#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_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_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
ITGA8	8516	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	15559198	15559198	+	Missense_Mutation	SNP	C	C	T	rs561911227		TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr10:15559198C>T	ENST00000378076.3	-	30	3504	c.3151G>A	c.(3151-3153)Gac>Aac	p.D1051N		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	1051					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)			NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						TGTTCCCTGTCGGTCATGTCC	0.443													C|||	1	0.000199681	0.0008	0.0	5008	,	,		14264	0.0		0.0	False		,,,				2504	0.0															0													84.0	80.0	81.0					10																	15559198		2203	4300	6503	SO:0001583	missense	8516			L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"""Integrins"""	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.3151G>A	10.37:g.15559198C>T	ENSP00000367316:p.Asp1051Asn		B0YJ31|Q5VX94	Missense_Mutation	SNP	ENST00000378076.3	37	CCDS31155.1	.	.	.	.	.	.	.	.	.	.	C	18.29	3.591940	0.66219	.	.	ENSG00000077943	ENST00000378076;ENST00000538044	T	0.78003	-1.14	5.74	5.74	0.90152	.	0.046141	0.85682	D	0.000000	D	0.85665	0.5749	L	0.56199	1.76	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.72338	0.977;0.95	D	0.84641	0.0695	10	0.45353	T	0.12	.	18.0979	0.89497	0.0:1.0:0.0:0.0	.	1036;1051	F5H818;P53708	.;ITA8_HUMAN	N	1051;1036	ENSP00000367316:D1051N	ENSP00000367316:D1051N	D	-	1	0	ITGA8	15599204	1.000000	0.71417	0.932000	0.37286	0.018000	0.09664	6.197000	0.72100	2.707000	0.92482	0.563000	0.77884	GAC		0.443	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638		21	36	21	36
GALNT18	374378	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	11642953	11642953	+	Missense_Mutation	SNP	A	A	G			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr11:11642953A>G	ENST00000227756.4	-	1	599	c.188T>C	c.(187-189)aTt>aCt	p.I63T	GALNT18_ENST00000526064.1_5'UTR	NM_198516.2	NP_940918.2	Q6P9A2	GLT18_HUMAN	polypeptide N-acetylgalactosaminyltransferase 18	63					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										CAGCCGCTCAATAATCTTCAG	0.622																																																0													135.0	126.0	129.0					11																	11642953		2201	4294	6495	SO:0001583	missense	374378			AK055111	CCDS7807.1	11p15	2014-03-13	2014-03-13	2013-01-25	ENSG00000110328	ENSG00000110328	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	30488	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 18"""	615136	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 4"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18"""	GALNTL4		22186971	Standard	NM_198516		Approved	MGC71806, GALNT15, GalNAc-T18	uc001mjo.2	Q6P9A2	OTTHUMG00000165707	ENST00000227756.4:c.188T>C	11.37:g.11642953A>G	ENSP00000227756:p.Ile63Thr		O95903|Q8NDY9	Missense_Mutation	SNP	ENST00000227756.4	37	CCDS7807.1	.	.	.	.	.	.	.	.	.	.	A	17.94	3.510853	0.64522	.	.	ENSG00000110328	ENST00000227756	T	0.56444	0.46	5.02	5.02	0.67125	.	0.189401	0.30575	N	0.009328	T	0.40619	0.1124	L	0.34521	1.04	0.45502	D	0.998464	B	0.23058	0.079	B	0.14578	0.011	T	0.22556	-1.0213	10	0.23891	T	0.37	.	13.6929	0.62559	1.0:0.0:0.0:0.0	.	63	Q6P9A2	GLTL4_HUMAN	T	63	ENSP00000227756:I63T	ENSP00000227756:I63T	I	-	2	0	GALNTL4	11599529	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.757000	0.91657	2.103000	0.63969	0.459000	0.35465	ATT		0.622	GALNT18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385848.1	NM_198516		62	141	62	141
GIF	2694	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	59611461	59611461	+	Silent	SNP	T	T	C			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr11:59611461T>C	ENST00000257248.2	-	2	194	c.147A>G	c.(145-147)tcA>tcG	p.S49S	GIF_ENST00000541311.1_Silent_p.S24S	NM_005142.2	NP_005133.2	P27352	IF_HUMAN	gastric intrinsic factor (vitamin B synthesis)	49					cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|lysosomal lumen (GO:0043202)|microvillus (GO:0005902)	cobalamin binding (GO:0031419)			large_intestine(4)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	17					Cyanocobalamin(DB00115)	GGTAGGCTGATGAAGTCACCG	0.522																																					NSCLC(53;1139 1245 16872 38474 42853)											0													129.0	112.0	118.0					11																	59611461		2201	4295	6496	SO:0001819	synonymous_variant	2694			X76562	CCDS7977.1	11q12.1	2013-09-20			ENSG00000134812	ENSG00000134812			4268	protein-coding gene	gene with protein product		609342				2071148	Standard	NM_005142		Approved	TCN3, IF, IFMH, INF	uc001noi.3	P27352	OTTHUMG00000167399	ENST00000257248.2:c.147A>G	11.37:g.59611461T>C			B2RAN8|B4DVZ1	Silent	SNP	ENST00000257248.2	37	CCDS7977.1																																																																																				0.522	GIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394497.1	NM_005142		15	64	15	64
BTG4	54766	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	111365994	111365994	+	Missense_Mutation	SNP	G	G	A	rs140812937	byFrequency	TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr11:111365994G>A	ENST00000356018.2	-	5	755	c.556C>T	c.(556-558)Cgc>Tgc	p.R186C		NM_017589.3	NP_060059.1	Q9NY30	BTG4_HUMAN	B-cell translocation gene 4	186					cell cycle arrest (GO:0007050)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|neuron differentiation (GO:0030182)			p.R186C(1)		large_intestine(2)|upper_aerodigestive_tract(1)	3		all_cancers(61;3.78e-13)|all_epithelial(67;5.29e-08)|Melanoma(852;3.15e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0204)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.22e-06)|BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|all cancers(92;2.18e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0509)		TTCTTTTTGCGGGGGATTTGT	0.448																																																1	Substitution - Missense(1)	large_intestine(1)						G	CYS/ARG	0,4402		0,0,2201	83.0	79.0	81.0		556	0.6	0.0	11	dbSNP_134	81	3,8591	3.0+/-9.4	0,3,4294	no	missense	BTG4	NM_017589.2	180	0,3,6495	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging	186/224	111365994	3,12993	2201	4297	6498	SO:0001583	missense	54766			AJ271351	CCDS8346.1	11q23	2008-05-27				ENSG00000137707			13862	protein-coding gene	gene with protein product		605673				10995567	Standard	NM_017589		Approved	PC3B	uc001plj.3	Q9NY30		ENST00000356018.2:c.556C>T	11.37:g.111365994G>A	ENSP00000348300:p.Arg186Cys		Q8NEH7	Missense_Mutation	SNP	ENST00000356018.2	37	CCDS8346.1	.	.	.	.	.	.	.	.	.	.	G	7.707	0.694385	0.15039	0.0	3.49E-4	ENSG00000137707	ENST00000356018	.	.	.	5.97	0.604	0.17547	.	0.408414	0.26776	N	0.022553	T	0.43942	0.1270	M	0.75447	2.3	0.09310	N	1	B	0.24618	0.107	B	0.17433	0.018	T	0.43829	-0.9367	9	0.87932	D	0	.	9.1067	0.36703	0.3769:0.0:0.623:0.0	.	186	Q9NY30	BTG4_HUMAN	C	186	.	ENSP00000348300:R186C	R	-	1	0	BTG4	110871204	0.921000	0.31238	0.002000	0.10522	0.107000	0.19398	0.935000	0.28924	-0.119000	0.11830	-0.136000	0.14681	CGC		0.448	BTG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391177.1			32	68	32	68
CNTN1	1272	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	41333261	41333261	+	Silent	SNP	G	G	A			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr12:41333261G>A	ENST00000551295.2	+	12	1470	c.1353G>A	c.(1351-1353)ggG>ggA	p.G451G	CNTN1_ENST00000347616.1_Silent_p.G451G|CNTN1_ENST00000547849.1_Silent_p.G451G|CNTN1_ENST00000547702.1_Silent_p.G451G|CNTN1_ENST00000360099.3_Silent_p.G451G|CNTN1_ENST00000348761.2_Silent_p.G440G	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	451	Ig-like C2-type 5.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				GGAGTAAAGGGACAGAGTGGC	0.373																																																0													74.0	74.0	74.0					12																	41333261		2203	4300	6503	SO:0001819	synonymous_variant	1272			Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"", ""Endogenous ligands"""	2171	protein-coding gene	gene with protein product	"""glycoprotein gP135"""	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.1353G>A	12.37:g.41333261G>A			A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Silent	SNP	ENST00000551295.2	37	CCDS8737.1																																																																																				0.373	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		11	39	11	39
MPHOSPH8	54737	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	20221185	20221185	+	Silent	SNP	C	C	T			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr13:20221185C>T	ENST00000361479.5	+	3	1040	c.972C>T	c.(970-972)acC>acT	p.T324T	MPHOSPH8_ENST00000414242.2_Silent_p.T324T	NM_017520.3	NP_059990.2	Q99549	MPP8_HUMAN	M-phase phosphoprotein 8	324					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of DNA methylation (GO:0044030)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nuclear nucleosome (GO:0000788)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	methylated histone binding (GO:0035064)	p.T324T(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_cancers(29;2.83e-16)|all_lung(29;1.16e-17)|all_epithelial(30;8.13e-16)|Lung NSC(5;6.91e-15)|Lung SC(185;0.0367)		all cancers(112;8.43e-05)|Epithelial(112;0.000426)|OV - Ovarian serous cystadenocarcinoma(117;0.00596)|Lung(94;0.015)|LUSC - Lung squamous cell carcinoma(192;0.0795)		AGGAGGATACCGATGTCAGAG	0.498																																																1	Substitution - coding silent(1)	lung(1)											64.0	66.0	66.0					13																	20221185		2203	4299	6502	SO:0001819	synonymous_variant	54737			AK056785, AJ293409	CCDS9287.1	13q12.11	2013-01-10			ENSG00000196199	ENSG00000196199		"""Ankyrin repeat domain containing"""	29810	protein-coding gene	gene with protein product		611626				8885239	Standard	NM_017520		Approved	mpp8, HSMPP8	uc001umh.3	Q99549	OTTHUMG00000016498	ENST00000361479.5:c.972C>T	13.37:g.20221185C>T			B7Z6F9|Q5JPE5|Q5JTQ0|Q86TK3|Q96MK4|Q9BTP1	Silent	SNP	ENST00000361479.5	37	CCDS9287.1																																																																																				0.498	MPHOSPH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044028.2	NM_017520		13	48	13	48
