diolein transacylation activity (GO:0051265)|mono-olein transacylation activity (GO:0051264)|phospholipase A2 activity (GO:0004623)|triglyceride lipase activity (GO:0004806)	p.S111Y(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|prostate(1)|skin(1)|stomach(2)	19		Ovarian(80;0.024)|all_neural(38;0.0416)				CAGCTCATCTCCGGCAAAATA	0.502																																																	1	Substitution - Missense(1)	kidney(1)											89.0	78.0	82.0					22																	44322959		2203	4300	6503	SO:0001583	missense	80339				CCDS14054.1	22q13.31	2014-03-14	2006-05-26	2006-05-26	ENSG00000100344	ENSG00000100344	3.1.1.3	"""Patatin-like phospholipase domain containing"""	18590	protein-coding gene	gene with protein product		609567	"""chromosome 22 open reading frame 20"", ""adiponutrin"""	C22orf20, ADPN		16799181, 19029121	Standard	NM_025225		Approved	dJ796I17.1, FLJ22012, adiponutrin, iPLA2epsilon	uc003bei.1	Q9NST1	OTTHUMG00000150555	ENST00000216180.3:c.332C>A	22.37:g.44322959C>A	ENSP00000216180:p.Ser111Tyr		B0QYI0|B2RCL3|B3KW00|Q6P1A1|Q96CB4	Missense_Mutation	SNP	ENST00000216180.3	37	CCDS14054.1	.	.	.	.	.	.	.	.	.	.	C	14.82	2.649278	0.47362	.	.	ENSG00000100344	ENST00000216180;ENST00000423180	T;T	0.80994	-1.44;-1.07	5.5	5.5	0.81552	Acyl transferase/acyl hydrolase/lysophospholipase (1);Patatin/Phospholipase A2-related (1);	0.000000	0.64402	D	0.000002	D	0.90920	0.7146	M	0.90309	3.105	0.52099	D	0.999947	D	0.89917	1.0	D	0.81914	0.995	D	0.92353	0.5891	10	0.87932	D	0	-26.7168	13.6947	0.62569	0.0:0.8453:0.1547:0.0	.	111	Q9NST1	PLPL3_HUMAN	Y	111;107	ENSP00000216180:S111Y;ENSP00000397987:S107Y	ENSP00000216180:S111Y	S	+	2	0	PNPLA3	42654292	0.797000	0.28877	0.198000	0.23420	0.007000	0.05969	5.346000	0.65992	2.568000	0.86640	0.643000	0.83706	TCC		0.502	PNPLA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318891.1		NM_025225	
PRKG1	5592	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	53921672	53921672	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr10:53921672G>A	ENST00000401604.2	+	9	1174	c.980G>A	c.(979-981)gGg>gAg	p.G327E	PRKG1_ENST00000373985.1_Missense_Mutation_p.G315E|PRKG1_ENST00000373975.2_Missense_Mutation_p.G45E|PRKG1_ENST00000373980.4_Missense_Mutation_p.G342E			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	327	cGMP-binding, low affinity.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)	p.G342E(1)|p.G327E(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		TTGATTGGAGGGCTGGATGAT	0.328																																																	2	Substitution - Missense(2)	kidney(2)											161.0	152.0	155.0					10																	53921672		2203	4300	6503	SO:0001583	missense	5592				CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.980G>A	10.37:g.53921672G>A	ENSP00000384200:p.Gly327Glu		A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	37	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	G	17.69	3.452392	0.63290	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000332193	T;T;T	0.27256	1.68;1.68;1.68	5.39	5.39	0.77823	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);	0.000000	0.85682	D	0.000000	T	0.20333	0.0489	N	0.16478	0.41	0.80722	D	1	B;P;P	0.45594	0.006;0.636;0.862	B;B;B	0.41946	0.025;0.254;0.371	T	0.01945	-1.1242	10	0.37606	T	0.19	-14.5411	18.2845	0.90110	0.0:0.0:1.0:0.0	.	45;342;327	B3KSF3;Q13976-2;Q13976	.;.;KGP1_HUMAN	E	327;315;342;45	ENSP00000384200:G327E;ENSP00000363097:G315E;ENSP00000363092:G342E	ENSP00000327642:G45E	G	+	2	0	PRKG1	53591678	1.000000	0.71417	0.994000	0.49952	0.992000	0.81027	7.260000	0.78391	2.675000	0.91044	0.573000	0.79308	GGG		0.328	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				
RIMKLB	57494	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	8906537	8906537	+	Missense_Mutation	SNP	A	A	G			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr12:8906537A>G	ENST00000538135.1	+	5	1370	c.545A>G	c.(544-546)cAt>cGt	p.H182R	RIMKLB_ENST00000357529.3_Missense_Mutation_p.H182R|RIMKLB_ENST00000299673.5_3'UTR|RIMKLB_ENST00000535829.1_Missense_Mutation_p.H182R			Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family member B	182	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|citrate-L-glutamate ligase activity (GO:0072591)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)	p.H182R(1)		central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						GATCTAAGCCATCTTATTCGC	0.438																																																	1	Substitution - Missense(1)	kidney(1)											128.0	111.0	117.0					12																	8906537		1894	4129	6023	SO:0001583	missense	57494			AB033064	CCDS41748.1	12p13.31	2011-09-21	2008-10-13	2008-10-13	ENSG00000166532	ENSG00000166532	6.3.2.N6		29228	protein-coding gene	gene with protein product	"""N-acetylaspartyl-glutamate synthetase"""	614054	"""family with sequence similarity 80, member B"""	FAM80B		10574462, 20643647	Standard	XM_006719116		Approved	KIAA1238, NAAGS, NAAGS-I	uc001qux.2	Q9ULI2		ENST00000538135.1:c.545A>G	12.37:g.8906537A>G	ENSP00000440943:p.His182Arg		B7Z834|D3DUV2|Q8N4P4|Q8WTW6	Missense_Mutation	SNP	ENST00000538135.1	37	CCDS41748.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.247172	0.80024	.	.	ENSG00000166532	ENST00000535829;ENST00000357529;ENST00000538135	.	.	.	4.83	4.83	0.62350	ATP-grasp fold (1);ATP-grasp fold, RimK-type (1);ATP-grasp fold, subdomain 1 (1);	0.000000	0.85682	U	0.000000	T	0.56140	0.1965	L	0.38838	1.175	0.80722	D	1	B;B	0.23490	0.031;0.086	B;B	0.32289	0.088;0.143	T	0.58222	-0.7674	9	0.62326	D	0.03	.	13.5059	0.61483	1.0:0.0:0.0:0.0	.	182;182	Q9ULI2-2;Q9ULI2	.;RIMKB_HUMAN	R	182	.	ENSP00000350136:H182R	H	+	2	0	RIMKLB	8797804	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.360000	0.90095	1.927000	0.55829	0.482000	0.46254	CAT		0.438	RIMKLB-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398874.1		NM_020734	
