#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	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_End_position_hg18	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_Start_position_hg18	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
THSD7A	221981	hgsc.bcm.edu	37	7	11675820	11675820	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr7:11675820T>C	ENST00000423059.4	-	2	1210	c.959A>G	c.(958-960)cAg>cGg	p.Q320R	THSD7A_ENST00000480061.1_5'Flank	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	320					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		ATATCCAATCTGGATGTCCCA	0.413										HNSCC(18;0.044)																																							0			7											160.0	157.0	158.0					7																	11675820		1889	4111	6000	11642345	SO:0001583	missense	221981				CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.959A>G	7.37:g.11675820T>C	ENSP00000406482:p.Gln320Arg		11642345		Missense_Mutation	SNP	ENST00000423059.4	37	CCDS47543.1	.	.	.	.	.	.	.	.	.	.	T	15.21	2.766098	0.49574	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.58940	0.3	5.62	4.47	0.54385	.	0.050105	0.85682	D	0.000000	T	0.44705	0.1306	L	0.34521	1.04	0.58432	D	0.999999	B	0.12013	0.005	B	0.12837	0.008	T	0.35325	-0.9793	10	0.33141	T	0.24	.	11.283	0.49206	0.0:0.0713:0.0:0.9286	.	320	Q9UPZ6	THS7A_HUMAN	R	320	ENSP00000406482:Q320R	ENSP00000262042:Q320R	Q	-	2	0	THSD7A	11642345	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.247000	0.72411	2.267000	0.75376	0.477000	0.44152	CAG		0.413	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2	
BBS9	27241	hgsc.bcm.edu	37	7	33380540	33380540	+	Silent	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr7:33380540C>T	ENST00000242067.6	+	11	1751	c.1230C>T	c.(1228-1230)gaC>gaT	p.D410D	BBS9_ENST00000396127.2_Silent_p.D410D|BBS9_ENST00000355070.2_Silent_p.D410D|BBS9_ENST00000350941.3_Silent_p.D410D|BBS9_ENST00000354265.4_Silent_p.D410D	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	410					cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)			BBS9/PKD1L1(2)	NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	50			GBM - Glioblastoma multiforme(11;0.0894)			GAGAAGATGACTTGAACGTTT	0.313									Bardet-Biedl syndrome																																								0			7											197.0	180.0	186.0					7																	33380540		2203	4300	6503	33347065	SO:0001819	synonymous_variant	27241	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome		CCDS5441.1, CCDS34618.1, CCDS43566.1, CCDS47572.1	7p14	2014-06-17			ENSG00000122507	ENSG00000122507			30000	protein-coding gene	gene with protein product	"""parathyroid hormone responsive B1 gene"""	607968				16380913, 10221542	Standard	XM_005249701		Approved	B1, PTHB1	uc003tdn.1	Q3SYG4	OTTHUMG00000128659	ENST00000242067.6:c.1230C>T	7.37:g.33380540C>T			33347065	E9PDC9|P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	Silent	SNP	ENST00000242067.6	37	CCDS43566.1																																																																																				0.313	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329064.1		
GLI3	2737	hgsc.bcm.edu	37	7	42064965	42064965	+	Silent	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr7:42064965C>T	ENST00000395925.3	-	9	1338	c.1254G>A	c.(1252-1254)acG>acA	p.T418T	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	418					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						CAGACTCACTCGTGGGCTTGT	0.527									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																																								0			7											131.0	109.0	116.0					7																	42064965		2203	4300	6503	42031490	SO:0001819	synonymous_variant	2737	Familial Cancer Database	;		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"""Zinc fingers, C2H2-type"""	4319	protein-coding gene	gene with protein product	"""zinc finger protein GLI3"", ""oncogene GLI3"", ""DNA-binding protein"""	165240	"""Greig cephalopolysyndactyly syndrome"", ""GLI-Kruppel family member GLI3"", ""glioma-associated oncogene family zinc finger 3"""	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.1254G>A	7.37:g.42064965C>T			42031490	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	37	CCDS5465.1																																																																																				0.527	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168	
STAG3	10734	hgsc.bcm.edu	37	7	99801743	99801743	+	Missense_Mutation	SNP	C	C	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr7:99801743C>G	ENST00000426455.1	+	26	3207	c.2800C>G	c.(2800-2802)Cag>Gag	p.Q934E	STAG3_ENST00000394018.2_Missense_Mutation_p.Q876E|GATS_ENST00000436886.2_Intron|GATS_ENST00000543273.1_RNA|STAG3_ENST00000317296.5_Missense_Mutation_p.Q934E|STAG3_ENST00000440830.1_3'UTR	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	934					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GAGCCTCAAGCAGGTGCGCCC	0.493																																																	0			7											122.0	98.0	106.0					7																	99801743		2203	4300	6503	99639679	SO:0001583	missense	10734			AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.2800C>G	7.37:g.99801743C>G	ENSP00000400359:p.Gln934Glu		99639679	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Missense_Mutation	SNP	ENST00000426455.1	37	CCDS34703.1	.	.	.	.	.	.	.	.	.	.	.	20.2	3.955845	0.73902	.	.	ENSG00000066923	ENST00000426455;ENST00000394018;ENST00000317296	T;T;T	0.21361	2.01;2.01;2.01	5.65	5.65	0.86999	.	0.000000	0.46442	D	0.000288	T	0.46288	0.1385	M	0.65498	2.005	0.80722	D	1	B;D;P	0.69078	0.427;0.997;0.604	B;D;B	0.75020	0.17;0.985;0.277	T	0.37056	-0.9722	10	0.72032	D	0.01	-16.4344	17.2163	0.86945	0.0:1.0:0.0:0.0	.	876;934;934	B4DZ10;D6W5U7;Q9UJ98	.;.;STAG3_HUMAN	E	934;876;934	ENSP00000400359:Q934E;ENSP00000377586:Q876E;ENSP00000319318:Q934E	ENSP00000319318:Q934E	Q	+	1	0	STAG3	99639679	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	5.744000	0.68664	2.674000	0.91012	0.655000	0.94253	CAG		0.493	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447	
KMT2E	55904	hgsc.bcm.edu	37	7	104749520	104749520	+	Silent	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr7:104749520C>T	ENST00000311117.3	+	23	4145	c.3600C>T	c.(3598-3600)gcC>gcT	p.A1200A	SRPK2_ENST00000493638.1_5'Flank|KMT2E_ENST00000257745.4_Silent_p.A1200A|KMT2E_ENST00000334877.4_Silent_p.A1200A|KMT2E_ENST00000334914.7_Silent_p.A255A	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	1200					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										ATGGCTGTGCCAGCAGTAATG	0.463																																																	0			7											110.0	94.0	100.0					7																	104749520		2203	4300	6503	104536756	SO:0001819	synonymous_variant	55904			AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	18541	protein-coding gene	gene with protein product		608444	"""myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"""	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.3600C>T	7.37:g.104749520C>T			104536756	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Silent	SNP	ENST00000311117.3	37	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	C	1.750	-0.489433	0.04352	.	.	ENSG00000005483	ENST00000473063	.	.	.	5.65	3.7	0.42460	.	.	.	.	.	.	.	.	.	.	.	0.21897	N	0.999485	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1311	0.65255	0.0:0.7144:0.2856:0.0	.	.	.	.	X	12	.	.	Q	+	1	0	MLL5	104536756	0.007000	0.16637	0.033000	0.17914	0.627000	0.37826	0.644000	0.24766	1.348000	0.45733	0.467000	0.42956	CAG		0.463	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1		