LATS2	26524	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	13	21562426	21562426	+	Missense_Mutation	SNP	C	C	A			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr13:21562426C>A	ENST00000382592.4	-	4	1898	c.1493G>T	c.(1492-1494)gGc>gTc	p.G498V	LATS2_ENST00000542899.1_Missense_Mutation_p.G498V|LATS2_ENST00000472754.1_5'Flank	NM_014572.2	NP_055387.2			large tumor suppressor kinase 2											breast(4)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(2)	45		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		CGGGAAGGCGCCTGCGCCGCC	0.766																																																0													7.0	9.0	8.0					13																	21562426		2169	4249	6418	SO:0001583	missense	26524			AB028019	CCDS9294.1	13q11-q12	2013-04-25	2013-04-25		ENSG00000150457	ENSG00000150457			6515	protein-coding gene	gene with protein product		604861	"""LATS (large tumor suppressor, Drosophila) homolog 2"", ""LATS, large tumor suppressor, homolog 2 (Drosophila)"""			10673337	Standard	NM_014572		Approved		uc001unr.4	Q9NRM7	OTTHUMG00000016531	ENST00000382592.4:c.1493G>T	13.37:g.21562426C>A	ENSP00000372035:p.Gly498Val			Missense_Mutation	SNP	ENST00000382592.4	37	CCDS9294.1	.	.	.	.	.	.	.	.	.	.	C	10.80	1.453014	0.26161	.	.	ENSG00000150457	ENST00000382592;ENST00000542899	T;T	0.58652	0.32;0.32	4.23	1.38	0.22167	.	0.835002	0.10498	N	0.667555	T	0.31606	0.0802	N	0.08118	0	0.09310	N	0.99999	B	0.24186	0.099	B	0.19391	0.025	T	0.17379	-1.0371	10	0.34782	T	0.22	.	4.2647	0.10757	0.0:0.379:0.3783:0.2427	.	498	Q9NRM7	LATS2_HUMAN	V	498	ENSP00000372035:G498V;ENSP00000441817:G498V	ENSP00000372035:G498V	G	-	2	0	LATS2	20460426	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	0.197000	0.17197	0.431000	0.26258	0.549000	0.68633	GGC		0.766	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1			8	9	8	9
CCDC113	29070	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	58287907	58287907	+	Silent	SNP	A	A	G			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr16:58287907A>G	ENST00000219299.4	+	3	313	c.234A>G	c.(232-234)cgA>cgG	p.R78R	CCDC113_ENST00000443128.2_Intron	NM_014157.3	NP_054876.2	Q9H0I3	CC113_HUMAN	coiled-coil domain containing 113	78						cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)				large_intestine(4)|lung(6)|ovary(1)|urinary_tract(1)	12						TGCAGTTTCGAGGCAGGCGTA	0.498																																																0													100.0	90.0	94.0					16																	58287907		2198	4300	6498	SO:0001819	synonymous_variant	29070			AL136785	CCDS10795.1, CCDS45497.1	16q21	2008-02-05			ENSG00000103021	ENSG00000103021			25002	protein-coding gene	gene with protein product						11230166, 11042152	Standard	NM_014157		Approved	HSPC065, DKFZp434N1418	uc002ene.3	Q9H0I3	OTTHUMG00000133489	ENST00000219299.4:c.234A>G	16.37:g.58287907A>G			B2RAQ7|B4DR20|Q9NZX2	Silent	SNP	ENST00000219299.4	37	CCDS10795.1																																																																																				0.498	CCDC113-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257387.2	NM_014157		50	99	50	99
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7577094	7577094	+	Missense_Mutation	SNP	G	G	A	rs28934574		TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr17:7577094G>A	ENST00000269305.4	-	8	1033	c.844C>T	c.(844-846)Cgg>Tgg	p.R282W	TP53_ENST00000359597.4_Missense_Mutation_p.R282W|TP53_ENST00000455263.2_Missense_Mutation_p.R282W|TP53_ENST00000420246.2_Missense_Mutation_p.R282W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.R282W	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	282	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		DR -> EW (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in a sporadic cancer; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|Ref.22}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934574). {ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|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)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R282W(401)|p.R282G(29)|p.0?(8)|p.R282fs*24(4)|p.R282R(3)|p.?(2)|p.D281fs*63(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.R282fs*63(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCTGTGCGCCGGTCTCTCCCA	0.557		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	463	Substitution - Missense(430)|Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(5)|Insertion - Frameshift(4)|Substitution - coding silent(3)|Unknown(2)|Complex - frameshift(2)|Complex - compound substitution(2)|Insertion - In frame(1)	large_intestine(136)|oesophagus(49)|upper_aerodigestive_tract(43)|stomach(33)|central_nervous_system(29)|breast(29)|lung(26)|ovary(21)|skin(20)|urinary_tract(16)|haematopoietic_and_lymphoid_tissue(16)|pancreas(10)|biliary_tract(5)|liver(5)|bone(5)|vulva(4)|prostate(4)|endometrium(3)|peritoneum(2)|thyroid(2)|NS(2)|autonomic_ganglia(1)|soft_tissue(1)|salivary_gland(1)	GRCh37	CM056413|CM920678	TP53	M	rs28934574	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	83.0	71.0	75.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	844,844,844,844,448,448,448	1.5	0.3	17	dbSNP_125	75	2,8598	2.2+/-6.3	1,0,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	101,101,101,101,101,101,101	1,0,6502	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	282/394,282/394,282/347,282/342,150/262,150/210,150/215	7577094	2,13004	2203	4300	6503	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.844C>T	17.37:g.7577094G>A	ENSP00000269305:p.Arg282Trp		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.057525	0.76074	0.0	2.33E-4	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.75	1.49	0.22878	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	M	0.89968	3.075	0.58432	A	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.998;1.0;0.999	D	0.97713	1.0192	9	0.87932	D	0	-12.0909	8.7508	0.34613	0.0:0.1376:0.5833:0.2792	rs28934574	282;282;282;282	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	W	282;282;282;282;282;271;150	ENSP00000352610:R282W;ENSP00000269305:R282W;ENSP00000398846:R282W;ENSP00000391127:R282W;ENSP00000391478:R282W;ENSP00000425104:R150W	ENSP00000269305:R282W	R	-	1	2	TP53	7517819	1.000000	0.71417	0.327000	0.25402	0.901000	0.52897	4.477000	0.60223	0.174000	0.19809	0.462000	0.41574	CGG		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		22	46	22	46
GFAP	2670	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	42991175	42991175	+	Missense_Mutation	SNP	G	G	T			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr17:42991175G>T	ENST00000253408.5	-	3	604	c.539C>A	c.(538-540)aCc>aAc	p.T180N	GFAP_ENST00000435360.2_Missense_Mutation_p.T180N|GFAP_ENST00000586793.1_Missense_Mutation_p.T180N|GFAP_ENST00000591327.1_5'UTR|GFAP_ENST00000588735.1_Intron	NM_002055.4	NP_002046.1	P14136	GFAP_HUMAN	glial fibrillary acidic protein	180	Coil 1B.|Rod.				astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|extracellular matrix organization (GO:0030198)|intermediate filament organization (GO:0045109)|long-term synaptic potentiation (GO:0060291)|negative regulation of neuron projection development (GO:0010977)|neuron projection regeneration (GO:0031102)|positive regulation of Schwann cell proliferation (GO:0010625)|regulation of neurotransmitter uptake (GO:0051580)|response to wounding (GO:0009611)	astrocyte projection (GO:0097449)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|membrane (GO:0016020)	structural constituent of cytoskeleton (GO:0005200)			endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(11)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23		Prostate(33;0.0959)				ACGGGCCAGGGTGGCTTCATC	0.622																																																0													98.0	102.0	101.0					17																	42991175		2203	4300	6503	SO:0001583	missense	2670			S40719	CCDS11491.1, CCDS45708.1, CCDS59296.1	17q21	2013-01-16						"""Intermediate filaments type III"""	4235	protein-coding gene	gene with protein product	"""intermediate filament protein"""	137780				9693047	Standard	NM_002055		Approved	FLJ45472	uc002ihq.3	P14136		ENST00000253408.5:c.539C>A	17.37:g.42991175G>T	ENSP00000253408:p.Thr180Asn		B2RD44|D3DX59|E9PAX3|Q53H98|Q5D055|Q6ZQS3|Q7Z5J6|Q7Z5J7|Q96KS4|Q96P18|Q9UFD0	Missense_Mutation	SNP	ENST00000253408.5	37	CCDS11491.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.0|22.0	4.227526|4.227526	0.79576|0.79576	.|.	.|.	ENSG00000131095|ENSG00000131095	ENST00000376990|ENST00000253408;ENST00000421021;ENST00000435360	D|D;D	0.88896|0.90385	-2.44|-2.66;-2.66	4.15|4.15	4.15|4.15	0.48705|0.48705	.|Filament (1);	.|0.415710	.|0.24105	.|N	.|0.041518	D|D	0.91153|0.91153	0.7214|0.7214	L|L	0.55103|0.55103	1.725|1.725	0.30185|0.30185	N|N	0.800029|0.800029	.|P;B	.|0.43231	.|0.801;0.22	.|B;P	.|0.49012	.|0.197;0.598	D|D	0.88955|0.88955	0.3389|0.3389	7|10	0.13108|0.45353	T|T	0.6|0.12	.|.	16.4115|16.4115	0.83713|0.83713	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|180;180	.|E9PAX3;P14136	.|.;GFAP_HUMAN	T|N	160|180;155;180	ENSP00000366189:P160T|ENSP00000253408:T180N;ENSP00000403962:T180N	ENSP00000366189:P160T|ENSP00000253408:T180N	P|T	-|-	1|2	0|0	GFAP|GFAP	40346701|40346701	0.988000|0.988000	0.35896|0.35896	0.999000|0.999000	0.59377|0.59377	0.976000|0.976000	0.68499|0.68499	6.393000|6.393000	0.73217|0.73217	2.598000|2.598000	0.87819|0.87819	0.462000|0.462000	0.41574|0.41574	CCC|ACC		0.622	GFAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448701.1	NM_002055		76	118	76	118
ELANE	1991	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	852925	852925	+	Silent	SNP	C	C	T			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr19:852925C>T	ENST00000590230.1	+	3	258	c.117C>T	c.(115-117)caC>caT	p.H39H	ELANE_ENST00000263621.1_Silent_p.H39H			P08246	ELNE_HUMAN	elastase, neutrophil expressed	39	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				acute inflammatory response to antigenic stimulus (GO:0002438)|cellular calcium ion homeostasis (GO:0006874)|collagen catabolic process (GO:0030574)|defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of chemotaxis (GO:0050922)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neutrophil mediated killing of fungus (GO:0070947)|phagocytosis (GO:0006909)|positive regulation of immune response (GO:0050778)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein catabolic process (GO:0030163)|proteolysis (GO:0006508)|response to lipopolysaccharide (GO:0032496)|response to UV (GO:0009411)|response to yeast (GO:0001878)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)|transcriptional repressor complex (GO:0017053)	cytokine binding (GO:0019955)|endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|RNA polymerase II transcription corepressor activity (GO:0001106)|serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(1)|lung(4)|pancreas(1)	13					Alpha-1-proteinase inhibitor(DB00058)|Filgrastim(DB00099)|Pegfilgrastim(DB00019)	CGCGGCCCCACGCGTGGCCCT	0.721																																																0													8.0	10.0	10.0					19																	852925		2115	4134	6249	SO:0001819	synonymous_variant	1991				CCDS12045.1	19p13.3	2014-09-17	2009-05-05	2009-05-05	ENSG00000197561	ENSG00000197561	3.4.21.37		3309	protein-coding gene	gene with protein product	"""neutrophil elastase"", ""leukocyte elastase"", ""medullasin"""	130130	"""elastase 2, neutrophil"""	ELA2		2902087	Standard	XM_005259517		Approved	NE, HNE, HLE	uc002lqb.3	P08246		ENST00000590230.1:c.117C>T	19.37:g.852925C>T			P09649|Q6B0D9|Q6LDP5	Silent	SNP	ENST00000590230.1	37	CCDS12045.1																																																																																				0.721	ELANE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457890.2	NM_001972		6	29	6	29
