#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
ZMYND11	10771	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	285431	285431	+	Silent	SNP	A	A	G			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr10:285431A>G	ENST00000397962.3	+	7	1091	c.663A>G	c.(661-663)caA>caG	p.Q221Q	ZMYND11_ENST00000381584.1_Silent_p.Q204Q|ZMYND11_ENST00000381602.4_Silent_p.Q181Q|ZMYND11_ENST00000535374.1_Intron|ZMYND11_ENST00000403354.1_Silent_p.Q167Q|ZMYND11_ENST00000509513.2_Silent_p.Q221Q|ZMYND11_ENST00000381607.4_Silent_p.Q127Q|ZMYND11_ENST00000545619.1_Silent_p.Q127Q|ZMYND11_ENST00000558098.2_Silent_p.Q221Q|ZMYND11_ENST00000381591.1_Silent_p.Q221Q|ZMYND11_ENST00000381604.4_Silent_p.Q181Q|ZMYND11_ENST00000402736.1_Silent_p.Q190Q|ZMYND11_ENST00000309776.4_Silent_p.Q181Q|ZMYND11_ENST00000397959.3_Silent_p.Q136Q|ZMYND11_ENST00000602682.1_Silent_p.Q136Q			Q15326	ZMY11_HUMAN	zinc finger, MYND-type containing 11	221	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cell cycle (GO:0007049)|cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription elongation from RNA polymerase II promoter (GO:0034243)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	24		all_cancers(4;1.32e-05)|all_lung(4;3.67e-05)|Lung NSC(4;0.000301)|all_epithelial(10;0.000416)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.132)	Epithelial(11;0.00289)|all cancers(11;0.0108)|Lung(33;0.0689)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		CTGATGCCCAATTGCTTCTCC	0.348																																																0													169.0	158.0	162.0					10																	285431		2203	4300	6503	SO:0001819	synonymous_variant	10771			X86098	CCDS7052.1, CCDS7053.1, CCDS7052.2, CCDS55696.1, CCDS55697.1, CCDS7053.2, CCDS73060.1, CCDS73061.1	10p14	2011-01-26	2011-01-26		ENSG00000015171	ENSG00000015171		"""Zinc fingers, MYND-type"""	16966	protein-coding gene	gene with protein product		608668	"""zinc finger, MYND domain containing 11"""			7621829, 10734313	Standard	NM_006624		Approved	BS69	uc010pzx.2	Q15326	OTTHUMG00000017526	ENST00000397962.3:c.663A>G	10.37:g.285431A>G			B2R6G8|B7Z293|F6UH50|Q2LD45|Q2LD46|Q2LD47|Q2LD48|Q5VUI1|Q8N4B3	Silent	SNP	ENST00000397962.3	37	CCDS7052.2																																																																																				0.348	ZMYND11-206	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046382.4	NM_006624		91	149	91	149
SEMA4G	57715	hgsc.bcm.edu;ucsc.edu	37	10	102741298	102741298	+	Intron	SNP	T	T	A			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr10:102741298T>A	ENST00000370250.4	+	13	2063				SEMA4G_ENST00000517724.1_Intron|MRPL43_ENST00000318325.2_Intron|MRPL43_ENST00000370241.3_Intron|RP11-108L7.4_ENST00000447344.1_RNA|SEMA4G_ENST00000210633.3_Intron|MRPL43_ENST00000299179.5_Silent_p.I177I|MRPL43_ENST00000342071.1_Missense_Mutation_p.I220F|MRPL43_ENST00000370242.4_Intron	NM_017893.3	NP_060363.2	Q9NTN9	SEM4G_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G						cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Colorectal(252;0.234)		Epithelial(162;3.71e-09)|all cancers(201;2.1e-07)		ACTGAACTGATATCTGAAGAA	0.398																																																0													145.0	138.0	140.0					10																	102741298		2203	4300	6503	SO:0001627	intron_variant	84545			AB046839	CCDS7501.1, CCDS55724.1	10q24.31	2013-01-11			ENSG00000095539	ENSG00000095539		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10735	protein-coding gene	gene with protein product							Standard	NM_017893		Approved	FLJ20590, KIAA1619	uc001krw.2	Q9NTN9	OTTHUMG00000018922	ENST00000370250.4:c.1690+312T>A	10.37:g.102741298T>A			A1A5C6|A6NJY8|Q58EY1|Q9HCF3	Missense_Mutation	SNP	ENST00000370250.4	37		.	.	.	.	.	.	.	.	.	.	T	9.795	1.178915	0.21787	.	.	ENSG00000055950	ENST00000342071	.	.	.	3.37	-0.394	0.12434	.	.	.	.	.	T	0.18341	0.0440	.	.	.	0.09310	N	1	B	0.34015	0.435	B	0.26517	0.07	T	0.14172	-1.0482	7	0.30078	T	0.28	.	5.9102	0.19025	0.0:0.4336:0.0:0.5664	.	220	C9J5Q3	.	F	220	.	ENSP00000339844:I220F	I	-	1	0	MRPL43	102731288	0.001000	0.12720	0.004000	0.12327	0.079000	0.17450	0.237000	0.17985	-0.066000	0.12998	0.254000	0.18369	ATC		0.398	SEMA4G-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049920.2			48	213	48	213
LRRC4C	57689	hgsc.bcm.edu;broad.mit.edu	37	11	40136683	40136683	+	Missense_Mutation	SNP	A	A	G			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr11:40136683A>G	ENST00000278198.2	-	2	3123	c.1160T>C	c.(1159-1161)aTt>aCt	p.I387T	LRRC4C_ENST00000528697.1_Missense_Mutation_p.I387T|LRRC4C_ENST00000530763.1_Missense_Mutation_p.I387T|LRRC4C_ENST00000527150.1_Missense_Mutation_p.I387T			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	387	Ig-like C2-type.				regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)				NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				ATTTGGAGTAATCCAAGATAC	0.493																																																0													143.0	128.0	133.0					11																	40136683		2203	4300	6503	SO:0001583	missense	57689			AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"""Immunoglobulin superfamily / I-set domain containing"""	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.1160T>C	11.37:g.40136683A>G	ENSP00000278198:p.Ile387Thr		A8K0T1|Q7L0N3	Missense_Mutation	SNP	ENST00000278198.2	37	CCDS31464.1	.	.	.	.	.	.	.	.	.	.	A	15.08	2.726950	0.48833	.	.	ENSG00000148948	ENST00000278198;ENST00000527150;ENST00000528697;ENST00000530763	T;T;T;T	0.26660	1.72;1.72;1.72;1.72	5.72	5.72	0.89469	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.32852	0.0843	L	0.37507	1.11	0.80722	D	1	P	0.42357	0.777	P	0.49528	0.614	T	0.05053	-1.0909	10	0.72032	D	0.01	.	15.2327	0.73404	1.0:0.0:0.0:0.0	.	387	Q9HCJ2	LRC4C_HUMAN	T	387	ENSP00000278198:I387T;ENSP00000436976:I387T;ENSP00000437132:I387T;ENSP00000434761:I387T	ENSP00000278198:I387T	I	-	2	0	LRRC4C	40093259	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	9.261000	0.95576	2.197000	0.70478	0.529000	0.55759	ATT		0.493	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929		188	171	188	171
CFL1	1072	hgsc.bcm.edu;broad.mit.edu	37	11	65623202	65623202	+	Splice_Site	SNP	C	C	T			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr11:65623202C>T	ENST00000525451.2	-	4	1027		c.e4-1		CFL1_ENST00000531413.1_Splice_Site|CFL1_ENST00000531407.1_Splice_Site|CFL1_ENST00000524553.1_Splice_Site|CFL1_ENST00000534769.1_Splice_Site|CFL1_ENST00000527344.1_Splice_Site|CFL1_ENST00000308162.5_Splice_Site			P23528	COF1_HUMAN	cofilin 1 (non-muscle)						actin cytoskeleton organization (GO:0030036)|actin filament depolymerization (GO:0030042)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytoskeleton organization (GO:0007010)|establishment of cell polarity (GO:0030010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|mitotic cytokinesis (GO:0000281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell size (GO:0045792)|neural crest cell migration (GO:0001755)|neural fold formation (GO:0001842)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of actin filament depolymerization (GO:0030836)|protein import into nucleus (GO:0006606)|protein phosphorylation (GO:0006468)|regulation of cell morphogenesis (GO:0022604)|response to amino acid (GO:0043200)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)	cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				breast(1)|kidney(1)|large_intestine(2)|lung(2)	6				READ - Rectum adenocarcinoma(159;0.169)		CTCGGGGGCCCTGGACAGAAA	0.542																																					Esophageal Squamous(90;820 1366 3932 32351 42291)											0													38.0	36.0	37.0					11																	65623202		2201	4297	6498	SO:0001630	splice_region_variant	1072			X95404	CCDS8114.1	11q13.1	2010-12-03			ENSG00000172757	ENSG00000172757			1874	protein-coding gene	gene with protein product		601442		CFL		8800436	Standard	NM_005507		Approved		uc001ofs.3	P23528		ENST00000525451.2:c.312-1G>A	11.37:g.65623202C>T			B3KUQ1|Q53Y87|Q9UCA2	Splice_Site	SNP	ENST00000525451.2	37	CCDS8114.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.045816	0.36085	.	.	ENSG00000172757	ENST00000525451;ENST00000308162;ENST00000527344;ENST00000531407;ENST00000524553;ENST00000534769;ENST00000531413;ENST00000532134;ENST00000530413	.	.	.	4.95	4.02	0.46733	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8599	0.52459	0.0:0.909:0.0:0.091	.	.	.	.	.	-1	.	.	.	-	.	.	CFL1	65379778	1.000000	0.71417	0.994000	0.49952	0.292000	0.27327	4.943000	0.63554	2.449000	0.82847	0.655000	0.94253	.		0.542	CFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390701.3	NM_005507	Intron	6	89	6	89