COG5	10466	hgsc.bcm.edu	37	7	107204319	107204319	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr7:107204319A>G	ENST00000347053.3	-	1	166	c.116T>C	c.(115-117)gTc>gCc	p.V39A	DUS4L_ENST00000498786.1_Intron|DUS4L_ENST00000265720.3_5'Flank|COG5_ENST00000297135.3_Missense_Mutation_p.V39A|COG5_ENST00000393603.2_Missense_Mutation_p.V39A|DUS4L_ENST00000402620.1_5'Flank	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	39					intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						AGCTACAGCGACGCTGCCGCC	0.672																																																	0			7											28.0	29.0	29.0					7																	107204319		2189	4272	6461	106991555	SO:0001583	missense	10466			AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"""Components of oligomeric golgi complex"""	14857	protein-coding gene	gene with protein product		606821	"""golgi transport complex 1 (90 kDa subunit)"""	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.116T>C	7.37:g.107204319A>G	ENSP00000334703:p.Val39Ala		106991555	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Missense_Mutation	SNP	ENST00000347053.3	37	CCDS5743.1	.	.	.	.	.	.	.	.	.	.	A	9.248	1.040050	0.19669	.	.	ENSG00000164597	ENST00000347053;ENST00000297135;ENST00000393603	T;T;T	0.20881	2.06;2.04;2.04	5.83	0.211	0.15236	.	0.555807	0.16328	N	0.219237	T	0.07458	0.0188	N	0.08118	0	0.09310	N	0.999995	B;B	0.02656	0.0;0.0	B;B	0.09377	0.001;0.004	T	0.29941	-0.9995	10	0.21540	T	0.41	0.031	2.3962	0.04390	0.4742:0.2993:0.0821:0.1444	.	39;39	Q9UP83;Q9UP83-2	COG5_HUMAN;.	A	39	ENSP00000334703:V39A;ENSP00000297135:V39A;ENSP00000377228:V39A	ENSP00000297135:V39A	V	-	2	0	COG5	106991555	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-0.525000	0.06214	0.422000	0.26005	0.482000	0.46254	GTC		0.672	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4		
PTPRZ1	5803	hgsc.bcm.edu	37	7	121624099	121624099	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr7:121624099C>T	ENST00000393386.2	+	8	1267	c.856C>T	c.(856-858)Cga>Tga	p.R286*	PTPRZ1_ENST00000449182.1_Nonsense_Mutation_p.R286*	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	286	Alpha-carbonic anhydrase.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						AAACAATTTTCGAGAGCAACA	0.333																																																	0			7											158.0	153.0	155.0					7																	121624099		2203	4299	6502	121411335	SO:0001587	stop_gained	5803			M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.856C>T	7.37:g.121624099C>T	ENSP00000377047:p.Arg286*		121411335	A4D0W5|C9JFM0|O76043|Q9UDR6	Nonsense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	C	38	6.895991	0.97916	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	.	.	.	6.08	6.08	0.98989	.	0.000000	0.64402	D	0.000016	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.8306	0.70146	0.2592:0.7408:0.0:0.0	.	.	.	.	X	286	.	ENSP00000377047:R286X	R	+	1	2	PTPRZ1	121411335	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.349000	0.52217	2.894000	0.99253	0.655000	0.94253	CGA		0.333	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
ZNF800	168850	hgsc.bcm.edu	37	7	127014460	127014460	+	Silent	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr7:127014460A>G	ENST00000393313.1	-	5	1521	c.930T>C	c.(928-930)caT>caC	p.H310H	ZNF800_ENST00000485577.1_5'Flank|ZNF800_ENST00000393312.1_Silent_p.H310H|ZNF800_ENST00000265827.3_Silent_p.H310H			Q2TB10	ZN800_HUMAN	zinc finger protein 800	310					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(8)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	32						TTAGTCCTCTATGAACTTCAT	0.373																																																	0			7											95.0	94.0	94.0					7																	127014460		2203	4300	6503	126801696	SO:0001819	synonymous_variant	168850			AF218032	CCDS5795.1	7q31.33	2008-05-02			ENSG00000048405	ENSG00000048405		"""Zinc fingers, C2H2-type"""	27267	protein-coding gene	gene with protein product						12477932	Standard	NM_176814		Approved		uc003vly.1	Q2TB10	OTTHUMG00000023456	ENST00000393313.1:c.930T>C	7.37:g.127014460A>G			126801696	Q9HBN0	Silent	SNP	ENST00000393313.1	37	CCDS5795.1																																																																																				0.373	ZNF800-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141823.1	NM_176814	
EZH2	2146	hgsc.bcm.edu	37	7	148525837	148525837	+	Missense_Mutation	SNP	C	C	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr7:148525837C>G	ENST00000460911.1	-	6	708	c.620G>C	c.(619-621)cGa>cCa	p.R207P	EZH2_ENST00000536783.1_Missense_Mutation_p.R98P|EZH2_ENST00000350995.2_Missense_Mutation_p.R168P|EZH2_ENST00000320356.2_Missense_Mutation_p.R207P|EZH2_ENST00000478654.1_Missense_Mutation_p.R198P|EZH2_ENST00000483967.1_Missense_Mutation_p.R198P|EZH2_ENST00000541220.1_Missense_Mutation_p.R198P|EZH2_ENST00000476773.1_Missense_Mutation_p.R198P			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	207	Interaction with DNMT1, DNMT3A and DNMT3B.				cellular response to hydrogen peroxide (GO:0070301)|cerebellar cortex development (GO:0021695)|chromatin organization (GO:0006325)|DNA methylation (GO:0006306)|G1 to G0 transition (GO:0070314)|histone H3-K27 methylation (GO:0070734)|negative regulation of epidermal cell differentiation (GO:0045605)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|protein localization to chromatin (GO:0071168)|regulation of cell proliferation (GO:0042127)|regulation of circadian rhythm (GO:0042752)|regulation of gliogenesis (GO:0014013)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(313)|kidney(3)|large_intestine(8)|liver(1)|lung(23)|parathyroid(2)|skin(3)|upper_aerodigestive_tract(3)	359	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			CATACCATCTCGGTGATCCTC	0.388			Mis		DLBCL																																			Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	0			7											208.0	182.0	191.0					7																	148525837		2203	4300	6503	148156770	SO:0001583	missense	2146				CCDS5891.1, CCDS5892.1, CCDS56516.1, CCDS56517.1, CCDS56518.1	7q35-q36	2014-09-17	2014-05-28		ENSG00000106462	ENSG00000106462		"""Chromatin-modifying enzymes / K-methyltransferases"""	3527	protein-coding gene	gene with protein product		601573	"""enhancer of zeste (Drosophila) homolog 2"", ""enhancer of zeste homolog 2 (Drosophila)"""			8954776, 17172412	Standard	NM_152998		Approved	EZH1, ENX-1, KMT6, KMT6A	uc003wfb.2	Q15910	OTTHUMG00000158973	ENST00000460911.1:c.620G>C	7.37:g.148525837C>G	ENSP00000419711:p.Arg207Pro		148156770	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Missense_Mutation	SNP	ENST00000460911.1	37	CCDS56516.1	.	.	.	.	.	.	.	.	.	.	c	10.44	1.349939	0.24426	.	.	ENSG00000106462	ENST00000478654;ENST00000320356;ENST00000460911;ENST00000350995;ENST00000541220;ENST00000476773;ENST00000483967;ENST00000536783	D;D;D;D;D;D;D;T	0.94138	-3.32;-3.35;-3.35;-3.36;-3.32;-3.32;-3.35;0.9	5.54	3.7	0.42460	SANT domain, DNA binding (1);	0.469946	0.22276	N	0.062193	D	0.84202	0.5420	L	0.29908	0.895	0.09310	N	1	P;B;B;B;B;B	0.42757	0.789;0.042;0.185;0.025;0.395;0.002	B;B;B;B;B;B	0.35931	0.214;0.014;0.177;0.058;0.07;0.008	T	0.74945	-0.3491	10	0.28530	T	0.3	.	3.3036	0.06992	0.1434:0.5711:0.1386:0.1469	.	207;198;198;207;168;207	B7Z8K5;Q15910-4;Q15910-5;Q15910;Q15910-3;Q15910-2	.;.;.;EZH2_HUMAN;.;.	P	198;207;207;168;198;198;198;98	ENSP00000417062:R198P;ENSP00000320147:R207P;ENSP00000419711:R207P;ENSP00000223193:R168P;ENSP00000443219:R198P;ENSP00000419050:R198P;ENSP00000419856:R198P;ENSP00000439305:R98P	ENSP00000320147:R207P	R	-	2	0	EZH2	148156770	0.876000	0.30132	0.053000	0.19242	0.818000	0.46254	0.998000	0.29744	0.682000	0.31407	0.585000	0.79938	CGA		0.388	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456	
PTPRA	5786	hgsc.bcm.edu	37	20	3007801	3007801	+	Silent	SNP	G	G	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr20:3007801G>A	ENST00000216877.6	+	18	2116	c.1716G>A	c.(1714-1716)cgG>cgA	p.R572R	PTPRA_ENST00000356147.3_Silent_p.R572R|PTPRA_ENST00000399903.2_Silent_p.R581R|PTPRA_ENST00000318266.5_Silent_p.R572R|PTPRA_ENST00000358719.4_Silent_p.R437R|PTPRA_ENST00000380393.3_Silent_p.R581R|PTPRA_ENST00000425918.2_Silent_p.R592R	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	581	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						CAGTTAAGCGGGGCGAAGAGA	0.483																																																	0			20											227.0	201.0	210.0					20																	3007801		2203	4300	6503	2955801	SO:0001819	synonymous_variant	5786				CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.1716G>A	20.37:g.3007801G>A			2955801	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Silent	SNP	ENST00000216877.6	37	CCDS13039.1																																																																																				0.483	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3		