LRP3	4037	hgsc.bcm.edu;broad.mit.edu	37	19	33696671	33696671	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr19:33696671G>A	ENST00000253193.7	+	5	1197	c.995G>A	c.(994-996)cGg>cAg	p.R332Q	CTD-2540B15.13_ENST00000609744.1_RNA	NM_002333.3	NP_002324.2	O75074	LRP3_HUMAN	low density lipoprotein receptor-related protein 3	332	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)	15	Esophageal squamous(110;0.137)					AGCAACCACCGGCCCGTGAGC	0.706																																																0													6.0	9.0	8.0					19																	33696671		2069	4098	6167	SO:0001583	missense	4037			AB009462	CCDS12430.1	19q13.11	2013-05-30			ENSG00000130881	ENSG00000130881		"""Low density lipoprotein receptors"""	6695	protein-coding gene	gene with protein product		603159				9693042, 7959795	Standard	NM_002333		Approved	LRP-3, hLRp105	uc010edh.3	O75074	OTTHUMG00000180343	ENST00000253193.7:c.995G>A	19.37:g.33696671G>A	ENSP00000253193:p.Arg332Gln		B3KQD6|B4DKF2	Missense_Mutation	SNP	ENST00000253193.7	37	CCDS12430.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.515485	0.44763	.	.	ENSG00000130881	ENST00000431491;ENST00000253193	T	0.51325	0.71	5.02	3.99	0.46301	CUB (5);	0.137892	0.44902	N	0.000416	T	0.33381	0.0861	L	0.45581	1.43	0.37320	D	0.909516	B;B;B	0.31193	0.312;0.04;0.019	B;B;B	0.26094	0.066;0.028;0.02	T	0.19484	-1.0304	10	0.15952	T	0.53	-30.3961	6.7438	0.23451	0.2836:0.0:0.7164:0.0	.	206;332;250	C9J8W0;O75074;B7ZAJ9	.;LRP3_HUMAN;.	Q	206;332	ENSP00000253193:R332Q	ENSP00000253193:R332Q	R	+	2	0	LRP3	38388511	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	3.611000	0.54132	1.129000	0.42072	0.313000	0.20887	CGG		0.706	LRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450842.4			9	1	9	1
LILRA1	11024	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	55105741	55105741	+	Missense_Mutation	SNP	T	T	A			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr19:55105741T>A	ENST00000251372.3	+	2	214	c.32T>A	c.(31-33)cTc>cAc	p.L11H	LILRA1_ENST00000453777.1_Missense_Mutation_p.L11H|LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000473156.1_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	11					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		CTGATCTGTCTCAGTGAGATT	0.587																																																0													82.0	106.0	98.0					19																	55105741		2203	4300	6503	SO:0001583	missense	11024			AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.32T>A	19.37:g.55105741T>A	ENSP00000251372:p.Leu11His		O75018|Q3MJA6	Missense_Mutation	SNP	ENST00000251372.3	37	CCDS12901.1	.	.	.	.	.	.	.	.	.	.	T	12.75	2.030108	0.35797	.	.	ENSG00000104974	ENST00000251372;ENST00000453777	T;T	0.00568	6.53;6.53	2.42	1.35	0.21983	.	0.339827	0.20653	N	0.088178	T	0.03136	0.0092	H	0.98218	4.175	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.982	T	0.30238	-0.9985	10	0.87932	D	0	.	4.5628	0.12168	0.0:0.1802:0.0:0.8198	.	11;11	O75019-2;O75019	.;LIRA1_HUMAN	H	11	ENSP00000251372:L11H;ENSP00000413715:L11H	ENSP00000251372:L11H	L	+	2	0	LILRA1	59797553	0.012000	0.17670	0.004000	0.12327	0.031000	0.12232	2.924000	0.48876	0.172000	0.19760	0.163000	0.16589	CTC		0.587	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863		65	77	65	77
DNAJC28	54943	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	21	34860571	34860571	+	Missense_Mutation	SNP	A	A	T			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr21:34860571A>T	ENST00000314399.3	-	2	1568	c.1130T>A	c.(1129-1131)aTg>aAg	p.M377K	DNAJC28_ENST00000381947.3_Missense_Mutation_p.M377K|DNAJC28_ENST00000402202.1_Missense_Mutation_p.M377K	NM_017833.3	NP_060303.2	Q9NX36	DJC28_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 28	377				LIVPILTRQKVHFDAQKEIVRAQKIYETLIKTKEVTDRNPN NLDQGEGEKTPEIKKGFLNWMNLWKFIKIRSF -> CSHPD QAKSPF (in Ref. 2; BAA91185). {ECO:0000305}.						endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(5)|skin(1)|urinary_tract(1)	18						CCACAGATTCATCCAGTTTAA	0.299																																																0													94.0	91.0	92.0					21																	34860571		2201	4299	6500	SO:0001583	missense	54943			AK000468	CCDS13626.1	21q22.11	2011-09-02	2008-06-17	2008-06-17	ENSG00000177692	ENSG00000177692		"""Heat shock proteins / DNAJ (HSP40)"""	1297	protein-coding gene	gene with protein product	"""Orf28"""		"""chromosome 21 open reading frame 55"""	C21orf55			Standard	NM_017833		Approved	C21orf78	uc002yrw.3	Q9NX36	OTTHUMG00000065531	ENST00000314399.3:c.1130T>A	21.37:g.34860571A>T	ENSP00000320303:p.Met377Lys		D3DSF2	Missense_Mutation	SNP	ENST00000314399.3	37	CCDS13626.1	.	.	.	.	.	.	.	.	.	.	A	7.127	0.579158	0.13686	.	.	ENSG00000177692	ENST00000381947;ENST00000314399;ENST00000402202	.	.	.	5.44	0.167	0.15006	.	0.560382	0.20359	N	0.093886	T	0.24967	0.0606	L	0.33485	1.01	0.19300	N	0.999972	B	0.02656	0.0	B	0.01281	0.0	T	0.13255	-1.0516	9	0.51188	T	0.08	-0.2591	2.6954	0.05133	0.6211:0.1251:0.1341:0.1197	.	377	Q9NX36	DJC28_HUMAN	K	377	.	ENSP00000320303:M377K	M	-	2	0	DNAJC28	33782441	0.991000	0.36638	0.108000	0.21378	0.277000	0.26821	2.327000	0.43858	-0.124000	0.11724	0.528000	0.53228	ATG		0.299	DNAJC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140454.3			8	26	8	26
HDAC10	83933	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	22	50689416	50689416	+	Missense_Mutation	SNP	G	G	T			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr22:50689416G>T	ENST00000216271.5	-	1	398	c.46C>A	c.(46-48)Ctg>Atg	p.L16M	MAPK12_ENST00000497036.1_5'UTR|HDAC10_ENST00000448072.1_Missense_Mutation_p.L16M|HDAC10_ENST00000349505.4_Missense_Mutation_p.L16M|HDAC10_ENST00000498366.1_Intron	NM_001159286.1|NM_032019.5	NP_001152758.1|NP_114408.3	Q969S8	HDA10_HUMAN	histone deacetylase 10	16	Histone deacetylase.				chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|oligodendrocyte development (GO:0014003)|protein deacetylation (GO:0006476)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)			endometrium(2)|kidney(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	8		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TCCCAGAGCAGCCGGGTGGCC	0.667																																																0													49.0	49.0	49.0					22																	50689416		2194	4299	6493	SO:0001583	missense	83933			AF393962	CCDS14088.1, CCDS54545.1	22q13.31	2008-06-10			ENSG00000100429	ENSG00000100429			18128	protein-coding gene	gene with protein product		608544				11677242, 11726666	Standard	NM_032019		Approved	DKFZP761B039	uc003bkg.3	Q969S8	OTTHUMG00000044647	ENST00000216271.5:c.46C>A	22.37:g.50689416G>T	ENSP00000216271:p.Leu16Met		Q08AP4|Q6STF9|Q96P77|Q96P78|Q9H028|Q9UGX1|Q9UGX2	Missense_Mutation	SNP	ENST00000216271.5	37	CCDS14088.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.177642	0.78564	.	.	ENSG00000100429	ENST00000216271;ENST00000448072;ENST00000349505	T;T;T	0.55930	0.49;0.9;0.89	3.28	3.28	0.37604	Histone deacetylase domain (1);	0.000000	0.64402	D	0.000018	T	0.69342	0.3100	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.998	T	0.70022	-0.4986	10	0.34782	T	0.22	-12.0259	15.4214	0.75015	0.0:0.0:1.0:0.0	.	16;16;16	Q969S8-2;C9J8B8;Q969S8	.;.;HDA10_HUMAN	M	16	ENSP00000216271:L16M;ENSP00000397542:L16M;ENSP00000343540:L16M	ENSP00000216271:L16M	L	-	1	2	HDAC10	49031543	1.000000	0.71417	0.996000	0.52242	0.986000	0.74619	6.294000	0.72738	2.147000	0.66899	0.313000	0.20887	CTG		0.667	HDAC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104141.4	NM_032019		31	57	31	57
OTOF	9381	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	26686908	26686908	+	Missense_Mutation	SNP	C	C	T	rs143889717		TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr2:26686908C>T	ENST00000272371.2	-	40	5153	c.5027G>A	c.(5026-5028)cGc>cAc	p.R1676H	OTOF_ENST00000403946.3_Missense_Mutation_p.R1676H|OTOF_ENST00000338581.6_Missense_Mutation_p.R909H|OTOF_ENST00000402415.3_Missense_Mutation_p.R986H|OTOF_ENST00000339598.3_Missense_Mutation_p.R909H	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1676					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCAGCCTGCGCGGGGGATGTC	0.667																																					GBM(102;732 1451 20652 24062 31372)											0								C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	69.0	72.0	71.0		2726,5027,2957,2726	4.4	0.9	2	dbSNP_134	71	0,8600		0,0,4300	no	missense,missense,missense,missense	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	29,29,29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	909/1231,1676/1998,986/1308,909/1231	26686908	1,13005	2203	4300	6503	SO:0001583	missense	9381			AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.5027G>A	2.37:g.26686908C>T	ENSP00000272371:p.Arg1676His		B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	37	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.356612	0.82243	2.27E-4	0.0	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	T;T;T;T;T	0.57595	0.39;0.39;0.39;0.39;0.39	4.4	4.4	0.53042	.	0.120976	0.56097	D	0.000026	T	0.64505	0.2604	M	0.68952	2.095	0.80722	D	1	P;P;D;P	0.58970	0.946;0.793;0.984;0.601	P;B;P;B	0.54238	0.542;0.417;0.746;0.417	T	0.68845	-0.5301	10	0.52906	T	0.07	-19.7042	16.7839	0.85569	0.0:1.0:0.0:0.0	.	1676;909;986;909	Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4	OTOF_HUMAN;.;.;.	H	909;909;986;1676;1676	ENSP00000345137:R909H;ENSP00000344521:R909H;ENSP00000383906:R986H;ENSP00000272371:R1676H;ENSP00000385255:R1676H	ENSP00000272371:R1676H	R	-	2	0	OTOF	26540412	0.992000	0.36948	0.911000	0.35937	0.418000	0.31294	5.898000	0.69838	2.264000	0.75181	0.561000	0.74099	CGC		0.667	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			76	172	76	172