RNF115	27246	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	145684607	145684607	+	Missense_Mutation	SNP	C	C	G	rs377184933		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr1:145684607C>G	ENST00000369291.5	+	7	800	c.596C>G	c.(595-597)aCa>aGa	p.T199R		NM_014455.2	NP_055270.1			ring finger protein 115									p.T199R(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13						CTGGAAAACACAGGCCCTCCC	0.433																																																	1	Substitution - Missense(1)	kidney(1)											79.0	79.0	79.0					1																	145684607		2203	4300	6503	SO:0001583	missense	27246			AF419857	CCDS72863.1	1q12	2013-01-09	2008-06-16	2008-06-16	ENSG00000121848	ENSG00000265491		"""RING-type (C3HC4) zinc fingers"""	18154	protein-coding gene	gene with protein product			"""zinc finger protein 364"""	ZNF364			Standard	NM_014455		Approved	CL469780	uc001eoj.3	Q9Y4L5	OTTHUMG00000013758	ENST00000369291.5:c.596C>G	1.37:g.145684607C>G	ENSP00000358297:p.Thr199Arg			Missense_Mutation	SNP	ENST00000369291.5	37	CCDS922.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.713353	0.89112	.	.	ENSG00000121848	ENST00000369291	T	0.12672	2.66	5.2	5.2	0.72013	.	0.051402	0.85682	D	0.000000	T	0.10252	0.0251	L	0.41573	1.285	0.80722	D	1	P	0.50272	0.933	P	0.49665	0.618	T	0.17077	-1.0381	10	0.18710	T	0.47	-9.1469	16.28	0.82672	0.0:1.0:0.0:0.0	.	199	Q9Y4L5	RN115_HUMAN	R	199	ENSP00000358297:T199R	ENSP00000358297:T199R	T	+	2	0	RNF115	144395964	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.195000	0.77798	2.691000	0.91804	0.655000	0.94253	ACA		0.433	RNF115-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038554.2		NM_014455	
RNF213	57674	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	78328249	78328249	+	Silent	SNP	T	T	C			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr17:78328249T>C	ENST00000582970.1	+	36	10878	c.10735T>C	c.(10735-10737)Ttg>Ctg	p.L3579L	RNF213_ENST00000508628.2_Silent_p.L3628L|CTD-2047H16.4_ENST00000575034.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000336301.6_Silent_p.L1652L	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3579					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L3628L(1)|p.L1652L(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			AGCCTCTTTCTTGCGGGTATC	0.547																																																	2	Substitution - coding silent(2)	kidney(2)											95.0	89.0	91.0					17																	78328249		2203	4300	6503	SO:0001819	synonymous_variant	57674			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.10735T>C	17.37:g.78328249T>C			C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																				0.547	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1		NM_020914	
RTN3	10313	broad.mit.edu	37	11	63517659	63517659	+	Silent	SNP	C	C	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr11:63517659C>A	ENST00000377819.5	+	4	2881	c.2727C>A	c.(2725-2727)ggC>ggA	p.G909G	RTN3_ENST00000356000.3_Silent_p.G132G|RTN3_ENST00000339997.4_Silent_p.G890G|RTN3_ENST00000537981.1_Silent_p.G113G|RTN3_ENST00000354497.4_Silent_p.G113G|RTN3_ENST00000341307.2_Silent_p.G113G|RTN3_ENST00000540798.1_Silent_p.G797G	NM_001265589.1	NP_001252518.1	O95197	RTN3_HUMAN	reticulon 3	909	Reticulon. {ECO:0000255|PROSITE- ProRule:PRU00170}.				apoptotic process (GO:0006915)|endoplasmic reticulum tubular network organization (GO:0071786)|response to stress (GO:0006950)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.G132G(1)|p.G890G(1)|p.G113G(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	20						CAGAAGAAGGCCATCCATTCA	0.428																																																	3	Substitution - coding silent(3)	kidney(3)											85.0	65.0	71.0					11																	63517659		2201	4298	6499	SO:0001819	synonymous_variant	10313			AF059524	CCDS8048.1, CCDS8049.1, CCDS8050.1, CCDS41664.1, CCDS58141.1, CCDS58142.1, CCDS58143.1	11q13	2011-01-14			ENSG00000133318	ENSG00000133318			10469	protein-coding gene	gene with protein product	"""neuroendocrine-specific protein-like 2"", ""NSP-like protein II"", ""isoforme III"", ""ASY interacting protein"", ""homolog of ASY protein"""	604249				10331947	Standard	NM_006054		Approved	NSPL2, NSPLII, ASYIP, HAP, RTN3-A1	uc001nxq.3	O95197		ENST00000377819.5:c.2727C>A	11.37:g.63517659C>A			B3KQS2|B7Z308|B7Z4M0|F5H774|Q147U9|Q496K2|Q53GN3|Q59EP0|Q5UEP2|Q6T930|Q7RTM7|Q7RTM8|Q7RTN3	Silent	SNP	ENST00000377819.5	37	CCDS58141.1																																																																																				0.428	RTN3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397846.1		NM_006054	