ARNTL2	56938	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	27542188	27542188	+	Missense_Mutation	SNP	C	C	T			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr12:27542188C>T	ENST00000266503.5	+	8	752	c.734C>T	c.(733-735)tCt>tTt	p.S245F	ARNTL2_ENST00000311001.5_Missense_Mutation_p.S231F|ARNTL2_ENST00000261178.5_Missense_Mutation_p.S197F|RP11-165P7.1_ENST00000500498.2_RNA|ARNTL2_ENST00000546179.1_Missense_Mutation_p.S208F|ARNTL2_ENST00000395901.2_Missense_Mutation_p.S208F|ARNTL2_ENST00000544915.1_Missense_Mutation_p.S211F|ARNTL2_ENST00000542388.1_Missense_Mutation_p.S160F			Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear translocator-like 2	245	Interaction with PER2. {ECO:0000250|UniProtKB:Q2VPD4}.|PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	E-box binding (GO:0070888)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	21	Colorectal(261;0.0847)|Lung SC(9;0.184)					CAACTTTCTTCTTTTGATATT	0.323																																																0													87.0	85.0	86.0					12																	27542188		2202	4298	6500	SO:0001583	missense	56938			AF246961	CCDS8712.1, CCDS58219.1, CCDS58220.1, CCDS58221.1, CCDS58222.1	12p12.2-p11.2	2013-05-21			ENSG00000029153	ENSG00000029153		"""Basic helix-loop-helix proteins"""	18984	protein-coding gene	gene with protein product		614517				10864977, 10964693	Standard	NM_020183		Approved	BMAL2, MOP9, CLIF, PASD9, bHLHe6	uc001rht.2	Q8WYA1	OTTHUMG00000169257	ENST00000266503.5:c.734C>T	12.37:g.27542188C>T	ENSP00000266503:p.Ser245Phe		B7Z429|F5H402|Q8WYA2|Q8WYA3|Q8WYA4|Q96J63|Q9H2M4|Q9NS70|Q9NYQ4|Q9NYQ5	Missense_Mutation	SNP	ENST00000266503.5	37	CCDS8712.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.48|18.48	3.633955|3.633955	0.67130|0.67130	.|.	.|.	ENSG00000029153|ENSG00000029153	ENST00000457040|ENST00000544915;ENST00000395901;ENST00000546179;ENST00000311001;ENST00000261178;ENST00000266503;ENST00000542388	.|T;T;T;T;T;T;T	.|0.17691	.|2.26;2.26;2.26;2.26;2.26;2.26;2.26	3.99|3.99	3.05|3.05	0.35203|0.35203	.|PAS (1);	.|0.363697	.|0.29444	.|N	.|0.012129	T|T	0.42944|0.42944	0.1225|0.1225	M|M	0.80982|0.80982	2.52|2.52	0.48696|0.48696	D|D	0.999695|0.999695	.|D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D	.|0.87578	.|0.994;0.994;0.99;0.994;0.989;0.998	T|T	0.49283|0.49283	-0.8956|-0.8956	5|10	.|0.87932	.|D	.|0	.|.	13.5604|13.5604	0.61786|0.61786	0.0:0.8426:0.1574:0.0|0.0:0.8426:0.1574:0.0	.|.	.|208;211;208;197;231;245	.|F5H402;Q8WYA1-5;Q8WYA1-3;Q8WYA1-4;Q8WYA1-2;Q8WYA1	.|.;.;.;.;.;BMAL2_HUMAN	F|F	197|211;208;208;231;197;245;160	.|ENSP00000442438:S211F;ENSP00000379238:S208F;ENSP00000438545:S208F;ENSP00000312247:S231F;ENSP00000261178:S197F;ENSP00000266503:S245F;ENSP00000445836:S160F	.|ENSP00000261178:S197F	L|S	+|+	1|2	0|0	ARNTL2|ARNTL2	27433455|27433455	0.992000|0.992000	0.36948|0.36948	0.925000|0.925000	0.36789|0.36789	0.759000|0.759000	0.43091|0.43091	3.582000|3.582000	0.53921|0.53921	0.967000|0.967000	0.38186|0.38186	0.655000|0.655000	0.94253|0.94253	CTT|TCT		0.323	ARNTL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403162.1	NM_020183		55	110	55	110
KRT86	3892	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	52698737	52698737	+	Missense_Mutation	SNP	C	C	T	rs199678774		TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr12:52698737C>T	ENST00000423955.2	+	6	839	c.661C>T	c.(661-663)Cgc>Tgc	p.R221C	RP11-845M18.6_ENST00000552441.1_RNA|KRT86_ENST00000544024.1_Missense_Mutation_p.R221C|KRT86_ENST00000293525.5_Missense_Mutation_p.R221C			O43790	KRT86_HUMAN	keratin 86	221	Coil 1B.|Rod.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(357;0.189)		CGCCTACCTCCGCAAATCAGA	0.597													N|||	1	0.000199681	0.0008	0.0	5008	,	,		18252	0.0		0.0	False		,,,				2504	0.0															0								C	CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	137.0	145.0	142.0		661	3.8	1.0	12		142	0,8600		0,0,4300	no	missense	KRT86	NM_002284.3	180	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	221/487	52698737	2,13004	2203	4300	6503	SO:0001583	missense	3892			X99142	CCDS41785.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000170442		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6463	protein-coding gene	gene with protein product	"""hard keratin type II 6"""	601928	"""keratin, hair, basic, 6 (monilethrix)"""	KRTHB6		9241275, 16831889	Standard	NM_002284		Approved	MNX, Hb6	uc001sad.3	O43790		ENST00000423955.2:c.661C>T	12.37:g.52698737C>T	ENSP00000444533:p.Arg221Cys		P78387	Missense_Mutation	SNP	ENST00000423955.2	37	CCDS41785.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	12.08	1.829498	0.32329	4.54E-4	0.0	ENSG00000170442;ENSG00000170442;ENSG00000170442;ENSG00000258832	ENST00000544024;ENST00000423955;ENST00000293525;ENST00000553310	T;T;T	0.78924	-1.22;-1.22;-1.22	4.73	3.8	0.43715	Filament (1);	0.000000	0.42964	U	0.000628	T	0.63141	0.2486	N	0.25144	0.715	0.39093	D	0.961134	B	0.22480	0.07	B	0.24269	0.052	T	0.65001	-0.6274	10	0.62326	D	0.03	.	8.2292	0.31589	0.2896:0.5748:0.1356:0.0	.	221	O43790	KRT86_HUMAN	C	221	ENSP00000443169:R221C;ENSP00000444533:R221C;ENSP00000293525:R221C	ENSP00000293525:R221C	R	+	1	0	AC021066.1;KRT86	50985004	0.948000	0.32251	0.999000	0.59377	0.753000	0.42808	1.437000	0.34991	2.182000	0.69389	0.430000	0.28490	CGC		0.597	KRT86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404911.1	NM_002284		204	253	204	253
ESPL1	9700	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	53680351	53680351	+	Silent	SNP	A	A	G			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr12:53680351A>G	ENST00000257934.4	+	18	3922	c.3831A>G	c.(3829-3831)ctA>ctG	p.L1277L	ESPL1_ENST00000552462.1_Silent_p.L1277L	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1277					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						TCACAAAACTAGGTGGCCTCA	0.542																																					Colon(53;1069 1201 2587 5382)											0													74.0	80.0	78.0					12																	53680351		2203	4300	6503	SO:0001819	synonymous_variant	9700			D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.3831A>G	12.37:g.53680351A>G				Silent	SNP	ENST00000257934.4	37	CCDS8852.1																																																																																				0.542	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291		134	139	134	139
CTSG	1511	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	25043477	25043477	+	Missense_Mutation	SNP	G	G	A			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr14:25043477G>A	ENST00000216336.2	-	4	604	c.568C>T	c.(568-570)Cgg>Tgg	p.R190W		NM_001911.2	NP_001902.1	P08311	CATG_HUMAN	cathepsin G	190	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|defense response to fungus (GO:0050832)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|negative regulation of growth of symbiont in host (GO:0044130)|neutrophil mediated killing of gram-positive bacterium (GO:0070946)|positive regulation of immune response (GO:0050778)|proteolysis (GO:0006508)|response to lipopolysaccharide (GO:0032496)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	heparin binding (GO:0008201)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			autonomic_ganglia(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(265;0.0269)		CGTTCCCGCCGGTCCCCCACA	0.617																																																0													61.0	54.0	57.0					14																	25043477		2203	4300	6503	SO:0001583	missense	1511			M16117	CCDS9631.1	14q12	2013-02-25			ENSG00000100448	ENSG00000100448		"""Cathepsins"", ""Endogenous ligands"""	2532	protein-coding gene	gene with protein product		116830				2569462	Standard	NM_001911		Approved	CG	uc001wpq.3	P08311	OTTHUMG00000140182	ENST00000216336.2:c.568C>T	14.37:g.25043477G>A	ENSP00000216336:p.Arg190Trp		Q6IBJ6|Q9UCA5|Q9UCU6	Missense_Mutation	SNP	ENST00000216336.2	37	CCDS9631.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.193901	0.58017	.	.	ENSG00000100448	ENST00000216336	D	0.88975	-2.45	5.01	4.11	0.48088	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.667491	0.12388	N	0.473306	D	0.85410	0.5690	N	0.25957	0.775	0.09310	N	1	P	0.44690	0.841	P	0.47206	0.541	T	0.77005	-0.2748	10	0.87932	D	0	.	9.8913	0.41292	0.097:0.0:0.903:0.0	.	190	P08311	CATG_HUMAN	W	190	ENSP00000216336:R190W	ENSP00000216336:R190W	R	-	1	2	CTSG	24113317	0.021000	0.18746	0.010000	0.14722	0.024000	0.10985	1.778000	0.38614	1.419000	0.47118	0.561000	0.74099	CGG		0.617	CTSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276536.2	NM_001911		42	51	42	51