TMEM131	23505	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	98504555	98504555	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr2:98504555G>A	ENST00000186436.5	-	4	547	c.319C>T	c.(319-321)Ccc>Tcc	p.P107S	TMEM131_ENST00000425805.2_Missense_Mutation_p.P58S	NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	107						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						AATCGTATGGGCCTGCAATTC	0.338																																																0													79.0	74.0	76.0					2																	98504555		1816	4077	5893	SO:0001583	missense	23505			AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.319C>T	2.37:g.98504555G>A	ENSP00000186436:p.Pro107Ser			Missense_Mutation	SNP	ENST00000186436.5	37	CCDS46368.1	.	.	.	.	.	.	.	.	.	.	G	17.84	3.487438	0.63962	.	.	ENSG00000075568	ENST00000186436;ENST00000425805	T	0.32023	1.47	5.56	5.56	0.83823	.	.	.	.	.	T	0.44350	0.1289	L	0.31926	0.97	0.58432	D	0.999999	D	0.89917	1.0	D	0.80764	0.994	T	0.09729	-1.0661	9	0.18276	T	0.48	.	18.309	0.90192	0.0:0.0:1.0:0.0	.	107	Q92545	TM131_HUMAN	S	107;58	ENSP00000186436:P107S	ENSP00000186436:P107S	P	-	1	0	TMEM131	97870987	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.895000	0.87343	2.620000	0.88729	0.655000	0.94253	CCC		0.338	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542		10	30	10	30
RIF1	55183	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	152319418	152319418	+	Silent	SNP	C	C	T			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr2:152319418C>T	ENST00000243326.5	+	29	3867	c.3384C>T	c.(3382-3384)gaC>gaT	p.D1128D	RIF1_ENST00000453091.2_Silent_p.D1128D|RIF1_ENST00000428287.2_Silent_p.D1128D|RIF1_ENST00000444746.2_Silent_p.D1128D|RIF1_ENST00000430328.2_Silent_p.D1128D			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		TGGACAGTGACATTGTCATTC	0.393																																																0													61.0	56.0	57.0					2																	152319418		2203	4300	6503	SO:0001819	synonymous_variant	55183			AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"""RAP1 interacting factor homolog (yeast)"""			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.3384C>T	2.37:g.152319418C>T			A0AVS0|Q9NS16	Silent	SNP	ENST00000243326.5	37	CCDS2194.1																																																																																				0.393	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			21	42	21	42
GALNT13	114805	hgsc.bcm.edu;ucsc.edu	37	2	155306962	155306962	+	Missense_Mutation	SNP	G	G	C			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr2:155306962G>C	ENST00000392825.3	+	13	2137	c.1570G>C	c.(1570-1572)Gat>Cat	p.D524H	GALNT13_ENST00000409237.1_3'UTR|AC009227.2_ENST00000434635.1_RNA	NM_052917.2	NP_443149.2	Q8IUC8	GLT13_HUMAN	polypeptide N-acetylgalactosaminyltransferase 13	524	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|lung(37)|ovary(3)|pancreas(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	65						CCAATGTCTCGATGAACCTTC	0.438																																																0													127.0	108.0	114.0					2																	155306962		2203	4300	6503	SO:0001583	missense	114805			AB067505	CCDS2199.1	2q24.1	2014-03-13	2014-03-13		ENSG00000144278	ENSG00000144278	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	23242	protein-coding gene	gene with protein product	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13"", ""polypeptide GalNAc transferase 13"""	608369	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13)"""			11572484, 12407114	Standard	XM_005246267		Approved	KIAA1918, GalNAc-T13	uc002tyr.4	Q8IUC8	OTTHUMG00000131917	ENST00000392825.3:c.1570G>C	2.37:g.155306962G>C	ENSP00000376570:p.Asp524His		Q08ER7|Q68VI8|Q6ZWG1|Q96PX0|Q9UIE5	Missense_Mutation	SNP	ENST00000392825.3	37	CCDS2199.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.6|25.6	4.657184|4.657184	0.88154|0.88154	.|.	.|.	ENSG00000144278|ENSG00000144278	ENST00000392825|ENST00000450838	T|.	0.36340|.	1.26|.	6.03|6.03	6.03|6.03	0.97812|0.97812	Ricin B-related lectin (1);Ricin B lectin (3);|.	0.122893|.	0.53938|.	D|.	0.000045|.	D|D	0.84447|0.84447	0.5474|0.5474	M|M	0.89030|0.89030	3|3	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.87578|.	0.998|.	D|D	0.85839|0.85839	0.1396|0.1396	10|5	0.72032|.	D|.	0.01|.	.|.	18.1336|18.1336	0.89610|0.89610	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	524|.	Q8IUC8|.	GLT13_HUMAN|.	H|P	524|109	ENSP00000376570:D524H|.	ENSP00000376570:D524H|.	D|R	+|+	1|2	0|0	GALNT13|GALNT13	155015208|155015208	1.000000|1.000000	0.71417|0.71417	0.969000|0.969000	0.41365|0.41365	0.916000|0.916000	0.54674|0.54674	8.811000|8.811000	0.91954|0.91954	2.881000|2.881000	0.98747|0.98747	0.650000|0.650000	0.86243|0.86243	GAT|CGA		0.438	GALNT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254870.2	NM_052917		38	76	38	76
SCN2A	6326	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	166170182	166170182	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr2:166170182G>A	ENST00000375437.2	+	9	1377	c.1087G>A	c.(1087-1089)Ggc>Agc	p.G363S	SCN2A_ENST00000375427.2_Missense_Mutation_p.G363S|SCN2A_ENST00000283256.6_Missense_Mutation_p.G363S|SCN2A_ENST00000357398.3_Missense_Mutation_p.G363S	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	363					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CCCCAACTATGGCTACACGAG	0.433																																																0													148.0	138.0	142.0					2																	166170182		2203	4300	6503	SO:0001583	missense	6326			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10588	protein-coding gene	gene with protein product		182390	"""sodium channel, voltage-gated, type II, alpha 2 polypeptide"", ""sodium channel, voltage-gated, type II, alpha 1 polypeptide"""	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.1087G>A	2.37:g.166170182G>A	ENSP00000364586:p.Gly363Ser		A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	37	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	G	31	5.064197	0.93898	.	.	ENSG00000136531	ENST00000424833;ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D;D	0.97553	-4.43;-4.43;-4.43;-4.43;-4.43	5.77	5.77	0.91146	Ion transport (1);	0.083313	0.52532	D	0.000077	D	0.99048	0.9674	H	0.95780	3.72	0.58432	D	0.999998	D;D	0.89917	0.998;1.0	D;D	0.97110	0.984;1.0	D	0.99116	1.0848	10	0.87932	D	0	.	20.3626	0.98863	0.0:0.0:1.0:0.0	.	363;363	Q99250-2;Q99250	.;SCN2A_HUMAN	S	363	ENSP00000406454:G363S;ENSP00000364586:G363S;ENSP00000349973:G363S;ENSP00000283256:G363S;ENSP00000364576:G363S	ENSP00000283256:G363S	G	+	1	0	SCN2A	165878428	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.009000	0.88606	2.885000	0.99019	0.655000	0.94253	GGC		0.433	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		35	77	35	77
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			22	83	22	83
ANKRD17	26057	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	74012998	74012998	+	Silent	SNP	T	T	C			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr4:74012998T>C	ENST00000358602.4	-	9	1835	c.1719A>G	c.(1717-1719)caA>caG	p.Q573Q	ANKRD17_ENST00000330838.6_Silent_p.Q573Q|ANKRD17_ENST00000514252.1_Intron|ANKRD17_ENST00000509867.2_Silent_p.Q460Q	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	573					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AATGACCCTCTTGAGCAGCTT	0.398																																																0													90.0	93.0	92.0					4																	74012998		2202	4300	6502	SO:0001819	synonymous_variant	26057			AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"""Ankyrin repeat domain containing"""	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.1719A>G	4.37:g.74012998T>C			E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Silent	SNP	ENST00000358602.4	37	CCDS34004.1																																																																																				0.398	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		58	96	58	96
KIF25	3834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	168440828	168440828	+	Missense_Mutation	SNP	C	C	T	rs199989232	byFrequency	TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr6:168440828C>T	ENST00000443060.2	+	7	969	c.578C>T	c.(577-579)gCg>gTg	p.A193V	KIF25_ENST00000351261.3_Missense_Mutation_p.A193V|KIF25_ENST00000354419.2_Missense_Mutation_p.A193V			Q9UIL4	KIF25_HUMAN	kinesin family member 25	193	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of autophagy (GO:0010507)|organelle organization (GO:0006996)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		CTGGTGCACGCGGATTCCTCC	0.572													c|||	5	0.000998403	0.0023	0.0	5008	,	,		19339	0.0		0.0	False		,,,				2504	0.002															0								T	VAL/ALA,VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	84.0	73.0	77.0		578,578	2.7	0.0	6		77	0,8600		0,0,4300	no	missense,missense	KIF25	NM_005355.3,NM_030615.2	64,64	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	193/333,193/385	168440828	1,13005	2203	4300	6503	SO:0001583	missense	3834			AB012722	CCDS5305.1, CCDS43530.1	6q27	2008-02-05	2003-01-09	2003-01-10	ENSG00000125337	ENSG00000125337		"""Kinesins"""	6390	protein-coding gene	gene with protein product		603815	"""kinesin-like 3"""	KNSL3		9925910	Standard	NM_030615		Approved		uc003qwk.1	Q9UIL4	OTTHUMG00000016035	ENST00000443060.2:c.578C>T	6.37:g.168440828C>T	ENSP00000388878:p.Ala193Val		O94775|Q5SZU9	Missense_Mutation	SNP	ENST00000443060.2	37	CCDS5305.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	c	11.82	1.752096	0.31046	2.27E-4	0.0	ENSG00000125337	ENST00000443060;ENST00000354419;ENST00000351261	T;T;T	0.76060	-0.99;-0.99;-0.99	3.56	2.7	0.31948	Kinesin, motor domain (5);	0.256528	0.30879	N	0.008681	T	0.48840	0.1522	L	0.55743	1.74	0.25812	N	0.984389	B;B	0.19445	0.032;0.036	B;B	0.20384	0.029;0.009	T	0.50701	-0.8797	10	0.62326	D	0.03	-14.4088	6.9243	0.24405	0.0:0.8702:0.0:0.1298	.	193;193	Q9UIL4-2;Q9UIL4	.;KIF25_HUMAN	V	193	ENSP00000388878:A193V;ENSP00000346401:A193V;ENSP00000252688:A193V	ENSP00000252688:A193V	A	+	2	0	KIF25	168183677	0.002000	0.14202	0.009000	0.14445	0.004000	0.04260	-0.005000	0.12855	0.714000	0.32081	-0.473000	0.04963	GCG		0.572	KIF25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362509.1			16	51	16	51
KIAA1549	57670	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	138603027	138603027	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr7:138603027C>T	ENST00000422774.1	-	2	1393	c.1345G>A	c.(1345-1347)Gag>Aag	p.E449K	KIAA1549_ENST00000242365.4_Missense_Mutation_p.E399K|KIAA1549_ENST00000440172.1_Missense_Mutation_p.E449K			Q9HCM3	K1549_HUMAN	KIAA1549	449						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CACAGAGTCTCGGCACCATCC	0.517			O	BRAF	pilocytic astrocytoma																																NSCLC(119;1534 1718 44213 46230 50068)		Dom	yes		7	7q34	57670	KIAA1549		O	0													68.0	67.0	67.0					7																	138603027		2089	4216	6305	SO:0001583	missense	57670				CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.1345G>A	7.37:g.138603027C>T	ENSP00000416040:p.Glu449Lys		B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	C	16.96	3.265687	0.59431	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.48522	0.81;0.83;0.82	4.65	4.65	0.58169	.	0.000000	0.56097	D	0.000036	T	0.55609	0.1931	L	0.34521	1.04	0.45528	D	0.998488	D;D	0.89917	1.0;1.0	D;D	0.83275	0.991;0.996	T	0.47636	-0.9102	10	0.22109	T	0.4	.	14.8534	0.70316	0.0:1.0:0.0:0.0	.	449;449	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	K	449;399;449	ENSP00000406661:E449K;ENSP00000242365:E399K;ENSP00000416040:E449K	ENSP00000242365:E399K	E	-	1	0	KIAA1549	138253567	0.998000	0.40836	0.482000	0.27366	0.056000	0.15407	4.833000	0.62766	2.414000	0.81942	0.655000	0.94253	GAG		0.517	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			13	115	13	115