SALL3	27164	broad.mit.edu	37	18	76752286	76752286	+	Missense_Mutation	SNP	C	C	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr18:76752286C>A	ENST00000537592.2	+	2	295	c.295C>A	c.(295-297)Ccc>Acc	p.P99T	SALL3_ENST00000536229.3_5'UTR|SALL3_ENST00000575389.2_Missense_Mutation_p.P99T	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	99					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P99T(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		CGAGCCTTCGCCCGCCAGCTC	0.761																																																	1	Substitution - Missense(1)	kidney(1)											5.0	7.0	6.0					18																	76752286		1964	3860	5824	SO:0001583	missense	27164			AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"""Zinc fingers, C2H2-type"""	10527	protein-coding gene	gene with protein product		605079	"""sal (Drosophila)-like 3"", ""sal-like 3 (Drosophila)"""			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.295C>A	18.37:g.76752286C>A	ENSP00000441823:p.Pro99Thr		Q9UGH1	Missense_Mutation	SNP	ENST00000537592.2	37	CCDS12013.1	.	.	.	.	.	.	.	.	.	.	C	10.72	1.428366	0.25726	.	.	ENSG00000256463	ENST00000537592;ENST00000536229	T	0.10860	2.83	4.43	4.43	0.53597	.	0.000000	0.53938	D	0.000060	T	0.29190	0.0726	M	0.72894	2.215	0.80722	D	1	D	0.76494	0.999	D	0.64144	0.922	T	0.04650	-1.0936	10	0.23302	T	0.38	-29.6515	17.412	0.87488	0.0:1.0:0.0:0.0	.	99	Q9BXA9	SALL3_HUMAN	T	99	ENSP00000441823:P99T	ENSP00000299466:P99T	P	+	1	0	SALL3	74853274	1.000000	0.71417	0.085000	0.20634	0.021000	0.10359	5.355000	0.66046	2.194000	0.70268	0.491000	0.48974	CCC		0.761	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1		NM_171999	
SALL4	57167	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	50407915	50407915	+	Silent	SNP	C	C	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr20:50407915C>A	ENST00000217086.4	-	2	1218	c.1107G>T	c.(1105-1107)gtG>gtT	p.V369V	SALL4_ENST00000371539.3_Intron|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000395997.3_Silent_p.V369V	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	369					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V369V(1)		endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GTTTGACATCCACCGCGGAGA	0.567																																																	1	Substitution - coding silent(1)	kidney(1)											76.0	74.0	75.0					20																	50407915		2203	4300	6503	SO:0001819	synonymous_variant	57167			AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.1107G>T	20.37:g.50407915C>A			A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																				0.567	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			
SIRT1	23411	hgsc.bcm.edu;ucsc.edu	37	10	69672600	69672600	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr10:69672600delA	ENST00000212015.6	+	8	1780	c.1727delA	c.(1726-1728)gaafs	p.E577fs	SIRT1_ENST00000406900.1_Frame_Shift_Del_p.E274fs|SIRT1_ENST00000432464.1_Frame_Shift_Del_p.E282fs|SIRT1_ENST00000403579.1_Frame_Shift_Del_p.E274fs	NM_012238.4	NP_036370.2	Q96EB6	SIR1_HUMAN	sirtuin 1	577					angiogenesis (GO:0001525)|cell aging (GO:0007569)|cellular glucose homeostasis (GO:0001678)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to starvation (GO:0009267)|cellular response to tumor necrosis factor (GO:0071356)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|chromatin organization (GO:0006325)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|establishment of chromatin silencing (GO:0006343)|fatty acid homeostasis (GO:0055089)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of chromatin silencing (GO:0006344)|methylation-dependent chromatin silencing (GO:0006346)|muscle organ development (GO:0007517)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of cell growth (GO:0030308)|negative regulation of cellular response to testosterone stimulus (GO:2000655)|negative regulation of cellular senescence (GO:2000773)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of helicase activity (GO:0051097)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of neuron death (GO:1901215)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostaglandin biosynthetic process (GO:0031393)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|ovulation from ovarian follicle (GO:0001542)|peptidyl-lysine acetylation (GO:0018394)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular senescence (GO:2000774)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of chromatin silencing (GO:0031937)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of macroautophagy (GO:0016239)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deacetylation (GO:0006476)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cell proliferation (GO:0042127)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of glucose metabolic process (GO:0010906)|regulation of mitotic cell cycle (GO:0007346)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of smooth muscle cell apoptotic process (GO:0034391)|response to hydrogen peroxide (GO:0042542)|response to insulin (GO:0032868)|response to oxidative