SEL1L2	80343	hgsc.bcm.edu	37	20	13971154	13971154	+	Missense_Mutation	SNP	C	C	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr20:13971154C>G	ENST00000284951.5	-	1	101	c.27G>C	c.(25-27)gaG>gaC	p.E9D	SEL1L2_ENST00000378072.5_Missense_Mutation_p.E9D|SEL1L2_ENST00000486903.1_Intron			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	9						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						TTATCAATATCTCTATTAACA	0.423																																																	0			20											103.0	96.0	98.0					20																	13971154		1840	4098	5938	13919154	SO:0001583	missense	80343			AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"""chromosome 20 open reading frame 50"""	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.27G>C	20.37:g.13971154C>G	ENSP00000284951:p.Glu9Asp		13919154	B4DXX5	Missense_Mutation	SNP	ENST00000284951.5	37		.	.	.	.	.	.	.	.	.	.	C	13.33	2.205023	0.38905	.	.	ENSG00000101251	ENST00000378072;ENST00000284951	T;T	0.23950	1.88;2.22	6.07	4.13	0.48395	.	0.512796	0.17868	N	0.159288	T	0.13927	0.0337	N	0.19112	0.55	0.20074	N	0.999935	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.24905	-1.0147	10	0.14252	T	0.57	0.111	7.7472	0.28875	0.0:0.7511:0.1649:0.084	.	9;9	B4DXX5;Q5TEA6	.;SE1L2_HUMAN	D	9	ENSP00000367312:E9D;ENSP00000284951:E9D	ENSP00000284951:E9D	E	-	3	2	SEL1L2	13919154	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	0.809000	0.27168	1.570000	0.49709	0.585000	0.79938	GAG		0.423	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229	
KIF16B	55614	hgsc.bcm.edu	37	20	16360332	16360332	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr20:16360332T>C	ENST00000354981.2	-	19	2472	c.2315A>G	c.(2314-2316)aAg>aGg	p.K772R	KIF16B_ENST00000408042.1_Missense_Mutation_p.K772R|KIF16B_ENST00000378003.2_5'UTR|KIF16B_ENST00000355755.3_Missense_Mutation_p.K772R	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	772	Glu-rich.		K -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		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)	p.K772T(1)		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						CATCTCCTGCTTCTCTCGGAG	0.567																																																	1	Substitution - Missense(1)	breast(1)	20											111.0	105.0	107.0					20																	16360332		2203	4300	6503	16308332	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.2315A>G	20.37:g.16360332T>C	ENSP00000347076:p.Lys772Arg		16308332	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	12.26	1.883831	0.33255	.	.	ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000408042	T;T;T	0.18016	2.24;2.24;2.24	5.31	1.7	0.24286	.	0.275521	0.40064	N	0.001182	T	0.09992	0.0245	L	0.32530	0.975	0.80722	D	1	B;B;B;B	0.15930	0.015;0.011;0.003;0.002	B;B;B;B	0.17722	0.015;0.019;0.01;0.004	T	0.25676	-1.0125	10	0.11485	T	0.65	.	5.9259	0.19112	0.0:0.1431:0.1415:0.7154	.	772;772;772;772	Q96L93-4;Q96L93-2;Q96L93-6;Q96L93	.;.;.;KI16B_HUMAN	R	772	ENSP00000347076:K772R;ENSP00000347995:K772R;ENSP00000384164:K772R	ENSP00000347076:K772R	K	-	2	0	KIF16B	16308332	1.000000	0.71417	0.958000	0.39756	0.915000	0.54546	2.413000	0.44618	0.026000	0.15269	0.477000	0.44152	AAG		0.567	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683	
BPIFB3	359710	hgsc.bcm.edu	37	20	31660530	31660530	+	Silent	SNP	G	G	A	rs145354732	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr20:31660530G>A	ENST00000375494.3	+	14	1332	c.1332G>A	c.(1330-1332)ctG>ctA	p.L444L		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	444					innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										CAGTGGCCCTGGATGTTGGAA	0.493													G|||	5	0.000998403	0.0038	0.0	5008	,	,		20722	0.0		0.0	False		,,,				2504	0.0																0			20						G		4,4402	8.1+/-20.4	0,4,2199	164.0	154.0	157.0		1332	2.7	0.7	20	dbSNP_134	157	0,8600		0,0,4300	no	coding-synonymous	BPIFB3	NM_182658.1		0,4,6499	AA,AG,GG		0.0,0.0908,0.0308		444/477	31660530	4,13002	2203	4300	6503	31124191	SO:0001819	synonymous_variant	359710			AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"""BPI fold containing"""	16178	protein-coding gene	gene with protein product		615717	"""chromosome 20 open reading frame 185"""	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.1332G>A	20.37:g.31660530G>A			31124191	Q5TDX7	Silent	SNP	ENST00000375494.3	37	CCDS13212.1																																																																																				0.493	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658	
NCOA6	23054	hgsc.bcm.edu	37	20	33330093	33330093	+	Missense_Mutation	SNP	G	G	A	rs181662709		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr20:33330093G>A	ENST00000374796.2	-	12	6537	c.3967C>T	c.(3967-3969)Cgg>Tgg	p.R1323W	NCOA6_ENST00000359003.2_Missense_Mutation_p.R1323W			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1323					brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.R1323W(2)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						GGACTTGCCCGTTTTGTTGCT	0.453																																																	2	Substitution - Missense(2)	ovary(2)	20											139.0	138.0	138.0					20																	33330093		2203	4300	6503	32793754	SO:0001583	missense	23054			AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.3967C>T	20.37:g.33330093G>A	ENSP00000363929:p.Arg1323Trp		32793754	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	16.30	3.084708	0.55861	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.31510	1.49;1.49	5.98	5.02	0.67125	.	0.000000	0.64402	D	0.000007	T	0.45438	0.1342	L	0.32530	0.975	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	T	0.46775	-0.9167	10	0.87932	D	0	-14.3735	14.9392	0.70980	0.0:0.0:0.7266:0.2734	.	1323	Q14686	NCOA6_HUMAN	W	1323	ENSP00000363929:R1323W;ENSP00000351894:R1323W	ENSP00000351894:R1323W	R	-	1	2	NCOA6	32793754	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.918000	0.48829	1.503000	0.48686	0.591000	0.81541	CGG		0.453	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071	
PRR14L	253143	hgsc.bcm.edu	37	22	32108222	32108222	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr22:32108222G>A	ENST00000327423.6	-	4	5792	c.5603C>T	c.(5602-5604)tCc>tTc	p.S1868F	PRR14L_ENST00000434485.1_Missense_Mutation_p.S1868F|PRR14L_ENST00000397493.2_Missense_Mutation_p.S1868F	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like	1868										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						GTCTGCTATGGAGGCTGGAGA	0.527																																																	0			22											134.0	128.0	130.0					22																	32108222		2203	4300	6503	30438222	SO:0001583	missense	253143			BC040859	CCDS13900.2	22q12.2	2011-01-25	2011-01-25	2011-01-25	ENSG00000183530	ENSG00000183530			28738	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 30"""	C22orf30		12477932	Standard	NM_173566		Approved	MGC50372	uc003alp.4	Q5THK1	OTTHUMG00000030139	ENST00000327423.6:c.5603C>T	22.37:g.32108222G>A	ENSP00000331845:p.Ser1868Phe		30438222	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Missense_Mutation	SNP	ENST00000327423.6	37	CCDS13900.2	.	.	.	.	.	.	.	.	.	.	G	17.03	3.285310	0.59867	.	.	ENSG00000183530	ENST00000397493;ENST00000327423;ENST00000434485	T;T;T	0.39997	1.05;1.05;1.05	5.66	5.66	0.87406	.	0.159398	0.44483	D	0.000460	T	0.60983	0.2311	L	0.56769	1.78	0.38691	D	0.952778	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.996;0.996	T	0.64309	-0.6438	10	0.62326	D	0.03	-9.0398	14.7978	0.69891	0.0:0.1449:0.8551:0.0	.	1868;1868;1868	Q5THK1-2;Q5THK1;Q5THK1-4	.;PR14L_HUMAN;.	F	1868	ENSP00000380630:S1868F;ENSP00000331845:S1868F;ENSP00000388314:S1868F	ENSP00000331845:S1868F	S	-	2	0	PRR14L	30438222	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	3.597000	0.54031	2.668000	0.90789	0.655000	0.94253	TCC		0.527	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566	