PKHD1L1	93035	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	110487479	110487479	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr8:110487479C>T	ENST00000378402.5	+	51	8842	c.8738C>T	c.(8737-8739)tCg>tTg	p.S2913L		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	2913					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TCATATACATCGACATTCTAT	0.338										HNSCC(38;0.096)																																						0													86.0	80.0	81.0					8																	110487479		1857	4109	5966	SO:0001583	missense	93035			AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.8738C>T	8.37:g.110487479C>T	ENSP00000367655:p.Ser2913Leu		Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.932465	0.73442	.	.	ENSG00000205038	ENST00000378402	D	0.85773	-2.03	5.69	5.69	0.88448	.	0.169362	0.39687	N	0.001287	T	0.76990	0.4065	L	0.44542	1.39	0.26601	N	0.973013	P	0.43412	0.806	B	0.34590	0.186	T	0.69606	-0.5100	10	0.07644	T	0.81	.	17.3018	0.87184	0.0:1.0:0.0:0.0	.	2913	Q86WI1	PKHL1_HUMAN	L	2913	ENSP00000367655:S2913L	ENSP00000367655:S2913L	S	+	2	0	PKHD1L1	110556655	0.967000	0.33354	0.998000	0.56505	0.984000	0.73092	3.440000	0.52886	2.671000	0.90904	0.655000	0.94253	TCG		0.338	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		8	14	8	14
CDC14B	8555	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	99296274	99296274	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr9:99296274G>A	ENST00000375241.1	-	9	1332	c.881C>T	c.(880-882)gCc>gTc	p.A294V	CDC14B_ENST00000463569.1_Missense_Mutation_p.A294V|CDC14B_ENST00000375240.3_Missense_Mutation_p.A294V|CDC14B_ENST00000375242.3_Missense_Mutation_p.A257V|CDC14B_ENST00000375236.1_Missense_Mutation_p.A294V|CDC14B_ENST00000265659.2_Missense_Mutation_p.A294V	NM_003671.3|NM_033331.2	NP_003662.1|NP_201588.1	O60729	CC14B_HUMAN	cell division cycle 14B	294	B.				activation of anaphase-promoting complex activity (GO:0051488)|DNA repair (GO:0006281)|G2 DNA damage checkpoint (GO:0031572)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)	15		Acute lymphoblastic leukemia(62;0.0559)				TTTGACAATGGCATCAGTAGG	0.423																																																0													58.0	51.0	54.0					9																	99296274		2203	4300	6503	SO:0001583	missense	8555			AF023158	CCDS6721.1, CCDS6722.1, CCDS43853.1	9q22.3	2013-01-17	2013-01-17		ENSG00000081377	ENSG00000081377		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"""	1719	protein-coding gene	gene with protein product		603505	"""CDC14 (cell division cycle 14, S. cerevisiae) homolog B"", ""CDC14 cell division cycle 14 homolog B (S. cerevisiae)"""			9367992	Standard	NM_003671		Approved	Cdc14B1, Cdc14B2, CDC14B3, hCDC14B	uc004awj.3	O60729	OTTHUMG00000020300	ENST00000375241.1:c.881C>T	9.37:g.99296274G>A	ENSP00000364389:p.Ala294Val		A6N5X8|A8MQ20|B1AL31|B1AL32|O43183|O60730|Q5JU08	Missense_Mutation	SNP	ENST00000375241.1	37	CCDS6722.1	.	.	.	.	.	.	.	.	.	.	G	15.14	2.745481	0.49151	.	.	ENSG00000081377	ENST00000265659;ENST00000375241;ENST00000375240;ENST00000375242;ENST00000463569;ENST00000375236	D;D;D;D;D;D	0.85773	-2.03;-2.03;-2.03;-2.03;-2.03;-2.03	5.42	3.48	0.39840	Dual specificity phosphatase, catalytic domain (1);	0.483799	0.24527	N	0.037753	D	0.84853	0.5564	M	0.81239	2.535	0.32621	N	0.523349	B;B;B	0.17038	0.003;0.02;0.004	B;B;B	0.12156	0.006;0.007;0.007	T	0.83306	-0.0025	10	0.33141	T	0.24	-18.6477	14.1807	0.65572	0.0:0.0:0.7267:0.2733	.	294;294;257	O60729-2;O60729;A8MQ20	.;CC14B_HUMAN;.	V	294;294;294;257;294;294	ENSP00000265659:A294V;ENSP00000364389:A294V;ENSP00000364388:A294V;ENSP00000364390:A257V;ENSP00000420572:A294V;ENSP00000364384:A294V	ENSP00000265659:A294V	A	-	2	0	CDC14B	98336095	1.000000	0.71417	0.988000	0.46212	0.972000	0.66771	2.563000	0.45922	0.763000	0.33175	0.650000	0.86243	GCC		0.423	CDC14B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053278.2	NM_033331		11	8	11	8
ARSF	416	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	3021883	3021883	+	Missense_Mutation	SNP	C	C	T	rs141853880	byFrequency	TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chrX:3021883C>T	ENST00000381127.1	+	9	1404	c.1183C>T	c.(1183-1185)Cgg>Tgg	p.R395W	ARSF_ENST00000537104.1_Missense_Mutation_p.R395W|ARSF_ENST00000359361.2_Missense_Mutation_p.R395W	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	395					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 vesicular exosome (GO:0070062)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	38		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ACCAGCTGGACGGTTGATTAA	0.478													c|||	4	0.0010596	0.0023	0.0014	3775	,	,		13190	0.0		0.0	False		,,,				2504	0.0															0								C	TRP/ARG,TRP/ARG,TRP/ARG	15,3820		1,10,3,1621,568	101.0	92.0	95.0		1183,1183,1183	-1.0	0.0	X	dbSNP_134	95	0,6728		0,0,0,2428,1872	yes	missense,missense,missense	ARSF	NM_001201538.1,NM_001201539.1,NM_004042.4	101,101,101	1,10,3,4049,2440	TT,TC,T,CC,C		0.0,0.3911,0.142	probably-damaging,probably-damaging,probably-damaging	395/591,395/591,395/591	3021883	15,10548	2203	4300	6503	SO:0001583	missense	416			X97868	CCDS14123.1	Xp22.3	2013-02-14			ENSG00000062096	ENSG00000062096		"""Arylsulfatase family"""	721	protein-coding gene	gene with protein product		300003				7720070	Standard	NM_004042		Approved		uc022brz.1	P54793	OTTHUMG00000021081	ENST00000381127.1:c.1183C>T	X.37:g.3021883C>T	ENSP00000370519:p.Arg395Trp		Q8TCC5	Missense_Mutation	SNP	ENST00000381127.1	37	CCDS14123.1	.	.	.	.	.	.	.	.	.	.	C	10.11	1.261285	0.23051	0.003911	0.0	ENSG00000062096	ENST00000381127;ENST00000537104;ENST00000359361	D;D;D	0.98889	-5.21;-5.21;-5.21	3.53	-0.967	0.10316	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.278461	0.32231	U	0.006400	D	0.97901	0.9310	M	0.86573	2.825	0.09310	N	1	B	0.23540	0.087	B	0.34346	0.18	D	0.94208	0.7456	10	0.42905	T	0.14	.	10.7878	0.46415	0.519:0.481:0.0:0.0	.	395	P54793	ARSF_HUMAN	W	395	ENSP00000370519:R395W;ENSP00000445594:R395W;ENSP00000352319:R395W	ENSP00000352319:R395W	R	+	1	2	ARSF	3031883	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.272000	0.18644	-0.716000	0.04962	-0.613000	0.04052	CGG		0.478	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055652.1			41	87	41	87
ZNF630	57232	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	47918328	47918328	+	Silent	SNP	A	A	C			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chrX:47918328A>C	ENST00000409324.3	-	5	1729	c.1503T>G	c.(1501-1503)ccT>ccG	p.P501P	ZNF630_ENST00000442455.3_Silent_p.P487P|ZNF630_ENST00000276054.4_Silent_p.P377P|ZNF630-AS1_ENST00000436124.1_RNA	NM_001037735.2	NP_001032824.2	Q2M218	ZN630_HUMAN	zinc finger protein 630	501					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(6)|lung(11)|ovary(1)	19						GTATGATAAGAGGTGATTTCT	0.413																																																0													71.0	66.0	68.0					X																	47918328		2194	4289	6483	SO:0001819	synonymous_variant	57232			AK000580	CCDS35237.2, CCDS75971.1	Xp11.3-p11.1	2013-01-08			ENSG00000221994	ENSG00000221994		"""Zinc fingers, C2H2-type"", ""-"""	28855	protein-coding gene	gene with protein product		300819					Standard	NM_001037735		Approved	BC037316, dJ54B20.2, FLJ20573, MGC138344	uc004div.4	Q2M218	OTTHUMG00000021463	ENST00000409324.3:c.1503T>G	X.37:g.47918328A>C			F8WAG4|Q5H8Z5	Silent	SNP	ENST00000409324.3	37	CCDS35237.2																																																																																				0.413	ZNF630-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327254.1	NM_001037735		33	49	33	49
TFE3	7030	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	48887870	48887870	+	Missense_Mutation	SNP	G	G	T			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chrX:48887870G>T	ENST00000315869.7	-	10	1786	c.1527C>A	c.(1525-1527)caC>caA	p.H509Q	TFE3_ENST00000487451.1_5'Flank	NM_006521.4	NP_006512.2	P19532	TFE3_HUMAN	transcription factor binding to IGHM enhancer 3	509					humoral immune response (GO:0006959)|positive regulation of cell adhesion (GO:0045785)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of osteoclast differentiation (GO:0045670)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)		NONO/TFE3(2)|PRCC/TFE3(25)|SFPQ/TFE3(6)|CLTC/TFE3(2)|ASPSCR1/TFE3(167)	central_nervous_system(1)	1						GGTCCCCCAGGTGGTCGCTGG	0.672			T	"""SFPQ, ASPSCR1, PRCC, NONO, CLTC"""	"""papillary renal, alveolar soft part sarcoma, renal"""																																		Dom	yes		X	Xp11.22	7030	transcription factor binding to IGHM enhancer 3		E	0													56.0	57.0	57.0					X																	48887870		2203	4296	6499	SO:0001583	missense	7030			X96717	CCDS14315.3	Xp11.22	2013-05-21			ENSG00000068323	ENSG00000068323		"""Basic helix-loop-helix proteins"""	11752	protein-coding gene	gene with protein product	transcription factor E family, member A	314310				1672758, 1685140	Standard	NM_006521		Approved	TFEA, bHLHe33	uc004dmb.3	P19532	OTTHUMG00000022690	ENST00000315869.7:c.1527C>A	X.37:g.48887870G>T	ENSP00000314129:p.His509Gln		A8MZL6|Q5JU74|Q92757|Q92758|Q99964	Missense_Mutation	SNP	ENST00000315869.7	37	CCDS14315.3	.	.	.	.	.	.	.	.	.	.	G	15.58	2.874319	0.51695	.	.	ENSG00000068323	ENST00000315869	T	0.63417	-0.04	5.51	3.75	0.43078	.	0.532611	0.17932	U	0.157144	T	0.49558	0.1564	L	0.39898	1.24	0.31195	N	0.700516	B	0.18166	0.026	B	0.17098	0.017	T	0.51553	-0.8691	10	0.54805	T	0.06	-7.8906	5.9547	0.19267	0.17:0.0:0.6763:0.1537	.	509	P19532	TFE3_HUMAN	Q	509	ENSP00000314129:H509Q	ENSP00000314129:H509Q	H	-	3	2	TFE3	48774814	0.950000	0.32346	1.000000	0.80357	0.924000	0.55760	-0.006000	0.12833	0.523000	0.28482	-0.329000	0.08387	CAC		0.672	TFE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058872.2	NM_006521		22	166	22	166
IRS4	8471	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	107978402	107978402	+	Silent	SNP	G	G	A			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chrX:107978402G>A	ENST00000372129.2	-	1	1249	c.1173C>T	c.(1171-1173)gaC>gaT	p.D391D	RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000608811.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	391					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						AAAGCATCTCGTCTTCCCCGT	0.652																																																0													61.0	57.0	58.0					X																	107978402		2203	4300	6503	SO:0001819	synonymous_variant	8471			AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.1173C>T	X.37:g.107978402G>A				Silent	SNP	ENST00000372129.2	37	CCDS14544.1																																																																																				0.652	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		50	104	50	104