stress (GO:0006979)|rRNA processing (GO:0006364)|single strand break repair (GO:0000012)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|triglyceride mobilization (GO:0006642)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|rDNA heterochromatin (GO:0033553)	bHLH transcription factor binding (GO:0043425)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|histone deacetylase activity (GO:0004407)|HLH domain binding (GO:0043398)|identical protein binding (GO:0042802)|keratin filament binding (GO:1990254)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent protein deacetylase activity (GO:0034979)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|protein deacetylase activity (GO:0033558)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	14						GGTTGTATGGAAGAAAAACCA	0.383																																																	0													97.0	100.0	99.0					10																	69672600		2203	4300	6503	SO:0001589	frameshift_variant	23411			AF083106	CCDS7273.1, CCDS44412.1	10q21	2010-06-25	2010-06-25		ENSG00000096717	ENSG00000096717			14929	protein-coding gene	gene with protein product		604479	"""sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 1"", ""sirtuin (silent mating type information regulation 2 homolog) 1 (S. cerevisiae)"""			10381378	Standard	NM_012238		Approved	SIR2L1	uc001jnd.3	Q96EB6	OTTHUMG00000018340	ENST00000212015.6:c.1727delA	10.37:g.69672600delA	ENSP00000212015:p.Glu577fs		Q2XNF6|Q5JVQ0|Q9GZR9|Q9Y6F0	Frame_Shift_Del	DEL	ENST00000212015.6	37	CCDS7273.1																																																																																				0.383	SIRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048296.1			
SLC15A1	6564	broad.mit.edu;ucsc.edu	37	13	99361816	99361824	+	Splice_Site	DEL	CGTCACCTA	CGTCACCTA	-	rs201817346|rs374337231		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	CGTCACCTA	CGTCACCTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr13:99361816_99361824delCGTCACCTA	ENST00000376503.5	-	14	1123		c.e14+1			NM_005073.3	NP_005064.1	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide transporter), member 1						digestion (GO:0007586)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	peptide:proton symporter activity (GO:0015333)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Captopril(DB01197)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftizoxime(DB01332)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Enalapril(DB00584)|Fluvastatin(DB01095)|Fosinopril(DB00492)|Glyburide(DB01016)|L-DOPA(DB01235)|Lisinopril(DB00722)|Methyldopa(DB00968)|Midodrine(DB00211)|Moexipril(DB00691)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CCAACCCACCCGTCACCTACGTGAAATTG	0.574																																																	0																																										SO:0001630	splice_region_variant	6564			U13173	CCDS9489.1	13q32.3	2013-05-22			ENSG00000088386	ENSG00000088386		"""Solute carriers"""	10920	protein-coding gene	gene with protein product	"""peptide transporter HPEPT1"", ""bA551M18.1.1 (solute carrier family 15 (oligopeptide transporter) member 1)"", ""solute carrier family 15 oligopeptide transporter member 1"""	600544				7896779	Standard	NM_005073		Approved	PEPT1, HPECT1, HPEPT1	uc001vno.3	P46059	OTTHUMG00000017255	ENST00000376503.5:c.1067+1TAGGTGACG>-	13.37:g.99361816_99361824delCGTCACCTA			Q5VW82	Splice_Site	DEL	ENST00000376503.5	37	CCDS9489.1																																																																																				0.574	SLC15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045560.3		NM_005073	Intron
SMG7	9887	broad.mit.edu;ucsc.edu	37	1	183515189	183515189	+	Missense_Mutation	SNP	A	A	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr1:183515189A>T	ENST00000347615.2	+	17	2578	c.2459A>T	c.(2458-2460)tAc>tTc	p.Y820F	SMG7_ENST00000515829.2_Missense_Mutation_p.Y774F|SMG7_ENST00000456731.2_Missense_Mutation_p.Y732F|SMG7_ENST00000367537.3_Missense_Mutation_p.Y803F|SMG7_ENST00000508461.1_Missense_Mutation_p.Y778F|SMG7_ENST00000507469.1_Missense_Mutation_p.Y774F	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor	820	Gln/Pro-rich.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)	p.Y820F(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						AAACAGCCCTACTACCTTCAG	0.463																																																	1	Substitution - Missense(1)	kidney(1)											78.0	86.0	83.0					1																	183515189		2203	4300	6503	SO:0001583	missense	9887			D87437	CCDS1355.1, CCDS41445.1, CCDS41445.2, CCDS53444.1, CCDS53445.1	1q25	2013-07-02	2013-07-02	2006-02-16	ENSG00000116698	ENSG00000116698			16792	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog C (S. cerevisiae)"""	610964	"""chromosome 1 open reading frame 16"", ""smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C1orf16		14636577, 15721257	Standard	NM_173156		Approved	KIAA0250, EST1C, SGA56M, SMG-7	uc001gqf.3	Q92540	OTTHUMG00000035221	ENST00000347615.2:c.2459A>T	1.37:g.183515189A>T	ENSP00000340766:p.Tyr820Phe		B4DRB2|E9PCI0|E9PEH2|Q5T1Q0|Q6PIE0|Q7Z7H9|Q8IXC1|Q8IXC2	Missense_Mutation	SNP	ENST00000347615.2	37	CCDS1355.1	.	.	.	.	.	.	.	.	.	.	A	11.55	1.671437	0.29693	.	.	