PARVB	29780	hgsc.bcm.edu	37	22	44489860	44489860	+	Silent	SNP	C	C	T	rs369214399		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr22:44489860C>T	ENST00000338758.7	+	2	228	c.165C>T	c.(163-165)ccC>ccT	p.P55P	PARVB_ENST00000404989.1_Silent_p.P18P|PARVB_ENST00000477795.1_3'UTR|PARVB_ENST00000406477.3_Silent_p.P88P	NM_013327.4	NP_037459.2	Q9HBI1	PARVB_HUMAN	parvin, beta	55					actin cytoskeleton reorganization (GO:0031532)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell projection assembly (GO:0030031)|establishment or maintenance of cell polarity regulating cell shape (GO:0071963)|lamellipodium assembly (GO:0030032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(3)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Ovarian(80;0.0246)|all_neural(38;0.0423)				CGATGTCCCCCGCCCTGGTGG	0.547																																																	0			22						T	,	0,4406		0,0,2203	99.0	99.0	99.0		264,165	-9.8	0.0	22		99	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	PARVB	NM_001003828.2,NM_013327.4	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	88/398,55/365	44489860	1,13005	2203	4300	6503	42821193	SO:0001819	synonymous_variant	29780			AF151814	CCDS14056.1, CCDS46724.1, CCDS58808.1, CCDS74874.1	22q13.2-q13.33	2013-01-24			ENSG00000188677	ENSG00000188677		"""Parvins"""	14653	protein-coding gene	gene with protein product	"""affixin"""	608121				10810093, 11171322	Standard	NM_001003828		Approved	CGI-56	uc003ben.3	Q9HBI1	OTTHUMG00000150665	ENST00000338758.7:c.165C>T	22.37:g.44489860C>T			42821193	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Silent	SNP	ENST00000338758.7	37	CCDS14056.1																																																																																				0.547	PARVB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319518.2	NM_001003828	
EXD2	55218	hgsc.bcm.edu	37	14	69704380	69704380	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr14:69704380T>C	ENST00000409018.3	+	8	1509	c.1381T>C	c.(1381-1383)Tcc>Ccc	p.S461P	EXD2_ENST00000409949.1_Missense_Mutation_p.S336P|EXD2_ENST00000449989.1_Missense_Mutation_p.S336P|EXD2_ENST00000409242.1_Missense_Mutation_p.S336P|EXD2_ENST00000312994.5_Missense_Mutation_p.S461P|RP11-363J20.2_ENST00000556316.1_lincRNA|EXD2_ENST00000409675.1_Missense_Mutation_p.S336P|EXD2_ENST00000492815.1_3'UTR|EXD2_ENST00000409014.1_Missense_Mutation_p.S336P	NM_001193361.1	NP_001180290.1	Q9NVH0	EXD2_HUMAN	exonuclease 3'-5' domain containing 2	461							3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|urinary_tract(1)	14						GCTCTGCACCTCCTGCCATGC	0.567																																																	0			14											64.0	52.0	56.0					14																	69704380		2203	4300	6503	68774133	SO:0001583	missense	55218			AK001600	CCDS9793.1, CCDS53902.1	14q24.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000081177	ENSG00000081177			20217	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 114"", ""exonuclease 3'-5' domain-like 2"""	C14orf114, EXDL2			Standard	NM_018199		Approved	FLJ10738	uc001xkv.3	Q9NVH0	OTTHUMG00000154496	ENST00000409018.3:c.1381T>C	14.37:g.69704380T>C	ENSP00000387331:p.Ser461Pro		68774133	B4DIH6|G5E947|Q6AWB6|Q8N3D3	Missense_Mutation	SNP	ENST00000409018.3	37	CCDS53902.1	.	.	.	.	.	.	.	.	.	.	T	14.93	2.683563	0.47991	.	.	ENSG00000081177	ENST00000409018;ENST00000409014;ENST00000409675;ENST00000409949;ENST00000409242;ENST00000312994;ENST00000449989	T;T;T;T;T;T;T	0.64085	0.32;-0.08;-0.08;-0.08;-0.08;0.32;-0.08	5.24	5.24	0.73138	.	0.281373	0.40144	N	0.001161	T	0.48447	0.1500	L	0.27053	0.805	0.53005	D	0.999966	B;B;B	0.20459	0.045;0.004;0.004	B;B;B	0.22386	0.039;0.005;0.005	T	0.42275	-0.9461	10	0.30078	T	0.28	-14.6992	11.9225	0.52799	0.0:0.0:0.1451:0.8549	.	461;336;336	G5E947;B3KP95;Q9NVH0	.;.;EXD2_HUMAN	P	461;336;336;336;336;461;336	ENSP00000387331:S461P;ENSP00000386915:S336P;ENSP00000386762:S336P;ENSP00000386632:S336P;ENSP00000386839:S336P;ENSP00000313140:S461P;ENSP00000392177:S336P	ENSP00000313140:S461P	S	+	1	0	EXD2	68774133	0.985000	0.35326	1.000000	0.80357	0.996000	0.88848	1.557000	0.36299	2.197000	0.70478	0.455000	0.32223	TCC		0.567	EXD2-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000335504.1		
ODF3L2	284451	hgsc.bcm.edu	37	19	463968	463968	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr19:463968G>A	ENST00000315489.4	-	4	981	c.746C>T	c.(745-747)aCc>aTc	p.T249I	SHC2_ENST00000264554.6_5'Flank|ODF3L2_ENST00000382696.3_Missense_Mutation_p.T213I	NM_182577.2	NP_872383.1	Q3SX64	OD3L2_HUMAN	outer dense fiber of sperm tails 3-like 2	249						cytoplasmic microtubule (GO:0005881)				large_intestine(1)|lung(2)	3						TTTGTTCACGGTGACCTGCTC	0.736																																																	0			19											24.0	28.0	27.0					19																	463968		2196	4290	6486	414968	SO:0001583	missense	284451			AK097378	CCDS12027.1	19p13.3	2010-04-23	2008-07-04	2008-07-04		ENSG00000181781			26841	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 19"""	C19orf19		14702039	Standard	NM_182577		Approved	FLJ40059	uc002lor.3	Q3SX64		ENST00000315489.4:c.746C>T	19.37:g.463968G>A	ENSP00000318029:p.Thr249Ile		414968	Q3SX65|Q8N1L2	Missense_Mutation	SNP	ENST00000315489.4	37	CCDS12027.1	.	.	.	.	.	.	.	.	.	.	G	13.69	2.311600	0.40895	.	.	ENSG00000181781	ENST00000315489;ENST00000382696	T;T	0.47869	1.36;0.83	3.81	3.81	0.43845	.	0.168517	0.51477	D	0.000099	T	0.54663	0.1872	L	0.53671	1.685	0.45261	D	0.998261	D;D	0.67145	0.996;0.991	P;P	0.62184	0.899;0.899	T	0.49835	-0.8897	10	0.23302	T	0.38	-16.8727	9.1293	0.36835	0.0:0.0:0.7816:0.2184	.	213;249	Q3SX64-2;Q3SX64	.;OD3L2_HUMAN	I	249;213	ENSP00000318029:T249I;ENSP00000372143:T213I	ENSP00000318029:T249I	T	-	2	0	ODF3L2	414968	1.000000	0.71417	0.873000	0.34254	0.425000	0.31504	6.593000	0.74100	1.850000	0.53721	0.555000	0.69702	ACC		0.736	ODF3L2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451849.2	NM_182577	
MLLT1	4298	hgsc.bcm.edu	37	19	6218019	6218019	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr19:6218019T>C	ENST00000252674.7	-	7	1307	c.1144A>G	c.(1144-1146)Agc>Ggc	p.S382G	MLLT1_ENST00000585588.1_5'Flank	NM_005934.3	NP_005925.2	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1	382	Poly-Ser.				negative regulation of protein kinase activity (GO:0006469)|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 elongation factor complex (GO:0008023)	DNA binding (GO:0003677)			endometrium(3)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|skin(2)	17						gagtctgagctggagCTGGAG	0.612			T	MLL	AL																																			Dom	yes		19	19p13.3	4298	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1 (ENL)"""		L	0			19											173.0	137.0	149.0					19																	6218019		2199	4298	6497	6169019	SO:0001583	missense	4298				CCDS12160.1	19p13.3	2012-10-04	2001-11-28		ENSG00000130382	ENSG00000130382			7134	protein-coding gene	gene with protein product		159556	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 1"""				Standard	XM_005259561		Approved	ENL, LTG19, YEATS1	uc002mek.3	Q03111	OTTHUMG00000180757	ENST00000252674.7:c.1144A>G	19.37:g.6218019T>C	ENSP00000252674:p.Ser382Gly		6169019	Q14768	Missense_Mutation	SNP	ENST00000252674.7	37	CCDS12160.1	.	.	.	.	.	.	.	.	.	.	T	17.74	3.463410	0.63513	.	.	ENSG00000130382	ENST00000252674	.	.	.	4.59	4.59	0.56863	.	0.084546	0.85682	D	0.000000	T	0.76948	0.4059	M	0.80183	2.485	0.48696	D	0.999698	P	0.52842	0.956	D	0.65010	0.931	T	0.77305	-0.2637	9	0.36615	T	0.2	-6.0912	12.807	0.57619	0.0:0.0:0.0:1.0	.	382	Q03111	ENL_HUMAN	G	382	.	ENSP00000252674:S382G	S	-	1	0	MLLT1	6169019	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.071000	0.57556	1.705000	0.51264	0.379000	0.24179	AGC		0.612	MLLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452909.1	NM_005934	