HS6ST2	90161	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	132091353	132091353	+	Splice_Site	SNP	C	C	T			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chrX:132091353C>T	ENST00000370836.2	-	3	845	c.430G>A	c.(430-432)Gtc>Atc	p.V144I	HS6ST2_ENST00000521489.1_Splice_Site_p.V144I|HS6ST2_ENST00000370833.2_5'Flank	NM_147175.3	NP_671704.3	Q96MM7	H6ST2_HUMAN	heparan sulfate 6-O-sulfotransferase 2	144					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(2)	9	Acute lymphoblastic leukemia(192;0.000127)					ATGTTCCCGACGCTGGGGGAA	0.627																																																0													35.0	36.0	36.0					X																	132091353		2030	4158	6188	SO:0001630	splice_region_variant	90161			AB067776	CCDS48169.1, CCDS48170.1	Xq26.2	2008-02-05			ENSG00000171004	ENSG00000171004		"""Sulfotransferases, membrane-bound"""	19133	protein-coding gene	gene with protein product		300545				10644753	Standard	NM_147175		Approved		uc011mvd.1	Q96MM7	OTTHUMG00000022430	ENST00000370836.2:c.429-1G>A	X.37:g.132091353C>T			B9WRT4|B9WRT5|E9PDY5|Q2TB13|Q4VC07|Q6PIC4|Q86SM9|Q8N3T4|Q8NBN4|Q96SJ4	Splice_Site	SNP	ENST00000370836.2	37	CCDS48169.1	.	.	.	.	.	.	.	.	.	.	C	17.74	3.464575	0.63513	.	.	ENSG00000171004	ENST00000370836;ENST00000521489	T;T	0.72725	-0.68;-0.68	5.18	5.18	0.71444	.	0.391191	0.19919	N	0.103130	T	0.44540	0.1298	N	0.08118	0	0.80722	D	1	P;P	0.48998	0.846;0.918	B;B	0.35813	0.125;0.211	T	0.47971	-0.9075	10	0.37606	T	0.19	-5.9095	9.0623	0.36442	0.0:0.8972:0.0:0.1028	.	144;144	Q96MM7;E9PDY5	H6ST2_HUMAN;.	I	144	ENSP00000359873:V144I;ENSP00000429473:V144I	ENSP00000359873:V144I	V	-	1	0	HS6ST2	131919035	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	0.286000	0.18902	2.292000	0.77174	0.529000	0.55759	GTC		0.627	HS6ST2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058332.3	NM_147174	Missense_Mutation	11	57	11	57
ADH1C	126	broad.mit.edu;ucsc.edu	37	4	100263953	100263953	+	RNA	SNP	A	A	G	rs78836241		TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr4:100263953A>G	ENST00000510055.1	-	0	872				ADH1C_ENST00000515683.1_RNA			P00326	ADH1G_HUMAN	alcohol dehydrogenase 1C (class I), gamma polypeptide						ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|zinc ion binding (GO:0008270)								OV - Ovarian serous cystadenocarcinoma(123;1.08e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	GGATCATACCATGGTGTCAAG	0.413																																																0													250.0	241.0	244.0					4																	100263953		2203	4300	6503			126			M12272		4q23	2010-03-16			ENSG00000248144	ENSG00000248144	1.1.1.1	"""Alcohol dehydrogenases"""	251	protein-coding gene	gene with protein product		103730		ADH3		3006456	Standard	NM_000669		Approved		uc031sgp.1	P00326	OTTHUMG00000161422		4.37:g.100263953A>G			Q4PJ18|Q5WRV0|Q6LBW4|Q6NWV0|Q6NZA7	RNA	SNP	ENST00000510055.1	37																																																																																					0.413	ADH1C-004	KNOWN	mRNA_end_NF|basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000365189.2	NM_000669		89	199	89	199
GPR50	9248	broad.mit.edu;ucsc.edu	37	X	150349612	150349612	+	Missense_Mutation	SNP	C	C	A			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chrX:150349612C>A	ENST00000218316.3	+	2	1626	c.1557C>A	c.(1555-1557)gaC>gaA	p.D519E	AF003625.3_ENST00000602313.1_lincRNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	519	Pro-rich.				cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|identical protein binding (GO:0042802)|melatonin receptor activity (GO:0008502)			breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					CCACTGCTGACTATCCCAAGC	0.617																																																0													64.0	77.0	72.0					X																	150349612		2173	4242	6415	SO:0001583	missense	9248			U52219	CCDS44012.1	Xq28	2012-08-21			ENSG00000102195	ENSG00000102195		"""GPCR / Class A : Orphans"""	4506	protein-coding gene	gene with protein product		300207				9933574, 18400093	Standard	NM_004224		Approved	H9, Mel1c	uc010ntg.2	Q13585	OTTHUMG00000024166	ENST00000218316.3:c.1557C>A	X.37:g.150349612C>A	ENSP00000218316:p.Asp519Glu		Q0VGG3|Q3ZAR0	Missense_Mutation	SNP	ENST00000218316.3	37	CCDS44012.1	.	.	.	.	.	.	.	.	.	.	C	11.42	1.632486	0.29068	.	.	ENSG00000102195	ENST00000218316	T	0.72051	-0.62	3.05	1.12	0.20585	.	0.857444	0.10108	N	0.715020	T	0.50240	0.1604	N	0.24115	0.695	0.09310	N	1	P	0.41673	0.759	B	0.34722	0.188	T	0.42327	-0.9458	10	0.87932	D	0	-11.9689	5.0412	0.14460	0.0:0.6142:0.2385:0.1474	.	519	Q13585	MTR1L_HUMAN	E	519	ENSP00000218316:D519E	ENSP00000218316:D519E	D	+	3	2	GPR50	150100270	0.000000	0.05858	0.001000	0.08648	0.272000	0.26649	-0.271000	0.08572	0.147000	0.19030	0.523000	0.50628	GAC		0.617	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224		80	196	80	196
AKR1CL1	340811	broad.mit.edu;ucsc.edu	37	10	5203897	5203897	+	Silent	SNP	C	C	T			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr10:5203897C>T	ENST00000334314.3	-	3	376	c.300G>A	c.(298-300)ccG>ccA	p.P100P	AKR1CL1_ENST00000465430.1_5'Flank			Q5T2L2	AKCL1_HUMAN	aldo-keto reductase family 1, member C-like 1	100						cytoplasm (GO:0005737)	oxidoreductase activity (GO:0016491)			cervix(1)|endometrium(1)|large_intestine(2)|lung(2)	6						TTTCTAGGGCCGGGTGAACCA	0.388																																					Ovarian(129;1623 1737 25446 28757 47467)											0													56.0	56.0	56.0					10																	5203897		2203	4300	6503	SO:0001819	synonymous_variant	340811					10p15.2	2014-05-06			ENSG00000196326	ENSG00000264006			23469	protein-coding gene	gene with protein product						15164054	Standard	NR_027916		Approved		uc009xhz.2	Q5T2L2	OTTHUMG00000184213	ENST00000334314.3:c.300G>A	10.37:g.5203897C>T			A6NF66|Q6ZN81	Silent	SNP	ENST00000334314.3	37																																																																																					0.388	AKR1CL1-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NR_027916		13	23	13	23
MIR517C	574492	broad.mit.edu;ucsc.edu	37	19	54245794	54245794	+	RNA	SNP	A	A	G			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr19:54245794A>G	ENST00000385103.1	+	0	95				RNU6-982P_ENST00000516216.1_RNA|MIR520H_ENST00000385126.1_RNA	NR_030214.1				microRNA 517c																		TAGAGGAAGCACTTTCTGTTT	0.388																																																0													114.0	111.0	112.0					19																	54245794		1568	3580	5148			574493					19q13.42	2011-09-12		2008-12-18	ENSG00000207838	ENSG00000207838		"""ncRNAs / Micro RNAs"""	32124	non-coding RNA	RNA, micro				MIRN517C			Standard	NR_030214		Approved	hsa-mir-517c	uc021var.1				19.37:g.54245794A>G				RNA	SNP	ENST00000385103.1	37																																																																																					0.388	MIR517C-201	KNOWN	basic	miRNA	miRNA		NR_030214		21	40	21	40
TBCK	93627	broad.mit.edu;ucsc.edu	37	4	107229997	107229997	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr4:107229997G>A	ENST00000273980.5	-	3	568	c.121C>T	c.(121-123)Cgc>Tgc	p.R41C	TBCK_ENST00000432496.2_Missense_Mutation_p.R41C|TBCK_ENST00000361687.4_Missense_Mutation_p.R41C|TBCK_ENST00000394706.3_Missense_Mutation_p.R41C|TBCK_ENST00000394708.2_Missense_Mutation_p.R41C					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						ATTTGAAAGCGCCCTAAAATT	0.413																																																0													139.0	145.0	143.0					4																	107229997		2203	4300	6503	SO:0001583	missense	93627				CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.121C>T	4.37:g.107229997G>A	ENSP00000273980:p.Arg41Cys			Missense_Mutation	SNP	ENST00000273980.5	37	CCDS54788.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.437867	0.83885	.	.	ENSG00000145348	ENST00000273980;ENST00000432496;ENST00000361687;ENST00000394706;ENST00000394708;ENST00000509532;ENST00000509862;ENST00000507696	T;T;T;T;T;T;T;T	0.11604	2.77;2.77;2.77;2.77;2.77;2.77;2.76;2.76	5.39	5.39	0.77823	Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.37812	0.1017	M	0.84773	2.715	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.994	T	0.27157	-1.0082	10	0.87932	D	0	.	14.9184	0.70815	0.0:0.0:0.8479:0.1521	.	41;41;41	Q8TEA7;Q8TEA7-2;Q8TEA7-3	TBCK_HUMAN;.;.	C	41	ENSP00000273980:R41C;ENSP00000405847:R41C;ENSP00000355338:R41C;ENSP00000378196:R41C;ENSP00000378198:R41C;ENSP00000420985:R41C;ENSP00000425197:R41C;ENSP00000423637:R41C	ENSP00000273980:R41C	R	-	1	0	TBCK	107449446	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	7.829000	0.86735	2.549000	0.85964	0.591000	0.81541	CGC		0.413	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115		25	72	25	72
RPS6KA3	6197	broad.mit.edu;ucsc.edu	37	X	20205954	20205954	+	Missense_Mutation	SNP	C	C	A			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chrX:20205954C>A	ENST00000379565.3	-	9	973	c.766G>T	c.(766-768)Gtg>Ttg	p.V256L	RPS6KA3_ENST00000540702.1_Missense_Mutation_p.V228L|RPS6KA3_ENST00000544447.1_Missense_Mutation_p.V228L|RPS6KA3_ENST00000379548.4_Missense_Mutation_p.V227L	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	256	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V256M(1)		breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	ACCATTAACACACCAAAAGAC	0.388																																																1	Substitution - Missense(1)	liver(1)											187.0	179.0	182.0					X																	20205954		2203	4300	6503	SO:0001583	missense	6197			U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"""ribosomal protein S6 kinase, 90kD, polypeptide 3"", ""mental retardation, X-linked 19"", ""Coffin-Lowry syndrome"""	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.766G>T	X.37:g.20205954C>A	ENSP00000368884:p.Val256Leu		B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Missense_Mutation	SNP	ENST00000379565.3	37	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.402335	0.83230	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702;ENST00000457145	T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53	4.76	4.76	0.60689	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	T	0.41511	0.1162	M	0.69248	2.105	0.80722	D	1	P;P;P;P	0.48640	0.844;0.913;0.517;0.845	P;B;P;B	0.46299	0.511;0.364;0.479;0.393	T	0.49513	-0.8932	10	0.87932	D	0	.	16.9773	0.86316	0.0:1.0:0.0:0.0	.	228;227;228;256	B4DG22;F5GYC4;B7ZB17;P51812	.;.;.;KS6A3_HUMAN	L	256;228;227;228;227	ENSP00000368884:V256L;ENSP00000440220:V228L;ENSP00000368865:V227L;ENSP00000444837:V228L;ENSP00000407655:V227L	ENSP00000368865:V227L	V	-	1	0	RPS6KA3	20115875	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.776000	0.85560	1.925000	0.55765	0.513000	0.50165	GTG		0.388	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		77	218	77	218