EXOC5	10640	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	57684716	57684716	+	Missense_Mutation	SNP	C	C	T			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr14:57684716C>T	ENST00000413566.2	-	15	1956	c.1597G>A	c.(1597-1599)Gat>Aat	p.D533N	EXOC5_ENST00000340918.7_Missense_Mutation_p.D468N	NM_006544.3	NP_006535.1	O00471	EXOC5_HUMAN	exocyst complex component 5	533					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|vesicle docking (GO:0048278)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(3)|endometrium(1)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	22						ATGCCAGTATCCAATTTCATC	0.294																																																0													83.0	86.0	85.0					14																	57684716		1798	4055	5853	SO:0001583	missense	10640			U85946	CCDS45111.1	14q22.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000070367	ENSG00000070367			10696	protein-coding gene	gene with protein product		604469	"""SEC10 (S. cerevisiae)-like 1"", ""SEC10-like 1 (S. cerevisiae)"""	SEC10L1		9119050	Standard	XM_005267272		Approved	SEC10, SEC10P	uc001xct.3	O00471	OTTHUMG00000171309	ENST00000413566.2:c.1597G>A	14.37:g.57684716C>T	ENSP00000389934:p.Asp533Asn		B2R6C5	Missense_Mutation	SNP	ENST00000413566.2	37	CCDS45111.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.590104	0.86851	.	.	ENSG00000070367	ENST00000413566;ENST00000340918	T;T	0.38401	1.14;1.15	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	T	0.47414	0.1444	L	0.39245	1.2	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.70487	0.964;0.969	T	0.23619	-1.0183	10	0.06365	T	0.9	-14.5611	18.6145	0.91297	0.0:1.0:0.0:0.0	.	468;533	F8W9B8;O00471	.;EXOC5_HUMAN	N	533;468	ENSP00000389934:D533N;ENSP00000342100:D468N	ENSP00000342100:D468N	D	-	1	0	EXOC5	56754469	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.542000	0.82095	2.462000	0.83206	0.555000	0.69702	GAT		0.294	EXOC5-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412905.1	NM_006544		45	62	45	62
MAX	4149	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	65544747	65544747	+	Missense_Mutation	SNP	C	C	T			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr14:65544747C>T	ENST00000358664.4	-	4	309	c.179G>A	c.(178-180)cGg>cAg	p.R60Q	MAX_ENST00000341653.2_Intron|MAX_ENST00000284165.6_Missense_Mutation_p.R60Q|MAX_ENST00000555419.1_Missense_Mutation_p.R24Q|MAX_ENST00000358402.4_Missense_Mutation_p.R51Q|MAX_ENST00000556979.1_Missense_Mutation_p.R60Q|MAX_ENST00000557277.1_5'UTR|MAX_ENST00000555667.1_Missense_Mutation_p.R51Q|MAX_ENST00000556443.1_Missense_Mutation_p.R51Q|MAX_ENST00000555932.1_Intron|MAX_ENST00000557746.1_Missense_Mutation_p.R51Q	NM_002382.4	NP_002373.3	P61244	MAX_HUMAN	MYC associated factor X	60	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cellular response to peptide hormone stimulus (GO:0071375)|cellular response to starvation (GO:0009267)|negative regulation of gene expression (GO:0010629)|neuron apoptotic process (GO:0051402)|protein complex assembly (GO:0006461)|response to axon injury (GO:0048678)|response to insulin (GO:0032868)|retina development in camera-type eye (GO:0060041)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)|PML body (GO:0016605)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)	p.R60Q(5)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	17				all cancers(60;0.000776)|OV - Ovarian serous cystadenocarcinoma(108;0.00359)|BRCA - Breast invasive adenocarcinoma(234;0.00999)		GATTTGGGCCCGGGATGCCTG	0.498																																																5	Substitution - Missense(5)	endometrium(4)|haematopoietic_and_lymphoid_tissue(1)											100.0	88.0	92.0					14																	65544747		2203	4300	6503	SO:0001583	missense	4149				CCDS9770.1, CCDS9771.1, CCDS9772.1, CCDS9774.1, CCDS41965.1	14q23	2014-09-17	2005-02-08		ENSG00000125952	ENSG00000125952		"""Basic helix-loop-helix proteins"""	6913	protein-coding gene	gene with protein product		154950	"""MAX protein"""			1557420	Standard	NM_002382		Approved	bHLHd4, bHLHd5, bHLHd6, bHLHd7, bHLHd8	uc001xif.2	P61244	OTTHUMG00000142809	ENST00000358664.4:c.179G>A	14.37:g.65544747C>T	ENSP00000351490:p.Arg60Gln		A6NH73|A8K265|A8K4G4|A8K824|P25912|P52163|Q14803|Q96CY8	Missense_Mutation	SNP	ENST00000358664.4	37	CCDS9771.1	.	.	.	.	.	.	.	.	.	.	C	18.61	3.661506	0.67700	.	.	ENSG00000125952	ENST00000358402;ENST00000284165;ENST00000358664;ENST00000555419;ENST00000441116;ENST00000556979;ENST00000555667;ENST00000557746;ENST00000556443	D;D;D;D;D;D;D;D	0.97870	-4.58;-4.58;-4.58;-4.32;-4.58;-4.58;-4.58;-4.58	5.72	3.91	0.45181	Helix-loop-helix DNA-binding (5);	0.119749	0.56097	D	0.000028	D	0.98492	0.9497	M	0.84326	2.69	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.998;0.991;0.994;0.995;0.985	D	0.98698	1.0699	10	0.87932	D	0	-3.6574	11.4065	0.49900	0.0:0.8517:0.0:0.1483	.	60;51;51;60;60	Q14803;Q6V3B1;P61244-2;P61244;P61244-3	.;.;.;MAX_HUMAN;.	Q	51;60;60;24;67;60;51;51;51	ENSP00000351175:R51Q;ENSP00000284165:R60Q;ENSP00000351490:R60Q;ENSP00000452405:R24Q;ENSP00000452378:R60Q;ENSP00000452286:R51Q;ENSP00000452197:R51Q;ENSP00000450818:R51Q	ENSP00000284165:R60Q	R	-	2	0	MAX	64614500	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.037000	0.70956	0.774000	0.33427	-0.140000	0.14226	CGG		0.498	MAX-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286386.1	NM_197957		53	74	53	74
ADAM20	8748	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	70989595	70989595	+	Missense_Mutation	SNP	C	C	T			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr14:70989595C>T	ENST00000256389.3	-	2	2274	c.2030G>A	c.(2029-2031)aGt>aAt	p.S677N	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	627					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		ATGAACCATACTGGCACACTT	0.463																																																0													500.0	375.0	417.0					14																	70989595		2203	4300	6503	SO:0001583	missense	8748			AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"""ADAM metallopeptidase domain containing"""	199	protein-coding gene	gene with protein product		603712	"""a disintegrin and metalloproteinase domain 20"""			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.2030G>A	14.37:g.70989595C>T	ENSP00000256389:p.Ser677Asn		Q6GTZ1|Q9UKJ9	Missense_Mutation	SNP	ENST00000256389.3	37	CCDS32111.1	.	.	.	.	.	.	.	.	.	.	C	2.673	-0.277020	0.05679	.	.	ENSG00000134007	ENST00000256389	T	0.00976	5.48	4.8	-6.71	0.01760	ADAM, cysteine-rich (1);	1.571450	0.04482	N	0.377987	T	0.00552	0.0018	N	0.16201	0.385	0.09310	N	1	B	0.06786	0.001	B	0.12837	0.008	T	0.47711	-0.9096	10	0.02654	T	1	.	4.2609	0.10740	0.1152:0.1385:0.115:0.6313	.	627	O43506	ADA20_HUMAN	N	677	ENSP00000256389:S677N	ENSP00000256389:S677N	S	-	2	0	ADAM20	70059348	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.077000	0.00615	-1.437000	0.01967	-0.768000	0.03414	AGT		0.463	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2			269	413	269	413
TEX9	374618	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	56686922	56686922	+	Missense_Mutation	SNP	C	C	G			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr15:56686922C>G	ENST00000352903.2	+	9	742	c.718C>G	c.(718-720)Cag>Gag	p.Q240E	TEX9_ENST00000558083.2_Missense_Mutation_p.Q165E|RP11-48G14.2_ENST00000564401.1_lincRNA|TEX9_ENST00000561221.2_Missense_Mutation_p.Q240E|TEX9_ENST00000537232.1_Missense_Mutation_p.Q165E|TEX9_ENST00000560582.1_5'UTR	NM_198524.1	NP_940926.1	Q8N6V9	TEX9_HUMAN	testis expressed 9	240										cervix(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	14				all cancers(107;0.0394)|GBM - Glioblastoma multiforme(80;0.056)		TATGAGACAGCAGCGAACAAT	0.284																																																0													38.0	41.0	40.0					15																	56686922		2192	4278	6470	SO:0001583	missense	374618			BC028119	CCDS10157.1, CCDS66776.1	15q21.3	2007-03-13	2007-03-13		ENSG00000151575	ENSG00000151575			29585	protein-coding gene	gene with protein product			"""testis expressed sequence 9"""				Standard	XM_005254361		Approved		uc002adp.3	Q8N6V9	OTTHUMG00000132035	ENST00000352903.2:c.718C>G	15.37:g.56686922C>G	ENSP00000342169:p.Gln240Glu		B4DH73	Missense_Mutation	SNP	ENST00000352903.2	37	CCDS10157.1	.	.	.	.	.	.	.	.	.	.	C	13.65	2.300631	0.40694	.	.	ENSG00000151575	ENST00000352903;ENST00000537232	T;T	0.75477	-0.94;-0.94	5.25	4.28	0.50868	.	0.053416	0.85682	D	0.000000	T	0.68622	0.3021	L	0.55103	1.725	0.80722	D	1	B;B	0.30727	0.033;0.292	B;B	0.27380	0.027;0.079	T	0.66937	-0.5797	10	0.26408	T	0.33	-12.628	16.258	0.82526	0.0:0.8552:0.1448:0.0	.	165;240	B4DH73;Q8N6V9	.;TEX9_HUMAN	E	240;165	ENSP00000342169:Q240E;ENSP00000438745:Q165E	ENSP00000342169:Q240E	Q	+	1	0	TEX9	54474214	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.392000	0.59659	2.453000	0.82957	0.591000	0.81541	CAG		0.284	TEX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255048.2	NM_198524		12	79	12	79