ENSG00000116698	ENST00000456731;ENST00000367537;ENST00000508461;ENST00000419169;ENST00000347615;ENST00000507469;ENST00000515829	T;T;T;T;T;T;T	0.22336	2.28;2.26;2.26;1.96;2.26;2.25;2.28	5.62	4.47	0.54385	.	0.586968	0.18821	N	0.130241	T	0.10723	0.0262	N	0.11560	0.145	0.43512	D	0.995775	B;B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.001;0.0	B;B;B;B;B;B	0.04013	0.0;0.0;0.0;0.001;0.0;0.001	T	0.09796	-1.0658	10	0.10377	T	0.69	-1.3608	11.6948	0.51538	0.9302:0.0:0.0698:0.0	.	778;803;732;774;820;774	E9PCI0;E9PD50;E9PCE5;Q92540-2;Q92540;E9PEH2	.;.;.;.;SMG7_HUMAN;.	F	732;803;778;732;820;774;774	ENSP00000407629:Y732F;ENSP00000356507:Y803F;ENSP00000426915:Y778F;ENSP00000388390:Y732F;ENSP00000340766:Y820F;ENSP00000425133:Y774F;ENSP00000421358:Y774F	ENSP00000340766:Y820F	Y	+	2	0	SMG7	181781812	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.670000	0.61583	0.921000	0.36994	0.533000	0.62120	TAC		0.463	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1		NM_014837	
SON	6651	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	21	34922737	34922737	+	Silent	SNP	T	T	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr21:34922737T>A	ENST00000356577.4	+	3	1675	c.1200T>A	c.(1198-1200)acT>acA	p.T400T	SON_ENST00000300278.4_Silent_p.T400T|SON_ENST00000381692.2_Intron|SON_ENST00000290239.6_Silent_p.T400T|SON_ENST00000381679.4_Silent_p.T400T	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	400					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.T400T(2)		breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						CCCCTGTGACTCCAGTGCTGG	0.677																																																	2	Substitution - coding silent(2)	kidney(2)											33.0	39.0	37.0					21																	34922737		2203	4300	6503	SO:0001819	synonymous_variant	6651			AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"""G patch domain containing"""	11183	protein-coding gene	gene with protein product	"""NRE-binding protein"", ""negative regulatory element-binding protein"", ""Bax antagonist selected in Saccharomyces 1"""	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.1200T>A	21.37:g.34922737T>A			D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Silent	SNP	ENST00000356577.4	37	CCDS13629.1																																																																																				0.677	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2		NM_138927	
SORCS3	22986	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	107015522	107015522	+	Silent	SNP	G	G	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr10:107015522G>T	ENST00000369701.3	+	24	3527	c.3300G>T	c.(3298-3300)ggG>ggT	p.G1100G		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	1100					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)	p.G1100G(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TGAAGCCGGGGGTACAAGTCA	0.453																																					NSCLC(116;1497 1690 7108 13108 14106)												1	Substitution - coding silent(1)	kidney(1)											120.0	104.0	109.0					10																	107015522		2203	4300	6503	SO:0001819	synonymous_variant	22986			AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.3300G>T	10.37:g.107015522G>T			Q5VXF9|Q9NQJ2	Silent	SNP	ENST00000369701.3	37	CCDS7558.1																																																																																				0.453	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1		NM_014978	
TCP10	6953	hgsc.bcm.edu	37	6	167789488	167789488	+	Silent	SNP	C	C	T	rs9355636	byFrequency	TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr6:167789488C>T	ENST00000397829.4	-	6	821	c.654G>A	c.(652-654)acG>acA	p.T218T	TCP10_ENST00000366827.2_Silent_p.T218T	NM_004610.3	NP_004601.3	Q12799	TCP10_HUMAN	t-complex 10	245						cytosol (GO:0005829)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(6)	18		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)|GBM - Glioblastoma multiforme(31;0.0386)		GCTCCTGCAGCGTGGTGGCCT	0.577																																																	0													22.0	27.0	25.0					6																	167789488		1978	4165	6143	SO:0001819	synonymous_variant	6953			U03399	CCDS43527.1	6q27	2012-09-20	2012-09-20		ENSG00000203690	ENSG00000203690			11656	protein-coding gene	gene with protein product		187020	"""t-complex 10 (a murine tcp homolog)"", ""t-complex 10 (mouse)"", ""t-complex 10 homolog (mouse)"""			8111376	Standard	NM_004610		Approved		uc003qvv.1	Q12799	OTTHUMG00000016026	ENST00000397829.4:c.654G>A	6.37:g.167789488C>T			Q5JR60|Q6P4F4	Silent	SNP	ENST00000397829.4	37	CCDS43527.1																																																																																				0.577	TCP10-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365570.1		NM_004610	