PKD1L1	168507	broad.mit.edu;ucsc.edu	37	7	47840379	47840379	+	Silent	SNP	G	G	A	rs138774842		TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr7:47840379G>A	ENST00000289672.2	-	54	8111	c.8061C>T	c.(8059-8061)ccC>ccT	p.P2687P	C7orf69_ENST00000418326.2_Intron|C7orf69_ENST00000258776.4_Intron	NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2687					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						ACAGCAGCCCGGGGAAGGCGT	0.567													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16896	0.0		0.0	False		,,,				2504	0.0															0								G	,	0,4406		0,0,2203	83.0	88.0	86.0		,8061	-4.4	0.0	7	dbSNP_134	86	1,8599	1.2+/-3.3	0,1,4299	no	intron,coding-synonymous	C7orf69,PKD1L1	NM_025031.2,NM_138295.3	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	,2687/2850	47840379	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	168507			AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.8061C>T	7.37:g.47840379G>A			Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																				0.567	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		46	125	46	125
RLF	6018	broad.mit.edu;hgsc.bcm.edu	37	1	40701977	40701978	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr1:40701977_40701978delAA	ENST00000372771.4	+	8	1630_1631	c.1603_1604delAA	c.(1603-1605)aaafs	p.K535fs		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	535					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			GCATAAGGAGAAAAGAGACAAA	0.356																																																0																																										SO:0001589	frameshift_variant	6018				CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"""Zinc fingers, C2H2-type"""	10025	protein-coding gene	gene with protein product		180610	"""rearranged L-myc fusion sequence"""			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.1603_1604delAA	1.37:g.40701979_40701980delAA	ENSP00000361857:p.Lys535fs		Q14CQ1|Q9NU60	Frame_Shift_Del	DEL	ENST00000372771.4	37	CCDS448.1																																																																																				0.356	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		29	31	29	31
ALMS1	7840	broad.mit.edu;hgsc.bcm.edu	37	2	73746974	73746976	+	In_Frame_Del	DEL	AAC	AAC	-			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr2:73746974_73746976delAAC	ENST00000264448.6	+	11	9720_9722	c.9609_9611delAAC	c.(9607-9612)ataaca>ata	p.T3205del	ALMS1_ENST00000409009.1_In_Frame_Del_p.T3163del	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3205					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						TCACTCAGATAACAACAGAAAGT	0.384																																																0																																										SO:0001651	inframe_deletion	7840			AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.9609_9611delAAC	2.37:g.73746977_73746979delAAC	ENSP00000264448:p.Thr3205del		Q53S05|Q580Q8|Q86VP9|Q9Y4G4	In_Frame_Del	DEL	ENST00000264448.6	37	CCDS42697.1																																																																																				0.384	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		12	41	12	41
EPC2	26122	broad.mit.edu;hgsc.bcm.edu	37	2	149539217	149539218	+	Frame_Shift_Del	DEL	AG	AG	-	rs201178099		TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr2:149539217_149539218delAG	ENST00000258484.6	+	11	1759_1760	c.1725_1726delAG	c.(1723-1728)acagggfs	p.G577fs		NM_015630.3	NP_056445.3	Q52LR7	EPC2_HUMAN	enhancer of polycomb homolog 2 (Drosophila)	577					chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0516)		TACCAGTAACAGGGGGTATCAC	0.376																																																0										0,3700		0,0,1850						5.0	1.0			70	1,7931		0,1,3965	no	frameshift	EPC2	NM_015630.3		0,1,5815	A1A1,A1R,RR		0.0126,0.0,0.0086				1,11631				SO:0001589	frameshift_variant	26122			AF286904	CCDS46422.1	2q23	2008-02-05			ENSG00000135999	ENSG00000135999			24543	protein-coding gene	gene with protein product		611000					Standard	NM_015630		Approved	DKFZP566F2124	uc010zbt.2	Q52LR7	OTTHUMG00000153739	ENST00000258484.6:c.1725_1726delAG	2.37:g.149539217_149539218delAG	ENSP00000258484:p.Gly577fs		B3KWT7|D3DP89|Q7L9J1|Q96RR7|Q9NUT8|Q9NVR1|Q9UFM9	Frame_Shift_Del	DEL	ENST00000258484.6	37	CCDS46422.1																																																																																				0.376	EPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332278.1	NM_015630		16	32	16	32
SKIV2L2	23517	broad.mit.edu;hgsc.bcm.edu	37	5	54706365	54706367	+	In_Frame_Del	DEL	CTT	CTT	-			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr5:54706365_54706367delCTT	ENST00000230640.5	+	23	2913_2915	c.2659_2661delCTT	c.(2659-2661)cttdel	p.L888del	SKIV2L2_ENST00000545714.1_In_Frame_Del_p.L787del	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	888					maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				TGATGAGCTCCTTCTAACTGAGA	0.35																																					Melanoma(2;92 134 23744 29976 33782)											0																																										SO:0001651	inframe_deletion	23517			D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 118"""		"""KIAA0052"""	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.2659_2661delCTT	5.37:g.54706365_54706367delCTT	ENSP00000230640:p.Leu888del		Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	In_Frame_Del	DEL	ENST00000230640.5	37	CCDS3967.1																																																																																				0.350	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1			31	103	31	103
IPO11	51194	broad.mit.edu;hgsc.bcm.edu	37	5	61779947	61779949	+	In_Frame_Del	DEL	GAA	GAA	-			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr5:61779947_61779949delGAA	ENST00000325324.6	+	11	1301_1303	c.1132_1134delGAA	c.(1132-1134)gaadel	p.E380del	KIF2A_ENST00000509663.2_Intron|IPO11_ENST00000409296.3_In_Frame_Del_p.E420del	NM_016338.4	NP_057422.3	Q9UI26	IPO11_HUMAN	importin 11	380					ribosomal protein import into nucleus (GO:0006610)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			endometrium(2)|kidney(3)|large_intestine(5)|lung(14)|skin(4)|stomach(2)	30		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		CCTATTAACTGAAGAAGAACTGA	0.33																																																0																																										SO:0001651	inframe_deletion	51194			AF111109	CCDS34167.1, CCDS47217.1	5q12.1	2008-09-19			ENSG00000086200	ENSG00000086200		"""Importins"""	20628	protein-coding gene	gene with protein product		610889					Standard	NM_016338		Approved	RanBP11	uc011cqr.2	Q9UI26	OTTHUMG00000154400	ENST00000325324.6:c.1132_1134delGAA	5.37:g.61779953_61779955delGAA	ENSP00000316651:p.Glu380del		A6NGJ5|B4DZ73|D3DW98|Q8N5R2|Q9NSJ6|Q9NVB1	In_Frame_Del	DEL	ENST00000325324.6	37	CCDS34167.1																																																																																				0.330	IPO11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335062.1	NM_016338		18	42	18	42
PIK3R1	5295	broad.mit.edu;hgsc.bcm.edu	37	5	67589550	67589552	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr5:67589550_67589552delAAG	ENST00000521381.1	+	11	1929_1931	c.1313_1315delAAG	c.(1312-1317)aaagaa>aaa	p.E439del	PIK3R1_ENST00000320694.8_In_Frame_Del_p.E139del|PIK3R1_ENST00000521657.1_In_Frame_Del_p.E439del|PIK3R1_ENST00000336483.5_In_Frame_Del_p.E169del|PIK3R1_ENST00000274335.5_In_Frame_Del_p.E439del|PIK3R1_ENST00000523872.1_In_Frame_Del_p.E76del|PIK3R1_ENST00000396611.1_In_Frame_Del_p.E439del	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	439					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	CAAGTTGTCAAAGAAGATAATAT	0.266			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																													Rec	yes		5	5q13.1	5295	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""		"""E, O"""	2	Whole gene deletion(1)|Unknown(1)	large_intestine(1)|lung(1)																																								SO:0001651	inframe_deletion	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1313_1315delAAG	5.37:g.67589553_67589555delAAG	ENSP00000428056:p.Glu439del		B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	In_Frame_Del	DEL	ENST00000521381.1	37	CCDS3993.1																																																																																				0.266	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		10	26	10	26
PIK3R1	5295	broad.mit.edu;hgsc.bcm.edu	37	5	67589623	67589624	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr5:67589623_67589624delAT	ENST00000521381.1	+	11	2002_2003	c.1386_1387delAT	c.(1384-1389)gaatatfs	p.Y463fs	PIK3R1_ENST00000320694.8_Frame_Shift_Del_p.Y163fs|PIK3R1_ENST00000521657.1_Frame_Shift_Del_p.Y463fs|PIK3R1_ENST00000336483.5_Frame_Shift_Del_p.Y193fs|PIK3R1_ENST00000274335.5_Frame_Shift_Del_p.Y463fs|PIK3R1_ENST00000523872.1_Frame_Shift_Del_p.Y100fs|PIK3R1_ENST00000396611.1_Frame_Shift_Del_p.Y463fs	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	463					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.D464fs*2(1)|p.0?(1)|p.?(1)|p.Y463fs*1(1)|p.E462_R465delEYDR(1)|p.Y463_L466del(1)|p.T454_D464del(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	AAAGTCGAGAATATGATAGATT	0.287			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																													Rec	yes		5	5q13.1	5295	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""		"""E, O"""	7	Deletion - In frame(3)|Whole gene deletion(1)|Insertion - Frameshift(1)|Deletion - Frameshift(1)|Unknown(1)	endometrium(4)|lung(2)|large_intestine(1)																																								SO:0001589	frameshift_variant	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1386_1387delAT	5.37:g.67589625_67589626delAT	ENSP00000428056:p.Tyr463fs		B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Frame_Shift_Del	DEL	ENST00000521381.1	37	CCDS3993.1																																																																																				0.287	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		17	36	17	36