COL5A3	50509	hgsc.bcm.edu	37	19	10090070	10090070	+	Silent	SNP	C	C	T	rs199880497	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr19:10090070C>T	ENST00000264828.3	-	38	2821	c.2736G>A	c.(2734-2736)ccG>ccA	p.P912P		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	912	Collagen-like 4.|Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			CTGGTCCAGGCGGGCCTGTCT	0.542													c|||	5	0.000998403	0.0	0.0	5008	,	,		17420	0.0		0.0	False		,,,				2504	0.0051																0			19											91.0	97.0	95.0					19																	10090070		2203	4300	6503	9951070	SO:0001819	synonymous_variant	50509			AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"""Collagens"""	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.2736G>A	19.37:g.10090070C>T			9951070	Q9NZQ6	Silent	SNP	ENST00000264828.3	37	CCDS12222.1																																																																																				0.542	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
SLC5A5	6528	hgsc.bcm.edu	37	19	17994774	17994774	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr19:17994774G>A	ENST00000222248.3	+	12	1792	c.1445G>A	c.(1444-1446)cGc>cAc	p.R482H		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	482					cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|iodide transport (GO:0015705)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	iodide transmembrane transporter activity (GO:0015111)|sodium:iodide symporter activity (GO:0008507)			NS(2)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						TCGGCTGCCCGCTGCGTGGCT	0.682																																					Melanoma(65;1008 1708 7910 46650)												0			19											10.0	8.0	9.0					19																	17994774		2174	4269	6443	17855774	SO:0001583	missense	6528				CCDS12368.1	19p13.11	2013-07-19	2013-07-19		ENSG00000105641	ENSG00000105641		"""Solute carriers"""	11040	protein-coding gene	gene with protein product		601843	"""solute carrier family 5 (sodium iodide symporter), member 5"""			9231811	Standard	NM_000453		Approved	NIS	uc002nhr.4	Q92911		ENST00000222248.3:c.1445G>A	19.37:g.17994774G>A	ENSP00000222248:p.Arg482His		17855774	O43702|Q2M335|Q9NYB6	Missense_Mutation	SNP	ENST00000222248.3	37	CCDS12368.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.195316	0.38806	.	.	ENSG00000105641	ENST00000222248	D	0.85171	-1.95	4.43	1.86	0.25419	.	0.710769	0.14031	N	0.346148	T	0.61652	0.2364	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.55704	-0.8099	10	0.44086	T	0.13	.	6.8823	0.24181	0.2848:0.0:0.7152:0.0	.	482	Q92911	SC5A5_HUMAN	H	482	ENSP00000222248:R482H	ENSP00000222248:R482H	R	+	2	0	SLC5A5	17855774	0.012000	0.17670	0.046000	0.18839	0.147000	0.21601	-0.023000	0.12456	0.991000	0.38814	0.555000	0.69702	CGC		0.682	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1		
DPY19L3	147991	hgsc.bcm.edu	37	19	32959705	32959705	+	Silent	SNP	G	G	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr19:32959705G>A	ENST00000342179.5	+	16	1898	c.1683G>A	c.(1681-1683)ctG>ctA	p.L561L	DPY19L3_ENST00000586987.1_Silent_p.L561L|DPY19L3_ENST00000392250.2_Silent_p.L561L|DPY19L3_ENST00000590651.1_3'UTR	NM_207325.2	NP_997208.2	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3 (C. elegans)	561						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(4)|pancreas(1)	32	Esophageal squamous(110;0.162)					CAGTGGAGCTGATGAACTGGA	0.333																																																	0			19											65.0	71.0	69.0					19																	32959705		2203	4300	6503	37651545	SO:0001819	synonymous_variant	147991				CCDS12422.1	19q13.11	2008-02-05				ENSG00000178904			27120	protein-coding gene	gene with protein product		613894					Standard	NM_207325		Approved		uc002ntg.3	Q6ZPD9		ENST00000342179.5:c.1683G>A	19.37:g.32959705G>A			37651545	Q68DC7|Q6ZTB7|Q6ZTS2	Silent	SNP	ENST00000342179.5	37	CCDS12422.1																																																																																				0.333	DPY19L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450311.1	NM_207325	
ZNF180	7733	hgsc.bcm.edu	37	19	44981815	44981815	+	Missense_Mutation	SNP	G	G	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr19:44981815G>T	ENST00000221327.4	-	5	1164	c.883C>A	c.(883-885)Cat>Aat	p.H295N	AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000391956.4_Missense_Mutation_p.H270N|ZNF180_ENST00000592529.1_Missense_Mutation_p.H268N	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	295					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				CCTCCTCCATGAATTTTTTCA	0.348																																					Esophageal Squamous(180;1353 2003 32862 46574 49854)												0			19											70.0	77.0	75.0					19																	44981815		2203	4299	6502	49673655	SO:0001583	missense	7733			AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.883C>A	19.37:g.44981815G>T	ENSP00000221327:p.His295Asn		49673655	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	G	6.869	0.529799	0.13127	.	.	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.26660	1.72;1.72	5.18	1.78	0.24846	.	1.110340	0.07032	N	0.828678	T	0.16471	0.0396	N	0.08118	0	0.29687	N	0.841251	P;P;P	0.42203	0.773;0.664;0.664	B;B;B	0.43274	0.414;0.235;0.235	T	0.21724	-1.0237	10	0.72032	D	0.01	-0.3399	6.6697	0.23062	0.1492:0.1535:0.6973:0.0	.	270;294;295	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	N	295;270	ENSP00000221327:H295N;ENSP00000375818:H270N	ENSP00000221327:H295N	H	-	1	0	ZNF180	49673655	0.297000	0.24408	0.000000	0.03702	0.340000	0.28889	2.163000	0.42377	0.149000	0.19098	0.655000	0.94253	CAT		0.348	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
GPR4	2828	hgsc.bcm.edu	37	19	46094082	46094082	+	Missense_Mutation	SNP	G	G	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr19:46094082G>T	ENST00000323040.4	-	2	1987	c.1043C>A	c.(1042-1044)tCc>tAc	p.S348Y	GPR4_ENST00000591614.1_5'Flank|OPA3_ENST00000544371.1_Intron	NM_005282.2	NP_005273.1	P46093	GPR4_HUMAN	G protein-coupled receptor 4	348					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(262;0.0071)|GBM - Glioblastoma multiforme(486;0.128)|Epithelial(262;0.223)		GTCCCCCTGGGAGGGCGGAGT	0.622																																					Esophageal Squamous(117;181 1612 1673 14956 42937)												0			19											58.0	59.0	59.0					19																	46094082		2203	4300	6503	50785922	SO:0001583	missense	2828			BC067536	CCDS12669.1	19q13.3	2012-08-21				ENSG00000177464		"""GPCR / Class A : Orphans"""	4497	protein-coding gene	gene with protein product		600551				8595909	Standard	NM_005282		Approved		uc002pcm.3	P46093		ENST00000323040.4:c.1043C>A	19.37:g.46094082G>T	ENSP00000319744:p.Ser348Tyr		50785922	A8K3T3|B0M0K1|Q6NWM4	Missense_Mutation	SNP	ENST00000323040.4	37	CCDS12669.1	.	.	.	.	.	.	.	.	.	.	G	10.56	1.383570	0.25031	.	.	ENSG00000177464	ENST00000323040	T	0.62364	0.03	4.53	4.53	0.55603	.	0.918642	0.08962	N	0.868555	T	0.49406	0.1555	N	0.14661	0.345	0.28453	N	0.91624	B	0.26258	0.145	B	0.28011	0.085	T	0.47799	-0.9089	10	0.66056	D	0.02	.	12.6317	0.56661	0.0:0.0:1.0:0.0	.	348	P46093	GPR4_HUMAN	Y	348	ENSP00000319744:S348Y	ENSP00000319744:S348Y	S	-	2	0	GPR4	50785922	0.279000	0.24239	0.924000	0.36721	0.452000	0.32318	0.502000	0.22594	2.356000	0.79943	0.455000	0.32223	TCC		0.622	GPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459603.1	NM_005282	
LENG8	114823	hgsc.bcm.edu	37	19	54966244	54966244	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr19:54966244C>T	ENST00000326764.5	+	7	1273	c.794C>T	c.(793-795)cCc>cTc	p.P265L	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	228										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		GGCCCCCAGCCCAACCCTGAG	0.602																																																	0			19											70.0	68.0	69.0					19																	54966244		2203	4300	6503	59658056	SO:0001583	missense	114823			AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.794C>T	19.37:g.54966244C>T	ENSP00000318374:p.Pro265Leu		59658056	B0VJY9|Q8IZ27|Q8NCX6	Missense_Mutation	SNP	ENST00000326764.5	37	CCDS12894.1	.	.	.	.	.	.	.	.	.	.	C	17.13	3.310150	0.60414	.	.	ENSG00000167615	ENST00000326764;ENST00000301196;ENST00000439657;ENST00000376526;ENST00000431846	T;T;T;T	0.44482	1.47;0.92;1.41;1.45	5.38	5.38	0.77491	.	0.247838	0.41605	D	0.000846	T	0.41627	0.1167	L	0.50333	1.59	0.80722	D	1	P;P	0.51933	0.617;0.949	B;P	0.45753	0.173;0.492	T	0.23762	-1.0179	10	0.42905	T	0.14	-33.8854	12.0197	0.53336	0.1726:0.8274:0.0:0.0	.	265;228	Q96PV6-2;F8W9Q9	.;.	L	265;228;265;228;265	ENSP00000318374:P265L;ENSP00000399507:P265L;ENSP00000365709:P228L;ENSP00000388053:P265L	ENSP00000301196:P228L	P	+	2	0	LENG8	59658056	1.000000	0.71417	0.997000	0.53966	0.932000	0.56968	2.432000	0.44784	2.688000	0.91661	0.655000	0.94253	CCC		0.602	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925	