HEATR6	63897	hgsc.bcm.edu;broad.mit.edu	37	17	58133572	58133572	+	Silent	SNP	G	G	A			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr17:58133572G>A	ENST00000184956.6	-	13	2122	c.2106C>T	c.(2104-2106)taC>taT	p.Y702Y	HEATR6_ENST00000585976.1_Intron	NM_022070.4	NP_071353.4	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	702							poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	44	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			TCATTGAAAAGTAGCCCCTTG	0.453																																																0													123.0	108.0	113.0					17																	58133572		2203	4300	6503	SO:0001819	synonymous_variant	63897			BX640819	CCDS11623.1	17q23.2	2007-05-01				ENSG00000068097			24076	protein-coding gene	gene with protein product	"""amplified in breast cancer 1"""					12755490	Standard	NM_022070		Approved	ABC1, FLJ22087	uc002iyk.1	Q6AI08		ENST00000184956.6:c.2106C>T	17.37:g.58133572G>A			B3KXP3|Q6MZX1|Q6MZY2|Q8TDM9|Q9H6B3|Q9H6M7	Silent	SNP	ENST00000184956.6	37	CCDS11623.1																																																																																				0.453	HEATR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449165.1	NM_022070		10	166	10	166
CLEC4M	10332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	7830088	7830088	+	Missense_Mutation	SNP	G	G	A	rs370560578		TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr19:7830088G>A	ENST00000327325.5	+	3	266	c.148G>A	c.(148-150)Gcc>Acc	p.A50T	CLEC4M_ENST00000596363.1_Missense_Mutation_p.A22T|CLEC4M_ENST00000359059.5_Intron|CLEC4M_ENST00000394122.2_Missense_Mutation_p.A42T|CLEC4M_ENST00000595496.1_Intron|CLEC4M_ENST00000334806.5_Missense_Mutation_p.A22T|CLEC4M_ENST00000248228.4_Missense_Mutation_p.A50T|CLEC4M_ENST00000596707.1_Intron|CLEC4M_ENST00000357361.2_Missense_Mutation_p.A50T|CLEC4M_ENST00000597522.1_Missense_Mutation_p.A50T	NM_001144909.1|NM_014257.4	NP_001138381.1|NP_055072.3	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M	50					antigen processing and presentation (GO:0019882)|cell-cell recognition (GO:0009988)|endocytosis (GO:0006897)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intracellular transport of virus (GO:0075733)|leukocyte cell-cell adhesion (GO:0007159)|modulation by virus of host morphology or physiology (GO:0019048)|peptide antigen transport (GO:0046968)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|viral genome replication (GO:0019079)|virion attachment to host cell (GO:0019062)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|ICAM-3 receptor activity (GO:0030369)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)|peptide antigen binding (GO:0042605)|receptor activity (GO:0004872)|virion binding (GO:0046790)	p.A50P(2)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(1)	26						TGGCCATGGCGCCCTGGTGCT	0.632																																																2	Substitution - Missense(2)	lung(2)						C	,,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	182.0	152.0	162.0		,,148,64,148,148,148,145,64	-4.7	0.0	19		162	0,8600		0,0,4300	no	intron,intron,missense,missense,missense,missense,missense,missense,missense	CLEC4M	NM_001144906.1,NM_001144907.1,NM_014257.4,NM_001144911.1,NM_001144910.1,NM_001144909.1,NM_001144908.1,NM_001144905.1,NM_001144904.1	,,58,58,58,58,58,58,58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,benign,benign,benign,benign,benign,benign,benign	,,50/400,22/297,50/377,50/354,50/233,49/376,22/349	7830088	1,13005	2203	4300	6503	SO:0001583	missense	10332			AB015629	CCDS12187.1, CCDS59346.1, CCDS59347.1, CCDS59348.1	19p13	2008-02-05	2005-02-04	2005-02-11		ENSG00000104938		"""C-type lectin domain containing"", ""CD molecules"""	13523	protein-coding gene	gene with protein product		605872	"""CD299 antigen"""	CD209L, CD299		10072769	Standard	NM_001144904		Approved	HP10347, DC-SIGNR, LSIGN, DCSIGNR, DC-SIGN2	uc010dvt.3	Q9H2X3		ENST00000327325.5:c.148G>A	19.37:g.7830088G>A	ENSP00000316228:p.Ala50Thr		A6NKI4|A8K8B3|Q69F40|Q969M4|Q96QP3|Q96QP4|Q96QP5|Q96QP6|Q9BXS3|Q9H2Q9|Q9H8F0|Q9Y2A8	Missense_Mutation	SNP	ENST00000327325.5	37	CCDS12187.1	.	.	.	.	.	.	.	.	.	.	g	14.03	2.414918	0.42817	2.27E-4	0.0	ENSG00000104938	ENST00000327325;ENST00000394122;ENST00000248228;ENST00000334806;ENST00000357361	T;T;T;T;T	0.03094	4.13;4.13;4.16;4.17;4.05	2.33	-4.65	0.03339	.	.	.	.	.	T	0.01353	0.0044	N	0.08118	0	0.09310	N	1	P;B;P;B;P;B	0.47604	0.898;0.389;0.516;0.031;0.611;0.252	B;B;B;B;B;B	0.31946	0.079;0.046;0.079;0.034;0.115;0.138	T	0.45249	-0.9274	9	0.44086	T	0.13	.	5.4105	0.16346	0.0:0.4043:0.1489:0.4468	.	22;50;42;50;22;50	B4E2Z5;Q9H2X3;E7ENS9;Q9H2X3-8;Q9H2X3-9;Q9H2X3-4	.;CLC4M_HUMAN;.;.;.;.	T	50;42;50;22;50	ENSP00000316228:A50T;ENSP00000377680:A42T;ENSP00000248228:A50T;ENSP00000335228:A22T;ENSP00000349924:A50T	ENSP00000248228:A50T	A	+	1	0	CLEC4M	7736088	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.079000	0.03410	-1.491000	0.01840	-2.622000	0.00156	GCC		0.632	CLEC4M-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461161.1	NM_014257		96	117	96	117
ZNF506	440515	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	19906098	19906098	+	Missense_Mutation	SNP	G	G	A			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr19:19906098G>A	ENST00000540806.2	-	4	686	c.598C>T	c.(598-600)Cgc>Tgc	p.R200C	CTC-559E9.6_ENST00000591884.1_RNA|ZNF506_ENST00000587461.1_Intron|CTC-559E9.6_ENST00000589657.1_RNA|CTC-559E9.4_ENST00000590274.1_lincRNA|ZNF506_ENST00000443905.2_Missense_Mutation_p.R200C|ZNF506_ENST00000450683.2_Missense_Mutation_p.R168C			Q5JVG8	ZN506_HUMAN	zinc finger protein 506	200					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(7)|lung(3)|skin(1)|stomach(1)	14						CATTTATAGCGTTTCTCTCCA	0.338																																																0													54.0	58.0	57.0					19																	19906098		2162	4278	6440	SO:0001583	missense	440515			AK095575	CCDS42531.1, CCDS46027.1	19p13.11	2013-01-08				ENSG00000081665		"""Zinc fingers, C2H2-type"", ""-"""	23780	protein-coding gene	gene with protein product							Standard	NM_001099269		Approved	DKFZp761G1812	uc010eci.2	Q5JVG8		ENST00000540806.2:c.598C>T	19.37:g.19906098G>A	ENSP00000440625:p.Arg200Cys		B3KTH6	Missense_Mutation	SNP	ENST00000540806.2	37	CCDS42531.1	.	.	.	.	.	.	.	.	.	.	g	15.31	2.795916	0.50208	.	.	ENSG00000081665	ENST00000443905;ENST00000540806;ENST00000450683	T;T;T	0.07688	3.17;3.17;3.17	0.974	0.974	0.19715	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08088	0.0202	N	0.19112	0.55	0.39329	D	0.965379	D;D	0.63046	0.978;0.992	B;P	0.51016	0.142;0.656	T	0.34976	-0.9807	9	0.59425	D	0.04	.	7.3873	0.26891	0.0:0.0:1.0:0.0	.	200;168	Q5JVG8;Q5JVG8-2	ZN506_HUMAN;.	C	200;200;168	ENSP00000393835:R200C;ENSP00000440625:R200C;ENSP00000408892:R168C	ENSP00000393835:R200C	R	-	1	0	ZNF506	19767098	0.018000	0.18449	0.139000	0.22197	0.119000	0.20118	0.070000	0.14573	0.423000	0.26033	0.423000	0.28283	CGC		0.338	ZNF506-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460794.1	XM_036218		6	123	6	123
FUBP1	8880	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	78429848	78429848	+	Splice_Site	SNP	C	C	T			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr1:78429848C>T	ENST00000370768.2	-	12	1022		c.e12-1		FUBP1_ENST00000370767.1_Splice_Site|FUBP1_ENST00000436586.2_Splice_Site	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1						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)			central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						GTCCCATCATCTTCAAAACAA	0.363			"""F, N"""		oligodendroglioma																																		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	0													180.0	174.0	176.0					1																	78429848		2203	4300	6503	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.941-1G>A	1.37:g.78429848C>T			Q12828	Splice_Site	SNP	ENST00000370768.2	37	CCDS683.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.179317	0.78564	.	.	ENSG00000162613	ENST00000370773;ENST00000370767;ENST00000370768;ENST00000394922;ENST00000436586	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.0643	0.97702	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FUBP1	78202436	1.000000	0.71417	1.000000	0.80357	0.725000	0.41563	7.773000	0.85462	2.737000	0.93849	0.650000	0.86243	.		0.363	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902	Intron	136	20	136	20