NOTCH1	4851	broad.mit.edu;hgsc.bcm.edu	37	9	139413070	139413072	+	In_Frame_Del	DEL	AGA	AGA	-			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr9:139413070_139413072delAGA	ENST00000277541.6	-	6	1145_1147	c.1070_1072delTCT	c.(1069-1074)ttctac>tac	p.F357del	MIR4673_ENST00000584777.1_RNA	NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	357	EGF-like 9; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F357delF(4)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		CACTCGCAGTAGAAGGAGGCCAC	0.655			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)																													Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	4	Deletion - In frame(4)	upper_aerodigestive_tract(2)|central_nervous_system(2)																																								SO:0001651	inframe_deletion	4851			AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.1070_1072delTCT	9.37:g.139413070_139413072delAGA	ENSP00000277541:p.Phe357del		Q59ED8|Q5SXM3	In_Frame_Del	DEL	ENST00000277541.6	37	CCDS43905.1																																																																																				0.655	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		12	43	12	43
TTBK2	146057	broad.mit.edu;hgsc.bcm.edu	37	15	43045062	43045066	+	Frame_Shift_Del	DEL	ACTTA	ACTTA	-			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr15:43045062_43045066delACTTA	ENST00000267890.6	-	14	2486_2490	c.2378_2382delTAAGT	c.(2377-2382)ttaagtfs	p.LS793fs		NM_173500.3	NP_775771.3	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2	793					cell death (GO:0008219)|cilium assembly (GO:0042384)|peptidyl-serine phosphorylation (GO:0018105)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	43		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		GCTGCCCTCTACTTAACTTCTCATC	0.4																																																0																																										SO:0001589	frameshift_variant	146057			AB020654	CCDS42029.1	15q15.2	2014-01-21			ENSG00000128881	ENSG00000128881			19141	protein-coding gene	gene with protein product		611695	"""spinocerebellar ataxia 11"""	SCA11		10048485	Standard	NM_173500		Approved	KIAA0847	uc001zqo.2	Q6IQ55	OTTHUMG00000175802	ENST00000267890.6:c.2378_2382delTAAGT	15.37:g.43045062_43045066delACTTA	ENSP00000267890:p.Leu793fs		O94932|Q6ZN52|Q8IVV1	Frame_Shift_Del	DEL	ENST00000267890.6	37	CCDS42029.1																																																																																				0.400	TTBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431106.2	NM_173500		27	85	27	85
IREB2	3658	broad.mit.edu;hgsc.bcm.edu	37	15	78764190	78764192	+	In_Frame_Del	DEL	CCT	CCT	-			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr15:78764190_78764192delCCT	ENST00000258886.8	+	7	956_958	c.807_809delCCT	c.(805-810)gacctc>gac	p.L271del	IREB2_ENST00000560440.1_In_Frame_Del_p.L271del	NM_004136.2	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	271					aging (GO:0007568)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|erythrocyte homeostasis (GO:0034101)|intestinal absorption (GO:0050892)|iron ion transport (GO:0006826)|osteoclast differentiation (GO:0030316)|post-embryonic development (GO:0009791)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to iron(II) ion (GO:0010040)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|translation repressor activity (GO:0030371)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	41				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		AAGAAAAAGACCTCCTCTTCCCA	0.399																																					NSCLC(200;764 2208 35157 49871 50830)											0																																										SO:0001651	inframe_deletion	3658			M58511	CCDS10302.1	15q25.1	2013-09-20			ENSG00000136381	ENSG00000136381			6115	protein-coding gene	gene with protein product		147582				2172968	Standard	NM_004136		Approved	IRP2	uc002bdr.2	P48200	OTTHUMG00000143861	ENST00000258886.8:c.807_809delCCT	15.37:g.78764193_78764195delCCT	ENSP00000258886:p.Leu271del		A8KAC7|E1CJT9|H0YKU0|Q13095|Q1HE21|Q59FQ7|Q8WVK6|Q9UF17	In_Frame_Del	DEL	ENST00000258886.8	37	CCDS10302.1																																																																																				0.399	IREB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290109.3	NM_004136		20	54	20	54
ACADVL	37	broad.mit.edu;hgsc.bcm.edu	37	17	7125570	7125572	+	In_Frame_Del	DEL	AGG	AGG	-	rs149680575		TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr17:7125570_7125572delAGG	ENST00000356839.5	+	9	1006_1008	c.827_829delAGG	c.(826-831)aaggag>aag	p.E277del	ACADVL_ENST00000350303.5_In_Frame_Del_p.E255del|ACADVL_ENST00000543245.2_In_Frame_Del_p.E300del|DLG4_ENST00000399510.2_5'Flank|MIR324_ENST00000362183.1_RNA	NM_000018.3|NM_001270448.1	NP_000009.1|NP_001257377.1	P49748	ACADV_HUMAN	acyl-CoA dehydrogenase, very long chain	277	Catalytic.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|energy derivation by oxidation of organic compounds (GO:0015980)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(1)|ovary(4)|skin(1)	21						GGAGCCGTGAAGGAGAAGATCAC	0.552																																																0									,	3,4261		1,1,2130					,	5.2	0.8		dbSNP_134	54	0,8254		0,0,4127	no	coding,coding	ACADVL	NM_001033859.1,NM_000018.2	,	1,1,6257	A1A1,A1R,RR		0.0,0.0704,0.024	,	,		3,12515				SO:0001651	inframe_deletion	37			BC012912	CCDS11090.1, CCDS42249.1, CCDS58509.1	17p13.1	2010-04-30	2010-04-30		ENSG00000072778	ENSG00000072778			92	protein-coding gene	gene with protein product		609575	"""acyl-Coenzyme A dehydrogenase, very long chain"""			8921384	Standard	NM_000018		Approved	VLCAD, LCACD, ACAD6	uc002gev.4	P49748	OTTHUMG00000102157	ENST00000356839.5:c.827_829delAGG	17.37:g.7125570_7125572delAGG	ENSP00000349297:p.Glu277del		B4DEB6|F5H2A9|O76056|Q8WUL0	In_Frame_Del	DEL	ENST00000356839.5	37	CCDS11090.1																																																																																				0.552	ACADVL-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220001.5	NM_000018		25	74	25	74
TSHZ1	10194	broad.mit.edu;hgsc.bcm.edu	37	18	72997649	72997651	+	In_Frame_Del	DEL	AGA	AGA	-			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr18:72997649_72997651delAGA	ENST00000580243.1	+	2	635_637	c.287_289delAGA	c.(286-291)gagaag>gag	p.K97del	TSHZ1_ENST00000322038.5_In_Frame_Del_p.K52del			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	97	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		TCTCGAGAAGAGAAGGAGGATCC	0.586																																																0																																										SO:0001651	inframe_deletion	10194			AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.287_289delAGA	18.37:g.72997649_72997651delAGA	ENSP00000464391:p.Lys97del		O60534|Q4LE29|Q53EU4	In_Frame_Del	DEL	ENST00000580243.1	37																																																																																					0.586	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786		14	31	14	31
EID2B	126272	broad.mit.edu;hgsc.bcm.edu	37	19	40023078	40023081	+	Frame_Shift_Del	DEL	ACAA	ACAA	-			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr19:40023078_40023081delACAA	ENST00000326282.4	-	1	413_416	c.362_365delTTGT	c.(361-366)tttgtgfs	p.FV121fs	CTB-60E11.9_ENST00000594676.1_RNA|EID2B_ENST00000601837.1_Intron	NM_152361.1	NP_689574.1			EP300 interacting inhibitor of differentiation 2B											endometrium(1)|lung(1)|urinary_tract(1)	3	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;8.61e-26)|all cancers(26;2.76e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GCAGCCTTCCACAAACAGCCTGCG	0.574																																																0										10,4254		4,2,2126						1.3	1.0			55	44,8210		22,0,4105	no	frameshift	EID2B	NM_152361.1		26,2,6231	A1A1,A1R,RR		0.5331,0.2345,0.4314				54,12464				SO:0001589	frameshift_variant	126272			AK096263	CCDS12539.1	19q13.2	2008-02-05				ENSG00000176401			26796	protein-coding gene	gene with protein product						15970276	Standard	NM_152361		Approved	EID-3, FLJ38944	uc002olz.1	Q96D98		ENST00000326282.4:c.362_365delTTGT	19.37:g.40023078_40023081delACAA	ENSP00000317564:p.Phe121fs			Frame_Shift_Del	DEL	ENST00000326282.4	37	CCDS12539.1																																																																																				0.574	EID2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464961.1	NM_152361		18	44	18	44
TRIM28	10155	broad.mit.edu;hgsc.bcm.edu	37	19	59061018	59061021	+	Splice_Site	DEL	GTGA	GTGA	-			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr19:59061018_59061021delGTGA	ENST00000253024.5	+	13	2271		c.e13+1		TRIM28_ENST00000341753.6_Splice_Site	NM_005762.2	NP_005753.1	Q13263	TIF1B_HUMAN	tripartite motif containing 28						convergent extension involved in axis elongation (GO:0060028)|DNA repair (GO:0006281)|embryonic placenta morphogenesis (GO:0060669)|epithelial to mesenchymal transition (GO:0001837)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|Krueppel-associated box domain binding (GO:0035851)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		ATGTACCAGGGTGAGTGTGAGGCT	0.574																																																0																																										SO:0001630	splice_region_variant	10155				CCDS12985.1	19q13.4	2014-06-13	2011-01-25			ENSG00000130726		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	16384	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 157"""	601742	"""tripartite motif-containing 28"""			11331580, 11226167	Standard	NM_005762		Approved	TIF1B, KAP1, TF1B, RNF96, PPP1R157	uc002qtg.1	Q13263		ENST00000253024.5:c.1982+1GTGA>-	19.37:g.59061018_59061021delGTGA			O00677|Q7Z632|Q93040|Q96IM1	Splice_Site	DEL	ENST00000253024.5	37	CCDS12985.1																																																																																				0.574	TRIM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467074.1	NM_005762	Intron	87	140	87	140
FUBP1	8880	broad.mit.edu	37	1	78433848	78433851	+	Splice_Site	DEL	CAGT	CAGT	-			TCGA-DU-7300-01A-21D-2086-08	TCGA-DU-7300-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41bb7bd2-c24e-41ae-881d-25b44ae287ad	2de73131-9a0c-46fc-aa61-6d35f76f75d2	g.chr1:78433848_78433851delCAGT	ENST00000370768.2	-	3	329_332	c.248_251delACTG	c.(247-252)gactgt>gt	p.DC83fs	FUBP1_ENST00000436586.2_Splice_Site_p.DC104fs|FUBP1_ENST00000370767.1_Splice_Site_p.DC83fs	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	83					positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)	p.?(1)		central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						GGAATACTTACAGTCATTTTGAGG	0.319			"""F, N"""		oligodendroglioma																																		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	1	Unknown(1)	central_nervous_system(1)																																								SO:0001630	splice_region_variant	8880			U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.250+1ACTG>-	1.37:g.78433848_78433851delCAGT			Q12828	Splice_Site	DEL	ENST00000370768.2	37	CCDS683.1																																																																																				0.319	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902	Frame_Shift_Del	8	14	8	14