TEX13A	56157	hgsc.bcm.edu	37	X	104464282	104464282	+	Splice_Site	DEL	C	C	-	rs56118606|rs367644904		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chrX:104464282delC	ENST00000413579.1	-	4	706	c.595delG	c.(595-597)gat>at	p.D199fs	TEX13A_ENST00000372575.1_Frame_Shift_Del_p.G199fs|IL1RAPL2_ENST00000372582.1_Intron|IL1RAPL2_ENST00000344799.4_Intron|TEX13A_ENST00000372578.3_Frame_Shift_Del_p.G199fs			Q9BXU3	TX13A_HUMAN	testis expressed 13A	199							zinc ion binding (GO:0008270)			large_intestine(5)|ovary(2)|upper_aerodigestive_tract(1)	8						CCTCCAACATCCCCTCTGCTC	0.652																																																	0													3.0	4.0	4.0					X																	104464282		1657	3597	5254	SO:0001630	splice_region_variant	56157			AF285597	CCDS76005.1	Xq28	2012-04-20	2007-03-13		ENSG00000133149	ENSG00000268629			11735	protein-coding gene	gene with protein product		300312	"""testis expressed sequence 13A"""			11279525	Standard	NM_031274		Approved		uc004ema.3	Q9BXU3	OTTHUMG00000022133	ENST00000413579.1:c.595-1G>-	X.37:g.104464282delC			B1B1G8|Q32NB6	Frame_Shift_Del	DEL	ENST00000413579.1	37																																																																																					0.652	TEX13A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			NM_031274	Frame_Shift_Del
TOPBP1	11073	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	133342007	133342007	+	Missense_Mutation	SNP	C	C	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr3:133342007C>T	ENST00000260810.5	-	19	3237	c.3106G>A	c.(3106-3108)Gta>Ata	p.V1036I		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1036					cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)	p.V1036I(1)|p.V949I(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						ATATTGTCTACATCATTTTCT	0.284								Other conserved DNA damage response genes																													Ovarian(21;193 658 4424 15423 17362)												2	Substitution - Missense(2)	kidney(2)											38.0	36.0	37.0					3																	133342007		1808	4060	5868	SO:0001583	missense	11073			AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.3106G>A	3.37:g.133342007C>T	ENSP00000260810:p.Val1036Ile		B7Z7W8|Q7LGC1|Q9UEB9	Missense_Mutation	SNP	ENST00000260810.5	37	CCDS46919.1	.	.	.	.	.	.	.	.	.	.	C	6.351	0.432937	0.12045	.	.	ENSG00000163781	ENST00000260810	T	0.11495	2.77	5.82	-4.7	0.03288	.	1.445680	0.03600	N	0.233264	T	0.05044	0.0135	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.40813	-0.9543	10	0.36615	T	0.2	.	9.6138	0.39679	0.0:0.525:0.2153:0.2597	.	949;1036	A0AV47;Q92547	.;TOPB1_HUMAN	I	1036	ENSP00000260810:V1036I	ENSP00000260810:V1036I	V	-	1	0	TOPBP1	134824697	0.000000	0.05858	0.001000	0.08648	0.581000	0.36288	-1.163000	0.03138	-0.732000	0.04856	0.655000	0.94253	GTA		0.284	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1		NM_007027	
UBR2	23304	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	42604791	42604791	+	Silent	SNP	C	C	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr6:42604791C>T	ENST00000372899.1	+	15	1975	c.1717C>T	c.(1717-1719)Ctg>Ttg	p.L573L	UBR2_ENST00000372883.3_Silent_p.L77L|UBR2_ENST00000372901.1_Silent_p.L573L	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	573					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L573L(1)		breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			TCTCGCTGTACTGATGCAGTG	0.373																																																	1	Substitution - coding silent(1)	kidney(1)											163.0	145.0	151.0					6																	42604791		2203	4300	6503	SO:0001819	synonymous_variant	23304			BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.1717C>T	6.37:g.42604791C>T			O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Silent	SNP	ENST00000372899.1	37	CCDS4870.1																																																																																				0.373	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2		NM_015255	
UGT1A4	54657	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	234627516	234627516	+	Missense_Mutation	SNP	T	T	C			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr2:234627516T>C	ENST00000373409.3	+	1	93	c.50T>C	c.(49-51)cTg>cCg	p.L17P	UGT1A6_ENST00000480628.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A10_ENST00000373445.1_Intron	NM_007120.2	NP_009051.1	P22310	UD14_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A4	17					cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.L17P(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	26		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;3.49e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000504)|Lung(119;0.0026)|LUSC - Lung squamous cell carcinoma(224;0.00624)	Asenapine(DB06216)|Clozapine(DB00363)|Ezogabine(DB04953)|Lamotrigine(DB00555)|Midazolam(DB00683)|Paricalcitol(DB00910)|Tamoxifen(DB00675)|Trifluoperazine(DB00831)|Valproic Acid(DB00313)	ACAGGACTGCTGCTCCTCCTC	0.657											OREG0003834	type=REGULATORY REGION|Gene=UGT1A4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									Melanoma(99;1011 1962 13201 26492)												1	Substitution - Missense(1)	kidney(1)											49.0	48.0	49.0					2																	234627516		2203	4300	6503	SO:0001583	missense	54657			M84128	CCDS33405.1	2q37.1	2014-01-10	2005-07-20		ENSG00000244474	ENSG00000244474		"""UDP glucuronosyltransferases"""	12536	other	complex locus constituent		606429	"""UDP glycosyltransferase 1 family, polypeptide A4"""			9295054, 1339448	Standard	NM_007120		Approved	HUG-BR2, UGT1D	uc002vux.3	P22310	OTTHUMG00000059119	ENST00000373409.3:c.50T>C	2.37:g.234627516T>C	ENSP00000362508:p.Leu17Pro	2375	B2R937|B8K288|Q5DT00	Missense_Mutation	SNP	ENST00000373409.3	37	CCDS33405.1	.	.	.	.	.	.	.	.	.	.	T	19.75	3.886145	0.72410	.	.	ENSG00000244474	ENST00000373409	T	0.64085	-0.08	4.14	4.14	0.48551	.	.	.	.	.	T	0.77398	0.4124	M	0.74467	2.265	0.58432	D	0.999992	D;D	0.76494	0.998;0.999	D;D	0.79784	0.993;0.959	T	0.80826	-0.1209	9	0.87932	D	0	.	13.4335	0.61071	0.0:0.0:0.0:1.0	.	17;17	B8K288;P22310	.;UD14_HUMAN	P	17	ENSP00000362508:L17P	ENSP00000362508:L17P	L	+	2	0	UGT1A4	234292255	0.031000	0.19500	0.037000	0.18230	0.131000	0.20780	2.353000	0.44089	1.621000	0.50320	0.402000	0.26972	CTG		0.657	UGT1A4-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130984.1		NM_007120	