KIF16B	55614	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	20	16360615	16360615	+	Missense_Mutation	SNP	T	T	C			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr20:16360615T>C	ENST00000354981.2	-	19	2189	c.2032A>G	c.(2032-2034)Aaa>Gaa	p.K678E	KIF16B_ENST00000378003.2_5'UTR|KIF16B_ENST00000355755.3_Missense_Mutation_p.K678E|KIF16B_ENST00000408042.1_Missense_Mutation_p.K678E	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	678	Glu-rich.				ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						TCTTCAAATTTTTCCTTCTCC	0.498																																																0													130.0	115.0	120.0					20																	16360615		2203	4300	6503	SO:0001583	missense	55614			AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"""Kinesins"""	15869	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 23"""	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.2032A>G	20.37:g.16360615T>C	ENSP00000347076:p.Lys678Glu		A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Missense_Mutation	SNP	ENST00000354981.2	37	CCDS13122.1	.	.	.	.	.	.	.	.	.	.	T	12.42	1.933109	0.34096	.	.	ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000377997;ENST00000408042	T;T;T	0.16743	2.32;2.32;2.32	5.58	4.47	0.54385	.	0.385575	0.27922	N	0.017304	T	0.15696	0.0378	L	0.54323	1.7	0.80722	D	1	B;P;B;B	0.36789	0.342;0.57;0.342;0.232	B;B;B;B	0.37047	0.142;0.24;0.142;0.067	T	0.02042	-1.1224	10	0.05833	T	0.94	.	12.8474	0.57837	0.0:0.0:0.1445:0.8555	.	678;678;678;678	Q96L93-4;Q96L93-2;Q96L93-6;Q96L93	.;.;.;KI16B_HUMAN	E	678	ENSP00000347076:K678E;ENSP00000347995:K678E;ENSP00000384164:K678E	ENSP00000347076:K678E	K	-	1	0	KIF16B	16308615	1.000000	0.71417	0.384000	0.26145	0.716000	0.41182	2.803000	0.47924	0.929000	0.37192	0.533000	0.62120	AAA		0.498	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		40	267	40	267
PREB	10113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	27355105	27355105	+	Missense_Mutation	SNP	C	C	T			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr2:27355105C>T	ENST00000260643.2	-	6	1172	c.919G>A	c.(919-921)Gat>Aat	p.D307N	PREB_ENST00000406567.3_Intron|PREB_ENST00000416802.1_5'Flank	NM_013388.4	NP_037520.1	Q9HCU5	PREB_HUMAN	prolactin regulatory element binding	307					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACCTGACATCGAGGCAGGAG	0.617																																																0													101.0	109.0	106.0					2																	27355105		2203	4300	6503	SO:0001583	missense	10113				CCDS1738.1	2p23	2013-01-10			ENSG00000138073	ENSG00000138073		"""WD repeat domain containing"""	9356	protein-coding gene	gene with protein product		606395				10194769, 12735795	Standard	NM_013388		Approved	SEC12	uc002rix.1	Q9HCU5	OTTHUMG00000097076	ENST00000260643.2:c.919G>A	2.37:g.27355105C>T	ENSP00000260643:p.Asp307Asn		Q53SZ8|Q9UH94	Missense_Mutation	SNP	ENST00000260643.2	37	CCDS1738.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	2.053|2.053	-0.417270|-0.417270	0.04766|0.04766	.|.	.|.	ENSG00000138073|ENSG00000138073	ENST00000260643;ENST00000546336|ENST00000456259;ENST00000430533	T|.	0.30448|.	1.53|.	6.08|6.08	2.34|2.34	0.29019|0.29019	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);|.	0.543359|.	0.23041|.	N|.	0.052602|.	T|T	0.09905|0.09905	0.0243|0.0243	N|N	0.02539|0.02539	-0.55|-0.55	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.31668|0.31668	-0.9935|-0.9935	10|5	0.40728|.	T|.	0.16|.	0.463|0.463	5.101|5.101	0.14759|0.14759	0.0:0.2216:0.1421:0.6362|0.0:0.2216:0.1421:0.6362	.|.	307|.	Q9HCU5|.	PREB_HUMAN|.	N|Q	307|50;62	ENSP00000260643:D307N|.	ENSP00000260643:D307N|.	D|R	-|-	1|2	0|0	PREB|PREB	27208609|27208609	0.998000|0.998000	0.40836|0.40836	0.086000|0.086000	0.20670|0.20670	0.024000|0.024000	0.10985|0.10985	1.421000|1.421000	0.34815|0.34815	0.157000|0.157000	0.19338|0.19338	-1.235000|-1.235000	0.01560|0.01560	GAT|CGA		0.617	PREB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214195.1	NM_013388		146	229	146	229
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	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			72	87	72	87
MKRN2	23609	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	12613687	12613687	+	Missense_Mutation	SNP	A	A	G			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr3:12613687A>G	ENST00000170447.7	+	4	594	c.457A>G	c.(457-459)Agt>Ggt	p.S153G	MKRN2_ENST00000448482.1_Missense_Mutation_p.S151G|MKRN2_ENST00000411987.1_Missense_Mutation_p.S110G	NM_001271707.1|NM_014160.3	NP_001258636.1|NP_054879.3	Q9H000	MKRN2_HUMAN	makorin ring finger protein 2	153					protein ubiquitination (GO:0016567)	intracellular (GO:0005622)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(3)	16						TGCCATCAGGAGTGGCCTTGA	0.627																																																0													72.0	71.0	71.0					3																	12613687		2203	4300	6503	SO:0001583	missense	23609				CCDS33702.1, CCDS63545.1	3p25	2008-08-13	2008-08-13		ENSG00000075975	ENSG00000075975		"""RING-type (C3HC4) zinc fingers"""	7113	protein-coding gene	gene with protein product		608426				11597136	Standard	NM_014160		Approved	RNF62, HSPC070	uc003bxd.4	Q9H000	OTTHUMG00000155371	ENST00000170447.7:c.457A>G	3.37:g.12613687A>G	ENSP00000170447:p.Ser153Gly		A6NIA2|B3KRC5|B4DPR4|Q8N391|Q96BD4|Q9BUY2|Q9NRY1	Missense_Mutation	SNP	ENST00000170447.7	37	CCDS33702.1	.	.	.	.	.	.	.	.	.	.	A	16.23	3.063537	0.55432	.	.	ENSG00000075975	ENST00000170447;ENST00000411987;ENST00000448482	T;T;T	0.24350	2.68;1.86;1.89	5.38	5.38	0.77491	.	0.249234	0.46442	D	0.000282	T	0.22126	0.0533	L	0.50333	1.59	0.44417	D	0.997338	P;B;B	0.37914	0.611;0.236;0.236	B;B;B	0.29353	0.101;0.075;0.075	T	0.03795	-1.1003	10	0.24483	T	0.36	.	15.566	0.76294	1.0:0.0:0.0:0.0	.	110;151;153	B4DPR4;C9J494;Q9H000	.;.;MKRN2_HUMAN	G	153;110;151	ENSP00000170447:S153G;ENSP00000396340:S110G;ENSP00000397983:S151G	ENSP00000170447:S153G	S	+	1	0	MKRN2	12588687	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.344000	0.59354	2.254000	0.74563	0.533000	0.62120	AGT		0.627	MKRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339679.1	NM_014160		57	59	57	59
TTC21A	199223	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	39170636	39170636	+	Missense_Mutation	SNP	T	T	C			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr3:39170636T>C	ENST00000431162.2	+	15	2125	c.1991T>C	c.(1990-1992)aTt>aCt	p.I664T	TTC21A_ENST00000301819.6_Missense_Mutation_p.I665T|TTC21A_ENST00000440121.1_Missense_Mutation_p.I616T			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	664										NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		CGCATCACCATTGCCAACGTG	0.522																																																0													95.0	97.0	96.0					3																	39170636		2156	4247	6403	SO:0001583	missense	199223			AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.1991T>C	3.37:g.39170636T>C	ENSP00000398211:p.Ile664Thr		A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.248678	0.80024	.	.	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.76578	-1.03;-0.28;-1.03	5.85	5.85	0.93711	Tetratricopeptide-like helical (1);	0.353602	0.26173	N	0.025914	T	0.81889	0.4918	M	0.75777	2.31	0.40827	D	0.983551	D;P;P	0.54772	0.968;0.873;0.799	P;B;B	0.48677	0.586;0.382;0.212	D	0.83619	0.0138	10	0.45353	T	0.12	-7.3352	15.2181	0.73285	0.0:0.0:0.0:1.0	.	616;665;664	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	T	665;647;664;616	ENSP00000301819:I665T;ENSP00000398211:I664T;ENSP00000410882:I616T	ENSP00000301819:I665T	I	+	2	0	TTC21A	39145640	0.972000	0.33761	0.908000	0.35775	0.718000	0.41266	7.650000	0.83521	2.238000	0.73509	0.533000	0.62120	ATT		0.522	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755		70	83	70	83
FBXL7	23194	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	15937211	15937211	+	Silent	SNP	C	C	T			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr5:15937211C>T	ENST00000504595.1	+	4	1873	c.1392C>T	c.(1390-1392)tgC>tgT	p.C464C	FBXL7_ENST00000510662.1_Silent_p.C417C|FBXL7_ENST00000329673.7_Silent_p.C452C|MIR887_ENST00000401258.1_RNA	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	464					cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						TCCAGGACTGCGAGGTCTCCG	0.607																																																0													30.0	33.0	32.0					5																	15937211		2111	4237	6348	SO:0001819	synonymous_variant	23194			AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580		"""F-boxes / Leucine-rich repeats"""	13604	protein-coding gene	gene with protein product		605656				10048485, 10531035	Standard	NM_012304		Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.1392C>T	5.37:g.15937211C>T			B9EGF1|D6RDY7|O94926	Silent	SNP	ENST00000504595.1	37	CCDS54833.1																																																																																				0.607	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304		18	51	18	51