CSMD1	64478	hgsc.bcm.edu	37	8	3015448	3015448	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr8:3015448C>T	ENST00000520002.1	-	40	6443	c.5888G>A	c.(5887-5889)cGt>cAt	p.R1963H	CSMD1_ENST00000539096.1_Missense_Mutation_p.R1962H|CSMD1_ENST00000537824.1_Missense_Mutation_p.R1962H|CSMD1_ENST00000602723.1_Missense_Mutation_p.R1963H|CSMD1_ENST00000400186.3_Missense_Mutation_p.R1963H|CSMD1_ENST00000542608.1_Missense_Mutation_p.R1962H|CSMD1_ENST00000602557.1_Missense_Mutation_p.R1963H|CSMD1_ENST00000523387.1_5'UTR			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1963	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		ATAGTTCCAACGGCGAACGGT	0.453																																																	0			8											55.0	53.0	54.0					8																	3015448		1959	4100	6059	3002855	SO:0001583	missense	64478					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.5888G>A	8.37:g.3015448C>T	ENSP00000430733:p.Arg1963His		3002855	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	C	19.45	3.829321	0.71258	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18	5.45	5.45	0.79879	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000001	T	0.75451	0.3851	L	0.47716	1.5	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;1.0;0.999;0.998	T	0.77051	-0.2731	10	0.72032	D	0.01	.	18.8862	0.92379	0.0:1.0:0.0:0.0	.	1963;1963;1962;1963	E5RIG2;Q96PZ7;F5H2I8;Q96PZ7-4	.;CSMD1_HUMAN;.;.	H	1963;1963;1824;1962;1962;1962	ENSP00000383047:R1963H;ENSP00000430733:R1963H;ENSP00000441462:R1962H;ENSP00000446243:R1962H;ENSP00000441675:R1962H	ENSP00000320445:R1824H	R	-	2	0	CSMD1	3002855	1.000000	0.71417	0.266000	0.24541	0.030000	0.12068	7.311000	0.78958	2.538000	0.85594	0.655000	0.94253	CGT		0.453	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
SLC7A13	157724	hgsc.bcm.edu	37	8	87235283	87235283	+	Silent	SNP	C	C	A	rs55902108	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr8:87235283C>A	ENST00000297524.3	-	2	838	c.735G>T	c.(733-735)gcG>gcT	p.A245A	SLC7A13_ENST00000520624.1_5'UTR|SLC7A13_ENST00000419776.2_Silent_p.A236A	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	245						integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						CCAGAGGTAACGCAGTAAATA	0.383																																																	0			8											158.0	161.0	160.0					8																	87235283		2203	4300	6503	87304399	SO:0001819	synonymous_variant	157724			AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"""Solute carriers"""	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.735G>T	8.37:g.87235283C>A			87304399	Q05C37|Q08AH9|Q96N84	Silent	SNP	ENST00000297524.3	37	CCDS34917.1																																																																																				0.383	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817	
CSMD3	114788	hgsc.bcm.edu	37	8	113358402	113358402	+	Silent	SNP	G	G	T	rs139487815	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr8:113358402G>T	ENST00000297405.5	-	41	6610	c.6366C>A	c.(6364-6366)atC>atA	p.I2122I	CSMD3_ENST00000352409.3_Silent_p.I2052I|CSMD3_ENST00000455883.2_Silent_p.I2018I|CSMD3_ENST00000343508.3_Silent_p.I2082I	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2122	CUB 12. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.I2122M(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CAGGACTGAGGATCACACCAC	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																							1	Substitution - Missense(1)	ovary(1)	8											111.0	112.0	112.0					8																	113358402		2203	4300	6503	113427578	SO:0001819	synonymous_variant	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.6366C>A	8.37:g.113358402G>T			113427578	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																				0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
ADCY8	114	hgsc.bcm.edu	37	8	131792656	131792656	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr8:131792656C>T	ENST00000286355.5	-	18	5828	c.3736G>A	c.(3736-3738)Gac>Aac	p.D1246N	ADCY8_ENST00000377928.3_Missense_Mutation_p.D1115N	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	1246					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			TCAGATTTGTCGGTGCCTTCA	0.358										HNSCC(32;0.087)																																							0			8											93.0	91.0	92.0					8																	131792656		2203	4300	6503	131861838	SO:0001583	missense	114			Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"""Adenylate cyclases"""	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.3736G>A	8.37:g.131792656C>T	ENSP00000286355:p.Asp1246Asn		131861838		Missense_Mutation	SNP	ENST00000286355.5	37	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.027473	0.75390	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	T;T	0.80304	-1.36;-1.34	5.68	5.68	0.88126	.	0.182120	0.44285	D	0.000473	D	0.83714	0.5314	L	0.27053	0.805	0.41093	D	0.985617	D;P	0.76494	0.999;0.649	D;B	0.68621	0.959;0.091	D	0.85809	0.1378	10	0.87932	D	0	.	16.9518	0.86247	0.0:1.0:0.0:0.0	.	1115;1246	E7EVL1;P40145	.;ADCY8_HUMAN	N	1246;1115	ENSP00000286355:D1246N;ENSP00000367161:D1115N	ENSP00000286355:D1246N	D	-	1	0	ADCY8	131861838	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.048000	0.76606	2.689000	0.91719	0.655000	0.94253	GAC		0.358	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1		
TG	7038	hgsc.bcm.edu	37	8	133899152	133899152	+	Missense_Mutation	SNP	G	G	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr8:133899152G>C	ENST00000220616.4	+	9	1575	c.1535G>C	c.(1534-1536)gGa>gCa	p.G512A	TG_ENST00000377869.1_Missense_Mutation_p.G512A	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	512					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		TTCTTGAATGGAGGGAGACAA	0.443																																																	0			8											44.0	47.0	46.0					8																	133899152		2203	4299	6502	133968334	SO:0001583	missense	7038			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.1535G>C	8.37:g.133899152G>C	ENSP00000220616:p.Gly512Ala		133968334	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	G	4.351	0.064592	0.08388	.	.	ENSG00000042832	ENST00000377869;ENST00000220616;ENST00000535932	T;T	0.63255	-0.03;-0.02	5.29	2.46	0.29980	.	1.403590	0.04446	N	0.371705	T	0.53302	0.1788	L	0.47716	1.5	0.09310	N	1	B	0.34372	0.451	B	0.27380	0.079	T	0.40757	-0.9546	10	0.33141	T	0.24	.	8.1981	0.31409	0.1456:0.1294:0.725:0.0	.	512	P01266	THYG_HUMAN	A	512	ENSP00000367100:G512A;ENSP00000220616:G512A	ENSP00000220616:G512A	G	+	2	0	TG	133968334	0.063000	0.20901	0.001000	0.08648	0.028000	0.11728	1.339000	0.33885	0.792000	0.33850	0.557000	0.71058	GGA		0.443	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
PRAMEF12	390999	hgsc.bcm.edu	37	1	12837469	12837469	+	Silent	SNP	G	G	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:12837469G>T	ENST00000357726.4	+	3	1206	c.1179G>T	c.(1177-1179)ctG>ctT	p.L393L		NM_001080830.1	NP_001074299.1	O95522	PRA12_HUMAN	PRAME family member 12	393					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					NS(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|urinary_tract(1)	23	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00818)|Colorectal(212;5.04e-06)|Kidney(185;4.99e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000198)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TGGCCGCCCTGGAGAACCTGC	0.627																																																	0			1											101.0	109.0	106.0					1																	12837469		2203	4300	6503	12760056	SO:0001819	synonymous_variant	390999				CCDS41254.1	1p36.21	2013-01-17			ENSG00000116726	ENSG00000116726		"""-"""	22125	protein-coding gene	gene with protein product							Standard	NM_001080830		Approved	OTTHUMG00000001927	uc001aui.3	O95522	OTTHUMG00000001927	ENST00000357726.4:c.1179G>T	1.37:g.12837469G>T			12760056		Silent	SNP	ENST00000357726.4	37	CCDS41254.1																																																																																				0.627	PRAMEF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005457.1	XM_372760	