GLUD1P2	100381203	broad.mit.edu	37	10	48968566	48968566	+	RNA	SNP	A	A	G	rs201727873		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr10:48968566A>G	ENST00000594520.1	+	0	723									glutamate dehydrogenase 1 pseudogene 2																		ACAGGATAACAAACTGGAAAA	0.318																																																	0																																												0			X66313, X66315, X66319		10q11.22	2013-02-15	2010-01-18	2010-01-18	ENSG00000227781				4337	pseudogene	pseudogene			"""glutamate dehydrogenase pseudogene 2"""	GLUDP2		8486350	Standard			Approved				OTTHUMG00000018156		10.37:g.48968566A>G				RNA	SNP	ENST00000594520.1	37																																																																																					0.318	GLUD1P2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000461126.1		NG_016765	
UPRT	139596	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	74517350	74517350	+	Missense_Mutation	SNP	T	T	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chrX:74517350T>A	ENST00000373383.4	+	4	691	c.524T>A	c.(523-525)tTt>tAt	p.F175Y	UPRT_ENST00000531704.1_3'UTR|UPRT_ENST00000530743.1_Missense_Mutation_p.F39Y|UPRT_ENST00000373379.1_Missense_Mutation_p.F175Y	NM_145052.3	NP_659489.1	Q96BW1	UPP_HUMAN	uracil phosphoribosyltransferase (FUR1) homolog (S. cerevisiae)	175					female pregnancy (GO:0007565)|lactation (GO:0007595)|response to insulin (GO:0032868)|UMP biosynthetic process (GO:0006222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.F175Y(1)		breast(1)|endometrium(7)|kidney(2)|large_intestine(4)|lung(4)	18						GGAGTGAAATTTGAGAAGGGA	0.368																																																	1	Substitution - Missense(1)	kidney(1)											214.0	197.0	203.0					X																	74517350		2203	4300	6503	SO:0001583	missense	139596			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.524T>A	X.37:g.74517350T>A	ENSP00000362481:p.Phe175Tyr		Q5JRL1|Q5JRL3|Q68DN0|Q96MW2	Missense_Mutation	SNP	ENST00000373383.4	37	CCDS14429.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.238239	0.79800	.	.	ENSG00000094841	ENST00000373383;ENST00000373379;ENST00000530743	D;D;D	0.91577	-2.87;-2.87;-2.87	5.24	4.05	0.47172	.	0.000000	0.85682	D	0.000000	D	0.89952	0.6864	L	0.35593	1.075	0.58432	D	0.999991	P;P	0.39862	0.692;0.692	P;P	0.53593	0.73;0.73	D	0.87349	0.2336	10	0.44086	T	0.13	-17.7988	10.3985	0.44216	0.0:0.0:0.1624:0.8376	.	175;175	A8KAF9;Q96BW1	.;UPP_HUMAN	Y	175;175;39	ENSP00000362481:F175Y;ENSP00000362477:F175Y;ENSP00000434037:F39Y	ENSP00000362477:F175Y	F	+	2	0	UPRT	74434075	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.649000	0.83500	0.629000	0.30376	0.486000	0.48141	TTT		0.368	UPRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057278.1		NM_145052	
VHL	7428	broad.mit.edu;ucsc.edu	37	3	10191499	10191499	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr3:10191499delG	ENST00000256474.2	+	3	1332	c.492delG	c.(490-492)cagfs	p.Q164fs	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Frame_Shift_Del_p.Q123fs	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	164	Interaction with Elongin BC complex.		Q -> H (in VHLD).|Q -> R (in VHLD; type II). {ECO:0000269|PubMed:8825918, ECO:0000269|PubMed:8956040}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.Q164H(3)|p.Q164fs*9(2)|p.V165fs*5(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GATGCCTCCAGGTTGTCCGGA	0.507		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	6	Substitution - Missense(3)|Deletion - Frameshift(3)	kidney(4)|adrenal_gland(2)	GRCh37	CM031757|CM074631	VHL	M							92.0	83.0	86.0					3																	10191499		2203	4300	6503	SO:0001589	frameshift_variant	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.492delG	3.37:g.10191499delG	ENSP00000256474:p.Gln164fs		B2RE45|Q13599|Q6PDA9	Frame_Shift_Del	DEL	ENST00000256474.2	37	CCDS2597.1																																																																																				0.507	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