MTX3	345778	hgsc.bcm.edu;broad.mit.edu	37	5	79282781	79282781	+	Missense_Mutation	SNP	C	C	T			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr5:79282781C>T	ENST00000512528.1	-	7	751	c.731G>A	c.(730-732)aGt>aAt	p.S244N	MTX3_ENST00000512560.1_Missense_Mutation_p.S183N|MTX3_ENST00000509852.1_Missense_Mutation_p.S244N			Q5HYI7	MTX3_HUMAN	metaxin 3	244					protein targeting to mitochondrion (GO:0006626)	mitochondrial outer membrane (GO:0005741)				endometrium(1)|large_intestine(3)|lung(2)|urinary_tract(1)	7		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.63e-45)|Epithelial(54;2.9e-40)|all cancers(79;4.68e-35)		ACCTCCAAGACTAAGCCTAAA	0.363																																																0													103.0	101.0	102.0					5																	79282781		1865	4101	5966	SO:0001583	missense	345778			BX538064	CCDS47239.1, CCDS47239.2, CCDS54872.1	5q14.1	2004-08-18				ENSG00000177034			24812	protein-coding gene	gene with protein product						15087125	Standard	NM_001010891		Approved		uc010jah.3	Q5HYI7		ENST00000512528.1:c.731G>A	5.37:g.79282781C>T	ENSP00000424798:p.Ser244Asn		B4DL65|E9PB57|Q7Z380|Q8NB92	Missense_Mutation	SNP	ENST00000512528.1	37		.	.	.	.	.	.	.	.	.	.	C	9.579	1.122955	0.20959	.	.	ENSG00000177034	ENST00000512560;ENST00000509852;ENST00000512528;ENST00000418095	T;T;T	0.44881	0.92;0.91;0.93	5.65	-0.447	0.12234	.	.	.	.	.	T	0.23370	0.0565	N	0.14661	0.345	0.09310	N	1	B;B	0.16603	0.0;0.018	B;B	0.15484	0.0;0.013	T	0.17837	-1.0356	9	0.48119	T	0.1	.	7.1304	0.25497	0.0:0.2292:0.263:0.5078	.	244;244	Q5HYI7-4;Q5HYI7	.;MTX3_HUMAN	N	183;244;244;244	ENSP00000423600:S183N;ENSP00000423302:S244N;ENSP00000424798:S244N	ENSP00000392181:S244N	S	-	2	0	MTX3	79318537	.	.	0.000000	0.03702	0.905000	0.53344	.	.	-0.279000	0.09167	-0.140000	0.14226	AGT		0.363	MTX3-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372567.1	XM_293971		8	158	8	158
VPS52	6293	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	33235064	33235064	+	Silent	SNP	G	G	A			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr6:33235064G>A	ENST00000445902.2	-	11	1244	c.1026C>T	c.(1024-1026)aaC>aaT	p.N342N	VPS52_ENST00000482399.1_3'UTR|VPS52_ENST00000478934.1_Intron|VPS52_ENST00000436044.2_Silent_p.N217N	NM_022553.4	NP_072047.4	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52 homolog (S. cerevisiae)	342					ectodermal cell differentiation (GO:0010668)|embryonic ectodermal digestive tract development (GO:0048611)|protein transport (GO:0015031)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(8)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28						TGAAAATGGTGTTCCTGCTGC	0.562																																																0													91.0	84.0	87.0					6																	33235064		2203	4300	6503	SO:0001819	synonymous_variant	6293			AJ223319	CCDS4770.2	6p21.3	2010-02-17	2006-12-19	2003-09-05	ENSG00000223501	ENSG00000223501			10518	protein-coding gene	gene with protein product		603443	"""SAC2 suppressor of actin mutations 2-like (yeast)"", ""vacuolar protein sorting 52 (yeast)"""	SACM2L		9790748	Standard	NM_022553		Approved	ARE1	uc003odm.1	Q8N1B4	OTTHUMG00000031276	ENST00000445902.2:c.1026C>T	6.37:g.33235064G>A			A2BF38|B0UZZ4|B4DNI9|Q53GR4|Q5JPA0|Q5SQW1|Q8IUN6|Q9NPT5	Silent	SNP	ENST00000445902.2	37	CCDS4770.2																																																																																				0.562	VPS52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076598.2	NM_022553		69	103	69	103
MRPL2	51069	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	43023893	43023893	+	Missense_Mutation	SNP	C	C	T			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr6:43023893C>T	ENST00000388752.3	-	4	870	c.446G>A	c.(445-447)cGc>cAc	p.R149H	MRPL2_ENST00000489623.1_Intron|MRPL2_ENST00000230413.5_Missense_Mutation_p.R149H|CUL7_ENST00000265348.3_5'Flank|CUL7_ENST00000535468.1_5'Flank	NM_015950.3	NP_057034.2	Q5T653	RM02_HUMAN	mitochondrial ribosomal protein L2	149					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(2)	9		Ovarian(999;0.0014)	Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00708)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)	BRCA - Breast invasive adenocarcinoma(397;0.0026)		GATGATCCAGCGTTTCCGGCT	0.537																																																0													135.0	123.0	127.0					6																	43023893		2203	4300	6503	SO:0001583	missense	51069			AB051617	CCDS34454.1, CCDS75458.1	6p21.3	2012-09-13			ENSG00000112651	ENSG00000112651		"""Mitochondrial ribosomal proteins / large subunits"""	14056	protein-coding gene	gene with protein product		611822					Standard	XM_005249161		Approved	MRP-L14, RPML14, CGI-22	uc003ots.1	Q5T653	OTTHUMG00000014719	ENST00000388752.3:c.446G>A	6.37:g.43023893C>T	ENSP00000373404:p.Arg149His		B2RC56|Q8WUL1|Q96Q56|Q9Y311	Missense_Mutation	SNP	ENST00000388752.3	37	CCDS34454.1	.	.	.	.	.	.	.	.	.	.	C	35	5.531720	0.96446	.	.	ENSG00000112651	ENST00000388752;ENST00000230413	T	0.52057	0.68	5.7	5.7	0.88788	Nucleic acid-binding, OB-fold-like (1);Ribosomal Proteins L2, RNA binding domain (1);Nucleic acid-binding, OB-fold (1);	0.000000	0.85682	D	0.000000	T	0.70842	0.3270	M	0.88775	2.98	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.76228	-0.3036	10	0.87932	D	0	-14.9332	18.0157	0.89239	0.0:1.0:0.0:0.0	.	149;149	B4DVE2;Q5T653	.;RM02_HUMAN	H	149	ENSP00000373404:R149H	ENSP00000230413:R149H	R	-	2	0	MRPL2	43131871	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.448000	0.80631	2.687000	0.91594	0.655000	0.94253	CGC		0.537	MRPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040577.2			56	90	56	90
NOTCH1	4851	hgsc.bcm.edu;ucsc.edu	37	9	139393712	139393712	+	Splice_Site	SNP	C	C	A			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr9:139393712C>A	ENST00000277541.6	-	32	6010		c.e32-1			NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1						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)			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)		GGATCAGGATCTGGGCAACAG	0.662			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)																													Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	0													41.0	46.0	44.0					9																	139393712		2193	4299	6492	SO:0001630	splice_region_variant	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.5935-1G>T	9.37:g.139393712C>A			Q59ED8|Q5SXM3	Splice_Site	SNP	ENST00000277541.6	37	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.440174	0.83993	.	.	ENSG00000148400	ENST00000277541	.	.	.	5.07	5.07	0.68467	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.7871	0.88541	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NOTCH1	138513533	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	7.306000	0.78905	2.512000	0.84698	0.561000	0.74099	.		0.662	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	Intron	6	65	6	65
DLG3	1741	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	69670626	69670626	+	Silent	SNP	C	C	T	rs370555109		TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chrX:69670626C>T	ENST00000374360.3	+	6	1211	c.978C>T	c.(976-978)taC>taT	p.Y326Y	DLG3_ENST00000374355.3_5'Flank|DLG3-AS1_ENST00000431103.1_RNA|RNU4-81P_ENST00000363561.1_RNA|DLG3_ENST00000194900.4_Silent_p.Y344Y|DLG3-AS1_ENST00000424211.1_RNA	NM_021120.3	NP_066943.2	Q92796	DLG3_HUMAN	discs, large homolog 3 (Drosophila)	326					axon guidance (GO:0007411)|establishment of planar polarity (GO:0001736)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|negative regulation of cell proliferation (GO:0008285)|negative regulation of phosphatase activity (GO:0010923)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)|tight junction (GO:0005923)	phosphatase binding (GO:0019902)	p.Y326Y(1)		endometrium(4)|kidney(1)|large_intestine(10)|lung(5)|pancreas(1)|urinary_tract(1)	22	Renal(35;0.156)					CCCCTGACTACGCCAGCAGTA	0.532																																																1	Substitution - coding silent(1)	large_intestine(1)						C		1,3834		0,1,1631,571	100.0	70.0	80.0		978	-0.9	1.0	X		80	0,6728		0,0,2428,1872	no	coding-synonymous	DLG3	NM_021120.3		0,1,4059,2443	TT,TC,CC,C		0.0,0.0261,0.0095		326/818	69670626	1,10562	2203	4300	6503	SO:0001819	synonymous_variant	1741			U49089	CCDS14403.1, CCDS43967.1, CCDS55439.1	Xq13.1	2014-06-12	2008-12-15		ENSG00000082458	ENSG00000082458			2902	protein-coding gene	gene with protein product	"""neuroendocrine-dlg"", ""protein phosphatase 1, regulatory subunit 82"""	300189	"""discs, large homolog 3 (neuroendocrine-dlg, Drosophila)"""			9598320	Standard	NM_021120		Approved	NE-Dlg, SAP102, SAP-102, NEDLG, KIAA1232, MRX90, PPP1R82	uc004dyi.2	Q92796	OTTHUMG00000021778	ENST00000374360.3:c.978C>T	X.37:g.69670626C>T			B4E0H1|D3DVU5|Q5JUW6|Q5JUW7|Q9ULI8	Silent	SNP	ENST00000374360.3	37	CCDS14403.1																																																																																				0.532	DLG3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057074.2	NM_021120		22	122	22	122