LRRC38	126755	hgsc.bcm.edu	37	1	13839913	13839913	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:13839913C>T	ENST00000376085.3	-	1	630	c.176G>A	c.(175-177)cGc>cAc	p.R59H	RP4-597A16.2_ENST00000563570.1_RNA	NM_001010847.1	NP_001010847.1	Q5VT99	LRC38_HUMAN	leucine rich repeat containing 38	59					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											CAGCAGCTTGCGCACGTCCAG	0.687																																																	0			1																																								13712500	SO:0001583	missense	126755			BC016048	CCDS53269.1	1p36.21	2008-02-05			ENSG00000162494	ENSG00000162494			27005	protein-coding gene	gene with protein product		615212				12477932	Standard	NM_001010847		Approved		uc001avb.3	Q5VT99	OTTHUMG00000007918	ENST00000376085.3:c.176G>A	1.37:g.13839913C>T	ENSP00000365253:p.Arg59His		13712500	Q96B32	Missense_Mutation	SNP	ENST00000376085.3	37	CCDS53269.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.433975	0.83776	.	.	ENSG00000162494	ENST00000376085	T	0.59772	0.24	4.14	4.14	0.48551	Leucine-rich repeat-containing N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.49355	0.1552	L	0.37800	1.135	0.58432	D	0.999996	D	0.61080	0.989	B	0.42625	0.393	T	0.58329	-0.7655	10	0.66056	D	0.02	.	14.9716	0.71238	0.0:1.0:0.0:0.0	.	59	Q5VT99	LRC38_HUMAN	H	59	ENSP00000365253:R59H	ENSP00000365253:R59H	R	-	2	0	LRRC38	13712500	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	5.873000	0.69644	1.837000	0.53436	0.297000	0.19635	CGC		0.687	LRRC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021793.1		
PUM1	9698	hgsc.bcm.edu	37	1	31440127	31440127	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:31440127T>C	ENST00000257075.5	-	12	1769	c.1676A>G	c.(1675-1677)tAt>tGt	p.Y559C	SNORD85_ENST00000363311.1_RNA|PUM1_ENST00000490546.1_5'UTR|PUM1_ENST00000373747.3_Missense_Mutation_p.Y560C|PUM1_ENST00000440538.2_Missense_Mutation_p.Y560C|PUM1_ENST00000423018.2_Intron|PUM1_ENST00000424085.2_Missense_Mutation_p.Y317C|PUM1_ENST00000373741.4_Missense_Mutation_p.Y595C|PUM1_ENST00000373742.2_Missense_Mutation_p.Y500C|PUM1_ENST00000426105.2_Missense_Mutation_p.Y559C	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	559	Ala-rich.				membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		AGTTTGGTCATAGTAAGCAGC	0.458																																																	0			1											117.0	104.0	108.0					1																	31440127		2203	4300	6503	31212714	SO:0001583	missense	9698			AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"""pumilio (Drosophila) homolog 1"", ""pumilio homolog 1 (Drosophila)"""				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.1676A>G	1.37:g.31440127T>C	ENSP00000257075:p.Tyr559Cys		31212714	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	ENST00000257075.5	37	CCDS338.1	.	.	.	.	.	.	.	.	.	.	T	29.0	4.972799	0.92919	.	.	ENSG00000134644	ENST00000424085;ENST00000257075;ENST00000373747;ENST00000373749;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000373742	T;T;T;T;T;T;T	0.35236	1.51;1.32;1.57;1.57;1.61;1.54;1.46	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.58018	0.2093	M	0.73217	2.22	0.80722	D	1	D;D;D;D;D;D;D	0.76494	0.999;0.994;0.963;0.991;0.984;0.991;0.991	P;P;P;P;P;P;P	0.62740	0.906;0.798;0.694;0.798;0.798;0.798;0.798	T	0.62253	-0.6893	10	0.87932	D	0	-7.2849	16.1778	0.81874	0.0:0.0:0.0:1.0	.	500;595;560;559;559;560;559	B4DG92;Q5T1Z8;Q14671-2;Q14671;E9PCJ0;Q5T1Z4;Q53HH5	.;.;.;PUM1_HUMAN;.;.;.	C	317;559;560;297;559;560;595;500	ENSP00000400141:Y317C;ENSP00000257075:Y559C;ENSP00000362852:Y560C;ENSP00000391723:Y559C;ENSP00000401777:Y560C;ENSP00000362846:Y595C;ENSP00000362847:Y500C	ENSP00000257075:Y559C	Y	-	2	0	PUM1	31212714	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.997000	0.88414	2.279000	0.76181	0.533000	0.62120	TAT		0.458	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1		
MACF1	23499	hgsc.bcm.edu	37	1	39824375	39824375	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:39824375C>T	ENST00000372915.3	+	45	12052	c.11965C>T	c.(11965-11967)Cga>Tga	p.R3989*	MACF1_ENST00000545844.1_Nonsense_Mutation_p.R1922*|MACF1_ENST00000289893.4_Nonsense_Mutation_p.R2424*|MACF1_ENST00000564288.1_Nonsense_Mutation_p.R3984*|MACF1_ENST00000539005.1_Nonsense_Mutation_p.R1922*|MACF1_ENST00000317713.7_Nonsense_Mutation_p.R1922*|MACF1_ENST00000567887.1_Nonsense_Mutation_p.R4021*|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000361689.2_Nonsense_Mutation_p.R1922*			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	3989					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.R2424*(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ACAGTGTACACGATTAGGATC	0.498																																																	1	Substitution - Nonsense(1)	central_nervous_system(1)	1											80.0	78.0	78.0					1																	39824375		2203	4300	6503	39596962	SO:0001587	stop_gained	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.11965C>T	1.37:g.39824375C>T	ENSP00000362006:p.Arg3989*		39596962	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Nonsense_Mutation	SNP	ENST00000372915.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	38|38	6.912323|6.912323	0.97928|0.97928	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893|ENST00000372925	.|T	.|0.35421	.|1.31	5.47|5.47	3.33|3.33	0.38152|0.38152	.|.	0.556344|.	0.15703|.	N|.	0.248842|.	.|T	.|0.32704	.|0.0838	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.31110	.|-0.9955	.|6	0.09338|0.62326	T|D	0.73|0.03	.|.	3.495|3.495	0.07651|0.07651	0.3168:0.4816:0.1139:0.0877|0.3168:0.4816:0.1139:0.0877	.|.	.|.	.|.	.|.	X|M	1922;3989;1922;1922;1922;2424|1055	.|ENSP00000362016:T1055M	ENSP00000289893:R2424X|ENSP00000362016:T1055M	R|T	+|+	1|2	2|0	MACF1|MACF1	39596962|39596962	0.054000|0.054000	0.20591|0.20591	0.674000|0.674000	0.29902|0.29902	0.938000|0.938000	0.57974|0.57974	1.867000|1.867000	0.39499|0.39499	1.442000|1.442000	0.47568|0.47568	0.655000|0.655000	0.94253|0.94253	CGA|ACG		0.498	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
HFM1	164045	hgsc.bcm.edu	37	1	91781507	91781507	+	Missense_Mutation	SNP	G	G	A	rs148381777		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:91781507G>A	ENST00000370425.3	-	28	3103	c.3005C>T	c.(3004-3006)aCg>aTg	p.T1002M	HFM1_ENST00000370424.3_Missense_Mutation_p.T681M|HFM1_ENST00000294696.5_Missense_Mutation_p.T234M|HFM1_ENST00000462405.1_5'UTR	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	1002	SEC63.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		TATTTCTGCCGTCGTATCACT	0.313																																																	0			1						G	MET/THR	1,4401	2.1+/-5.4	0,1,2200	52.0	52.0	52.0		3005	-10.5	0.0	1	dbSNP_134	52	1,8595	1.2+/-3.3	0,1,4297	no	missense	HFM1	NM_001017975.3	81	0,2,6497	AA,AG,GG		0.0116,0.0227,0.0154	benign	1002/1436	91781507	2,12996	2201	4298	6499	91554095	SO:0001583	missense	164045			AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"""SEC63 domain containing 1"""	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.3005C>T	1.37:g.91781507G>A	ENSP00000359454:p.Thr1002Met		91554095	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	37	CCDS30769.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	2.729|2.729	-0.264924|-0.264924	0.05754|0.05754	2.27E-4|2.27E-4	1.16E-4|1.16E-4	ENSG00000162669|ENSG00000162669	ENST00000430465|ENST00000370425;ENST00000294696;ENST00000370424;ENST00000370421	.|T;T;T	.|0.61158	.|0.13;0.13;0.13	5.25|5.25	-10.5|-10.5	0.00291|0.00291	.|Sec63 domain (2);	.|0.447307	.|0.25581	.|N	.|0.029700	T|T	0.08935|0.08935	0.0221|0.0221	N|N	0.11201|0.11201	0.11|0.11	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.25743	.|0.02;0.133;0.08	.|B;B;B	.|0.21546	.|0.006;0.035;0.022	T|T	0.08269|0.08269	-1.0730|-1.0730	5|10	.|0.33940	.|T	.|0.23	.|.	4.1282|4.1282	0.10138|0.10138	0.3899:0.0879:0.3937:0.1284|0.3899:0.0879:0.3937:0.1284	.|.	.|681;213;1002	.|A6NGI5;B1B0B5;A2PYH4	.|.;.;HFM1_HUMAN	W|M	214|1002;234;681;686	.|ENSP00000359454:T1002M;ENSP00000294696:T234M;ENSP00000359453:T681M	.|ENSP00000294696:T234M	R|T	-|-	1|2	2|0	HFM1|HFM1	91554095|91554095	0.000000|0.000000	0.05858|0.05858	0.004000|0.004000	0.12327|0.12327	0.009000|0.009000	0.06853|0.06853	1.121000|1.121000	0.31283|0.31283	-1.559000|-1.559000	0.01688|0.01688	-0.368000|-0.368000	0.07277|0.07277	CGG|ACG		0.313	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975	