WDR93	56964	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	90276249	90276249	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr15:90276249G>T	ENST00000268130.7	+	13	1444	c.1343G>T	c.(1342-1344)gGg>gTg	p.G448V	WDR93_ENST00000444934.2_Missense_Mutation_p.G165V|WDR93_ENST00000560294.1_Intron	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	448					electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)	p.G448V(1)		NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			TTCCCTCTTGGGGTCGCTGCT	0.507																																																	1	Substitution - Missense(1)	kidney(1)											96.0	107.0	104.0					15																	90276249		2200	4299	6499	SO:0001583	missense	56964				CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"""WD repeat domain containing"""	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.1343G>T	15.37:g.90276249G>T	ENSP00000268130:p.Gly448Val		Q8N7Y8|Q9NP89	Missense_Mutation	SNP	ENST00000268130.7	37	CCDS32326.1	.	.	.	.	.	.	.	.	.	.	G	18.13	3.555866	0.65425	.	.	ENSG00000140527	ENST00000268130;ENST00000444934	T;T	0.28666	1.6;2.39	5.73	3.68	0.42216	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.186928	0.37393	N	0.002117	T	0.47358	0.1441	M	0.70595	2.14	0.51482	D	0.999928	D	0.67145	0.996	P	0.59703	0.862	T	0.38908	-0.9639	10	0.40728	T	0.16	-29.6015	12.7926	0.57543	0.0:0.2414:0.7586:0.0	.	448	Q6P2C0	WDR93_HUMAN	V	448;165	ENSP00000268130:G448V;ENSP00000403871:G165V	ENSP00000268130:G448V	G	+	2	0	WDR93	88077253	0.999000	0.42202	0.983000	0.44433	0.984000	0.73092	1.180000	0.32005	2.710000	0.92621	0.644000	0.83932	GGG		0.507	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1		NM_020212	
ZNF181	339318	broad.mit.edu;hgsc.bcm.edu	37	19	35232767	35232767	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr19:35232767G>A	ENST00000492450.1	+	4	1570	c.1481G>A	c.(1480-1482)tGt>tAt	p.C494Y	ZNF181_ENST00000392232.3_Missense_Mutation_p.C538Y|ZNF181_ENST00000459757.2_Missense_Mutation_p.C493Y			Q2M3W8	ZN181_HUMAN	zinc finger protein 181	494					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C430Y(1)		endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(1)	22	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			TGTATTAAATGTGGGAAGACC	0.393																																																	1	Substitution - Missense(1)	kidney(1)											50.0	55.0	53.0					19																	35232767		2203	4300	6503	SO:0001583	missense	339318			BC104759, H54888	CCDS32990.2, CCDS46043.1	19q13.13	2013-01-08	2006-04-27		ENSG00000197841	ENSG00000197841		"""Zinc fingers, C2H2-type"", ""-"""	12971	protein-coding gene	gene with protein product		606741	"""zinc finger protein 181 (HHZ181)"""				Standard	NM_001029997		Approved	HHZ181, MGC44316	uc002nvu.3	Q2M3W8	OTTHUMG00000157508	ENST00000492450.1:c.1481G>A	19.37:g.35232767G>A	ENSP00000420727:p.Cys494Tyr		B7ZKX3|Q49A75	Missense_Mutation	SNP	ENST00000492450.1	37	CCDS32990.2	.	.	.	.	.	.	.	.	.	.	G	17.25	3.343079	0.61073	.	.	ENSG00000197841	ENST00000392232;ENST00000492450;ENST00000459757	D;D;D	0.85861	-2.04;-2.04;-2.04	3.12	3.12	0.35913	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94152	0.8124	H	0.96365	3.81	0.43025	D	0.994586	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.95346	0.8442	9	0.87932	D	0	.	12.4995	0.55948	0.0:0.0:1.0:0.0	.	493;494	B7ZKX3;Q2M3W8	.;ZN181_HUMAN	Y	538;494;493	ENSP00000376065:C538Y;ENSP00000420727:C494Y;ENSP00000419435:C493Y	ENSP00000376065:C538Y	C	+	2	0	ZNF181	39924607	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	8.284000	0.89912	2.041000	0.60428	0.655000	0.94253	TGT		0.393	ZNF181-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349005.3		NM_001029997	
ZNF395	55893	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	28206286	28206286	+	Missense_Mutation	SNP	A	A	G			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2c3c0f78-1c0a-48df-856e-0afbc2b5bceb	27bc1b1e-8214-4a64-95e7-9f94a435ed49	g.chr8:28206286A>G	ENST00000344423.5	-	10	1623	c.1492T>C	c.(1492-1494)Tgg>Cgg	p.W498R	ZNF395_ENST00000523095.1_Missense_Mutation_p.W498R|ZNF395_ENST00000523202.1_Missense_Mutation_p.W498R	NM_018660.2	NP_061130.1	Q9H8N7	ZN395_HUMAN	zinc finger protein 395	498					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.W498R(1)		cervix(1)|endometrium(1)|kidney(5)|large_intestine(6)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)		GCCGTGCACCACTGGTCCCGG	0.617																																																	1	Substitution - Missense(1)	kidney(1)											65.0	64.0	64.0					8																	28206286		2203	4300	6503	SO:0001583	missense	55893			AB044750	CCDS6067.1	8p21	2008-05-02			ENSG00000186918	ENSG00000186918		"""Zinc fingers, C2H2-type"""	18737	protein-coding gene	gene with protein product		609494				14625278	Standard	NM_018660		Approved	PRF-1, HDBP2, PBF, DKFZp434K1210	uc003xgr.3	Q9H8N7	OTTHUMG00000102137	ENST00000344423.5:c.1492T>C	8.37:g.28206286A>G	ENSP00000340494:p.Trp498Arg		B3KUY7|D3DST4|Q6F6H2|Q9BY72|Q9NPB2|Q9NS57|Q9NS58|Q9NS59	Missense_Mutation	SNP	ENST00000344423.5	37	CCDS6067.1	.	.	.	.	.	.	.	.	.	.	A	29.0	4.967128	0.92855	.	.	ENSG00000186918	ENST00000344423;ENST00000523202;ENST00000523095	T;T;T	0.35421	1.31;1.31;1.31	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.64249	0.2581	M	0.85630	2.765	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.70360	-0.4893	10	0.87932	D	0	-14.0604	14.0022	0.64439	1.0:0.0:0.0:0.0	.	498	Q9H8N7	ZN395_HUMAN	R	498	ENSP00000340494:W498R;ENSP00000429640:W498R;ENSP00000428452:W498R	ENSP00000340494:W498R	W	-	1	0	ZNF395	28262205	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.960000	0.93117	2.197000	0.70478	0.528000	0.53228	TGG		0.617	ZNF395-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219976.1			