AMMECR1	9949	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	109444269	109444269	+	Missense_Mutation	SNP	T	T	C			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chrX:109444269T>C	ENST00000262844.5	-	5	967	c.800A>G	c.(799-801)cAt>cGt	p.H267R	AMMECR1_ENST00000372057.1_Missense_Mutation_p.H144R|AMMECR1_ENST00000372059.2_Missense_Mutation_p.H230R	NM_015365.2	NP_056180.1	Q9Y4X0	AMMR1_HUMAN	Alport syndrome, mental retardation, midface hypoplasia and elliptocytosis chromosomal region gene 1	267	AMMECR1. {ECO:0000255|PROSITE- ProRule:PRU00467}.									large_intestine(1)|lung(4)|ovary(1)|stomach(1)	7						GGTCTGTATATGGTCCCATCC	0.373																																																0													190.0	164.0	173.0					X																	109444269		2203	4300	6503	SO:0001583	missense	9949			AJ007014	CCDS14551.1, CCDS35368.1, CCDS55476.1	Xq22.3	2014-06-17	2008-09-12		ENSG00000101935	ENSG00000101935			467	protein-coding gene	gene with protein product		300195				10049589, 9480748	Standard	NM_001171689		Approved		uc004eoo.3	Q9Y4X0	OTTHUMG00000022197	ENST00000262844.5:c.800A>G	X.37:g.109444269T>C	ENSP00000262844:p.His267Arg		Q5JYV9|Q6P9D8|Q8WX22|Q9UIQ8	Missense_Mutation	SNP	ENST00000262844.5	37	CCDS14551.1	.	.	.	.	.	.	.	.	.	.	T	16.05	3.011756	0.54468	.	.	ENSG00000101935	ENST00000262844;ENST00000372059;ENST00000372057	.	.	.	5.9	5.9	0.94986	AMMECR1 domain (2);	0.049541	0.85682	D	0.000000	T	0.42223	0.1193	N	0.16066	0.365	0.80722	D	1	B;B	0.26512	0.151;0.018	B;B	0.25614	0.062;0.03	T	0.30679	-0.9970	9	0.32370	T	0.25	-2.7743	15.2738	0.73726	0.0:0.0:0.0:1.0	.	230;267	Q9Y4X0-3;Q9Y4X0	.;AMER1_HUMAN	R	267;230;144	.	ENSP00000262844:H267R	H	-	2	0	AMMECR1	109330925	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.695000	0.84257	1.990000	0.58119	0.486000	0.48141	CAT		0.373	AMMECR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057907.1			147	178	147	178
GPC3	2719	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	132887716	132887716	+	Silent	SNP	G	G	A			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chrX:132887716G>A	ENST00000370818.3	-	3	1270	c.825C>T	c.(823-825)ggC>ggT	p.G275G	GPC3_ENST00000543339.1_Silent_p.G221G|GPC3_ENST00000394299.2_Silent_p.G275G	NM_001164618.1|NM_004484.3	NP_001158090.1|NP_004475.1	P51654	GPC3_HUMAN	glypican 3	275					anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|body morphogenesis (GO:0010171)|bone mineralization (GO:0030282)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cell proliferation involved in metanephros development (GO:0072203)|chondroitin sulfate metabolic process (GO:0030204)|coronary vasculature development (GO:0060976)|embryonic hindlimb morphogenesis (GO:0035116)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lung development (GO:0030324)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesonephric duct morphogenesis (GO:0072180)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of growth (GO:0045926)|negative regulation of smoothened signaling pathway (GO:0045879)|osteoclast differentiation (GO:0030316)|phototransduction, visible light (GO:0007603)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endocytosis (GO:0045807)|positive regulation of glucose import (GO:0046326)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of plasma membrane (GO:0046658)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	peptidyl-dipeptidase inhibitor activity (GO:0060422)			breast(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|prostate(1)|skin(2)	36	Acute lymphoblastic leukemia(192;0.000127)					TGCAGTAACCGCCACAGGGTT	0.483			"""T, D, Mis, N, F, S"""			Wilms tumour			Simpson-Golabi-Behmel syndrome																													yes	Rec/X		Simpson-Golabi-Behmel syndrome	X	Xq26.1	2719	glypican 3		O	0													556.0	353.0	422.0					X																	132887716		2203	4300	6503	SO:0001819	synonymous_variant	2719	Familial Cancer Database	SGBS	L47125	CCDS14638.1, CCDS55496.1	Xq26	2014-09-17			ENSG00000147257	ENSG00000147257		"""Proteoglycans / Cell Surface : Glypicans"""	4451	protein-coding gene	gene with protein product	"""glypican proteoglycan 3"""	300037		SDYS		8589713, 9787072	Standard	NM_004484		Approved	OCI-5, SGBS, SGBS1, SGB, DGSX	uc010nrn.2	P51654	OTTHUMG00000022448	ENST00000370818.3:c.825C>T	X.37:g.132887716G>A			C9JLE3|G3V1R0|Q2L880|Q2L882	Silent	SNP	ENST00000370818.3	37	CCDS14638.1	.	.	.	.	.	.	.	.	.	.	G	2.696	-0.272064	0.05716	.	.	ENSG00000147257	ENST00000406757	.	.	.	5.96	-4.88	0.03113	.	.	.	.	.	T	0.49949	0.1587	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49688	-0.8913	4	.	.	.	.	7.7324	0.28793	0.4281:0.2002:0.3717:0.0	.	.	.	.	V	5	.	.	A	-	2	0	GPC3	132715382	0.007000	0.16637	0.964000	0.40570	0.708000	0.40852	-0.763000	0.04740	-0.895000	0.03920	-1.281000	0.01382	GCG		0.483	GPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058356.1	NM_004484		194	196	194	196
GPR50	9248	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	150349210	150349210	+	Missense_Mutation	SNP	C	C	A			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chrX:150349210C>A	ENST00000218316.3	+	2	1224	c.1155C>A	c.(1153-1155)caC>caA	p.H385Q	GPR50-AS1_ENST00000454196.1_RNA|AF003625.3_ENST00000602313.1_lincRNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	385	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)					CCTCTGGCCACCCTAAGCCCC	0.582																																																0													95.0	107.0	103.0					X																	150349210		2130	4225	6355	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.1155C>A	X.37:g.150349210C>A	ENSP00000218316:p.His385Gln		Q0VGG3|Q3ZAR0	Missense_Mutation	SNP	ENST00000218316.3	37	CCDS44012.1	.	.	.	.	.	.	.	.	.	.	C	5.599	0.295259	0.10622	.	.	ENSG00000102195	ENST00000218316	T	0.75367	-0.93	3.96	0.8	0.18672	.	0.203527	0.49305	D	0.000151	T	0.52693	0.1750	N	0.19112	0.55	0.09310	N	1	B	0.15141	0.012	B	0.12156	0.007	T	0.41787	-0.9489	10	0.52906	T	0.07	-4.3925	3.9692	0.09446	0.1881:0.5695:0.0:0.2423	.	385	Q13585	MTR1L_HUMAN	Q	385	ENSP00000218316:H385Q	ENSP00000218316:H385Q	H	+	3	2	GPR50	150099868	0.000000	0.05858	0.003000	0.11579	0.216000	0.24613	-0.874000	0.04210	0.261000	0.21753	0.529000	0.55759	CAC		0.582	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224		124	160	124	160
GDI1	2664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	153668416	153668416	+	Missense_Mutation	SNP	C	C	T			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chrX:153668416C>T	ENST00000447750.2	+	5	852	c.517C>T	c.(517-519)Cgg>Tgg	p.R173W		NM_001493.2	NP_001484.1	P31150	GDIA_HUMAN	GDP dissociation inhibitor 1	173					negative regulation of axonogenesis (GO:0050771)|negative regulation of protein targeting to membrane (GO:0090315)|protein transport (GO:0015031)|Rab protein signal transduction (GO:0032482)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|midbody (GO:0030496)|neuron projection (GO:0043005)|protein complex (GO:0043234)	GDP-dissociation inhibitor activity (GO:0005092)|GTPase activator activity (GO:0005096)|Rab GDP-dissociation inhibitor activity (GO:0005093)	p.R173R(1)		autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	16	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TGACGTCTACCGGAAGTTTGA	0.577																																																1	Substitution - coding silent(1)	lung(1)											303.0	275.0	284.0					X																	153668416		2203	4300	6503	SO:0001583	missense	2664			X79353	CCDS35452.1	Xq28	2008-08-01			ENSG00000203879	ENSG00000203879			4226	protein-coding gene	gene with protein product	"""mental retardation, X-linked 41"", ""mental retardation, X-linked 48"", ""rab GDP-dissociation inhibitor, alpha"""	300104		MRX48, MRX41, GDIL		7543319, 7849400	Standard	NM_001493		Approved	RABGDIA, XAP-4, OPHN2, FLJ41411	uc004fli.4	P31150	OTTHUMG00000033293	ENST00000447750.2:c.517C>T	X.37:g.153668416C>T	ENSP00000394071:p.Arg173Trp		P50394|Q6FG50|Q7Z2G6|Q7Z2G9|Q7Z2H5|Q7Z2I6	Missense_Mutation	SNP	ENST00000447750.2	37	CCDS35452.1	.	.	.	.	.	.	.	.	.	.	C	20.0	3.930550	0.73327	.	.	ENSG00000203879	ENST00000447750;ENST00000369741	T	0.61510	0.1	4.78	2.78	0.32641	.	0.187016	0.47455	D	0.000237	T	0.63546	0.2520	L	0.48642	1.525	0.39569	D	0.96924	P;P	0.52061	0.95;0.81	P;B	0.61533	0.89;0.422	T	0.66200	-0.5983	10	0.87932	D	0	-23.7147	9.126	0.36816	0.5463:0.4537:0.0:0.0	.	173;173	B4DH24;P31150	.;GDIA_HUMAN	W	173;157	ENSP00000394071:R173W	ENSP00000358756:R157W	R	+	1	2	GDI1	153321610	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.036000	0.49767	0.972000	0.38314	0.529000	0.55759	CGG		0.577	GDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081649.2	NM_001493		311	551	311	551
DYX1C1	161582	broad.mit.edu;ucsc.edu	37	15	55731774	55731774	+	Silent	SNP	T	T	C			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr15:55731774T>C	ENST00000321149.3	-	7	1156	c.789A>G	c.(787-789)ctA>ctG	p.L263L	DYX1C1_ENST00000448430.2_Silent_p.L263L|DYX1C1_ENST00000348518.3_Silent_p.L263L|DYX1C1_ENST00000457155.2_Silent_p.L263L|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000380679.1_Silent_p.L263L	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	263					cilium movement (GO:0003341)|determination of left/right symmetry (GO:0007368)|inner dynein arm assembly (GO:0036159)|neuron migration (GO:0001764)|outer dynein arm assembly (GO:0036158)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of proteasomal protein catabolic process (GO:0061136)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18				all cancers(107;0.0118)|GBM - Glioblastoma multiforme(80;0.171)		CTTGTTTGTGTAGCCACTAGA	0.343																																																0													68.0	69.0	68.0					15																	55731774		2193	4292	6485	SO:0001819	synonymous_variant	161582				CCDS10154.1, CCDS32243.1, CCDS32244.1	15q21.3	2014-09-11			ENSG00000256061	ENSG00000256061		"""Tetratricopeptide (TTC) repeat domain containing"""	21493	protein-coding gene	gene with protein product		608706				12954984	Standard	NM_130810		Approved	EKN1, FLJ37882, CILD25	uc002adc.3	Q8WXU2	OTTHUMG00000132008	ENST00000321149.3:c.789A>G	15.37:g.55731774T>C			Q6P5Y9|Q8N1S6	Silent	SNP	ENST00000321149.3	37	CCDS10154.1																																																																																				0.343	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810		14	113	14	113
NOTCH1	4851	broad.mit.edu;ucsc.edu	37	9	139418369	139418369	+	Missense_Mutation	SNP	C	C	T			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr9:139418369C>T	ENST00000277541.6	-	3	278	c.203G>A	c.(202-204)tGc>tAc	p.C68Y	NOTCH1_ENST00000491649.1_5'Flank	NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	68	EGF-like 2. {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)			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)		GGCGTTCTTGCAGGGGGTGCT	0.677			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)																													Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	0													16.0	22.0	20.0					9																	139418369		2089	4197	6286	SO:0001583	missense	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.203G>A	9.37:g.139418369C>T	ENSP00000277541:p.Cys68Tyr		Q59ED8|Q5SXM3	Missense_Mutation	SNP	ENST00000277541.6	37	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.058201	0.76074	.	.	ENSG00000148400	ENST00000277541	D	0.99992	-12.4	4.62	3.71	0.42584	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.99994	0.9999	H	0.98507	4.25	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99982	1.2715	10	0.87932	D	0	.	13.2359	0.59969	0.0:0.8385:0.1615:0.0	.	68	P46531	NOTC1_HUMAN	Y	68	ENSP00000277541:C68Y	ENSP00000277541:C68Y	C	-	2	0	NOTCH1	138538190	1.000000	0.71417	0.620000	0.29132	0.942000	0.58702	7.551000	0.82182	0.887000	0.36136	0.561000	0.74099	TGC		0.677	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		3	15	3	15
AZU1	566	broad.mit.edu;ucsc.edu	37	19	831737	831737	+	Missense_Mutation	SNP	G	G	A	rs201462708		TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr19:831737G>A	ENST00000233997.2	+	5	637	c.616G>A	c.(616-618)Gtc>Atc	p.V206I		NM_001700.3	NP_001691.1	P20160	CAP7_HUMAN	azurocidin 1	206	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular extravasation (GO:0045123)|defense response to Gram-negative bacterium (GO:0050829)|glial cell migration (GO:0008347)|induction of positive chemotaxis (GO:0050930)|inflammatory response (GO:0006954)|macrophage chemotaxis (GO:0048246)|microglial cell activation (GO:0001774)|monocyte activation (GO:0042117)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fractalkine biosynthetic process (GO:0050754)|positive regulation of interleukin-1 beta biosynthetic process (GO:0050725)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of phagocytosis (GO:0050766)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of vascular permeability (GO:0043114)	azurophil granule (GO:0042582)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)|toxic substance binding (GO:0015643)			NS(1)|endometrium(1)|kidney(1)|lung(4)|pancreas(1)|upper_aerodigestive_tract(2)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CACCCCCCTCGTCTGCGAGGG	0.706													G|||	1	0.000199681	0.0	0.0	5008	,	,		13553	0.0		0.001	False		,,,				2504	0.0															0								G	ILE/VAL	0,4372		0,0,2186	14.0	16.0	15.0		616	-3.7	0.0	19		15	1,8565		0,1,4282	no	missense	AZU1	NM_001700.3	29	0,1,6468	AA,AG,GG		0.0117,0.0,0.0077	possibly-damaging	206/252	831737	1,12937	2186	4283	6469	SO:0001583	missense	566			X58794	CCDS12044.1	19p13.3	2012-03-30	2008-08-01		ENSG00000172232	ENSG00000172232			913	protein-coding gene	gene with protein product	"""cationic antimicrobial protein 37"", ""heparin-binding protein"", ""neutrophil azurocidin"""	162815				1919011	Standard	NM_001700		Approved	AZU, CAP37, AZAMP, HBP, NAZC, HUMAZUR	uc002lpz.1	P20160		ENST00000233997.2:c.616G>A	19.37:g.831737G>A	ENSP00000233997:p.Val206Ile		P80014|Q52LG4|Q9UCM1|Q9UCT5	Missense_Mutation	SNP	ENST00000233997.2	37	CCDS12044.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	0.661	-0.805819	0.02819	0.0	1.17E-4	ENSG00000172232	ENST00000233997	D	0.89270	-2.49	1.87	-3.73	0.04398	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.80944	0.4721	L	0.48362	1.52	0.09310	N	1	B	0.31503	0.326	B	0.19391	0.025	T	0.63941	-0.6523	9	0.45353	T	0.12	.	8.4979	0.33138	0.3028:0.0:0.6972:0.0	.	206	P20160	CAP7_HUMAN	I	206	ENSP00000233997:V206I	ENSP00000233997:V206I	V	+	1	0	AZU1	782737	0.000000	0.05858	0.010000	0.14722	0.212000	0.24457	-1.090000	0.03372	-1.361000	0.02169	-1.267000	0.01435	GTC		0.706	AZU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457472.2	NM_001700		21	25	21	25
ATRX	546	broad.mit.edu;ucsc.edu	37	X	76949414	76949414	+	Missense_Mutation	SNP	A	A	G			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chrX:76949414A>G	ENST00000373344.5	-	6	597	c.383T>C	c.(382-384)gTa>gCa	p.V128A	ATRX_ENST00000373341.1_Missense_Mutation_p.V89A|ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Intron	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	128					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						CTCTGGCTGTACAATCACTGT	0.348			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																																Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	1	Unknown(1)	bone(1)											140.0	122.0	128.0					X																	76949414		2202	4299	6501	SO:0001583	missense	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.383T>C	X.37:g.76949414A>G	ENSP00000362441:p.Val128Ala		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	A	18.97	3.736284	0.69189	.	.	ENSG00000085224	ENST00000373344;ENST00000400861;ENST00000373341	D	0.94184	-3.37	5.59	5.59	0.84812	.	0.086607	0.47852	D	0.000205	D	0.96147	0.8744	M	0.72118	2.19	0.49483	D	0.999791	D;D	0.76494	0.999;0.997	D;D	0.78314	0.991;0.978	D	0.96590	0.9437	10	0.87932	D	0	-8.4821	14.741	0.69455	1.0:0.0:0.0:0.0	.	128;128	A4LAA3;P46100	.;ATRX_HUMAN	A	128;89;89	ENSP00000362441:V128A	ENSP00000362438:V89A	V	-	2	0	ATRX	76836070	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.744000	0.85034	1.863000	0.54032	0.441000	0.28932	GTA		0.348	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		85	213	85	213
CIC	23152	broad.mit.edu;ucsc.edu	37	19	42799059	42799059	+	Missense_Mutation	SNP	C	C	T			TCGA-DH-5144-01A-01D-1468-08	TCGA-DH-5144-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b8626578-2105-4176-ad8c-5a2327743fa0	19e3a81b-ecb5-47d7-8d22-e1c55b6a25b7	g.chr19:42799059C>T	ENST00000575354.2	+	20	4583	c.4543C>T	c.(4543-4545)Cgc>Tgc	p.R1515C	CIC_ENST00000572681.2_Missense_Mutation_p.R2421C|CIC_ENST00000160740.3_Missense_Mutation_p.R1513C	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1515					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				CCGTGAGGTGCGCCAGAAGAT	0.632			"""Mis, F, S"""		oligodendroglioma																																		Rec	yes		19	19q13.2	23152	capicua homolog		O	0													47.0	47.0	47.0					19																	42799059		2203	4300	6503	SO:0001583	missense	23152			AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.4543C>T	19.37:g.42799059C>T	ENSP00000458663:p.Arg1515Cys		Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	37	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.159893	0.57368	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.49	2.33	0.28932	.	.	.	.	.	T	0.52901	0.1763	L	0.29908	0.895	0.51233	D	0.999917	D	0.89917	1.0	D	0.76575	0.988	T	0.55811	-0.8082	8	0.87932	D	0	-10.1007	2.833	0.05506	0.1907:0.5252:0.184:0.1001	.	1515	Q96RK0	CIC_HUMAN	C	1515	.	ENSP00000160740:R1515C	R	+	1	0	CIC	47490899	0.995000	0.38212	1.000000	0.80357	0.995000	0.86356	2.109000	0.41863	1.232000	0.43678	0.491000	0.48974	CGC		0.632	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			46	13	46	13