FNDC7	163479	hgsc.bcm.edu	37	1	109270590	109270590	+	Silent	SNP	G	G	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:109270590G>A	ENST00000370017.3	+	7	1549	c.1272G>A	c.(1270-1272)tcG>tcA	p.S424S	FNDC7_ENST00000271311.2_Silent_p.S425S	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	424	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|skin(4)|stomach(1)|urinary_tract(1)	20		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		GCACCCTTTCGGCTCTAGAGT	0.483																																																	0			1											242.0	208.0	219.0					1																	109270590		2203	4300	6503	109072113	SO:0001819	synonymous_variant	163479				CCDS44185.1	1p13.3	2013-02-11			ENSG00000143107	ENSG00000143107		"""Fibronectin type III domain containing"""	26668	protein-coding gene	gene with protein product						12477932	Standard	NM_001144937		Approved	FLJ35838	uc001dvx.3	Q5VTL7	OTTHUMG00000011120	ENST00000370017.3:c.1272G>A	1.37:g.109270590G>A			109072113	A1L468|E9PAZ5|Q6PF16|Q8NA51	Silent	SNP	ENST00000370017.3	37	CCDS44185.1	.	.	.	.	.	.	.	.	.	.	G	6.401	0.442051	0.12164	.	.	ENSG00000143107	ENST00000445274	.	.	.	5.73	-11.5	0.00074	.	.	.	.	.	T	0.24661	0.0598	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56745	-0.7928	4	.	.	.	-10.2511	7.5534	0.27810	0.1:0.0588:0.4515:0.3897	.	.	.	.	S	200	.	.	G	+	1	0	FNDC7	109072113	0.000000	0.05858	0.062000	0.19696	0.789000	0.44602	-3.528000	0.00441	-3.670000	0.00123	-1.036000	0.02392	GGC		0.483	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532	
GPR61	83873	hgsc.bcm.edu	37	1	110086221	110086221	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:110086221C>T	ENST00000527748.1	+	2	1260	c.577C>T	c.(577-579)Cca>Tca	p.P193S	RP5-1160K1.8_ENST00000526411.1_RNA	NM_031936.4	NP_114142.3	Q9BZJ8	GPR61_HUMAN	G protein-coupled receptor 61	193						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.P193S(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	23		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0426)|Colorectal(144;0.11)|Epithelial(280;0.128)|all cancers(265;0.132)|LUSC - Lung squamous cell carcinoma(189;0.228)		CAGTGTCCCCCCAGGCTGTTC	0.582																																																	1	Substitution - Missense(1)	central_nervous_system(1)	1											162.0	153.0	156.0					1																	110086221		2203	4300	6503	109887744	SO:0001583	missense	83873			AF317652	CCDS801.1	1p13.3	2012-08-21			ENSG00000156097	ENSG00000156097		"""GPCR / Class A : Orphans"""	13300	protein-coding gene	gene with protein product		606916				11165367, 11690637	Standard	NM_031936		Approved	BALGR	uc001dxy.2	Q9BZJ8	OTTHUMG00000011633	ENST00000527748.1:c.577C>T	1.37:g.110086221C>T	ENSP00000432456:p.Pro193Ser		109887744	A8K1W2|Q6NWS0|Q8TDV4|Q96PR4	Missense_Mutation	SNP	ENST00000527748.1	37	CCDS801.1	.	.	.	.	.	.	.	.	.	.	C	11.97	1.797278	0.31777	.	.	ENSG00000156097	ENST00000527748;ENST00000286603	T	0.36157	1.27	5.68	4.75	0.60458	GPCR, rhodopsin-like superfamily (1);	0.190927	0.42548	D	0.000698	T	0.08582	0.0213	N	0.08118	0	0.43574	D	0.995901	B	0.13594	0.008	B	0.14023	0.01	T	0.12167	-1.0558	10	0.10636	T	0.68	-2.3848	14.7202	0.69300	0.0:0.9283:0.0:0.0717	.	193	Q9BZJ8	GPR61_HUMAN	S	193;321	ENSP00000432456:P193S	ENSP00000286603:P321S	P	+	1	0	GPR61	109887744	0.026000	0.19158	1.000000	0.80357	0.980000	0.70556	1.287000	0.33284	2.664000	0.90586	0.655000	0.94253	CCA		0.582	GPR61-005	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385575.1		
HIPK1	204851	hgsc.bcm.edu	37	1	114483239	114483239	+	Silent	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:114483239T>C	ENST00000369558.1	+	2	466	c.234T>C	c.(232-234)gcT>gcC	p.A78A	HIPK1_ENST00000369561.4_Silent_p.A78A|HIPK1_ENST00000426820.2_Silent_p.A78A|HIPK1_ENST00000369555.2_Silent_p.A78A|HIPK1_ENST00000369559.4_Silent_p.A78A|HIPK1_ENST00000369554.2_Silent_p.A78A			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	78					anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCCTCCCAGCTCCTGCAGTGG	0.552																																																	0			1											100.0	101.0	101.0					1																	114483239		2203	4300	6503	114284762	SO:0001819	synonymous_variant	204851			AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.234T>C	1.37:g.114483239T>C			114284762	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Silent	SNP	ENST00000369558.1	37	CCDS867.1																																																																																				0.552	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268	
ECM1	1893	hgsc.bcm.edu	37	1	150483554	150483554	+	Silent	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:150483554A>G	ENST00000369047.4	+	6	713	c.588A>G	c.(586-588)ccA>ccG	p.P196P	ECM1_ENST00000470432.1_3'UTR|ECM1_ENST00000369049.4_Silent_p.P223P|ECM1_ENST00000346569.6_Silent_p.P196P	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	196	2 X approximate repeats.				angiogenesis (GO:0001525)|biomineral tissue development (GO:0031214)|inflammatory response (GO:0006954)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of peptidase activity (GO:0010466)|ossification (GO:0001503)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of T cell migration (GO:2000404)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type 2 immune response (GO:0002828)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	enzyme binding (GO:0019899)|laminin binding (GO:0043236)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)	p.P196P(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|urinary_tract(1)	22	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.29e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			GGAACCTACCACAGTCCAGCT	0.582																																					Melanoma(156;1696 2560 11093 19685)												1	Substitution - coding silent(1)	ovary(1)	1											144.0	147.0	146.0					1																	150483554		2203	4300	6503	148750178	SO:0001819	synonymous_variant	1893			U68186	CCDS953.1, CCDS954.1, CCDS55632.1	1q21	2008-02-05			ENSG00000143369	ENSG00000143369			3153	protein-coding gene	gene with protein product		602201				9367673, 9501329	Standard	NM_004425		Approved		uc001eus.3	Q16610	OTTHUMG00000012806	ENST00000369047.4:c.588A>G	1.37:g.150483554A>G			148750178	A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Silent	SNP	ENST00000369047.4	37	CCDS953.1																																																																																				0.582	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425	
TCHHL1	126637	hgsc.bcm.edu	37	1	152059508	152059508	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:152059508T>C	ENST00000368806.1	-	3	714	c.650A>G	c.(649-651)aAg>aGg	p.K217R		NM_001008536.1	NP_001008536.1	Q5QJ38	TCHL1_HUMAN	trichohyalin-like 1	217							calcium ion binding (GO:0005509)	p.K217M(1)		breast(4)|endometrium(1)|kidney(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(1)|skin(7)|stomach(1)	60	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			ACTGCTGGTCTTTTTTGATCC	0.448																																																	1	Substitution - Missense(1)	ovary(1)	1											137.0	122.0	127.0					1																	152059508		2203	4300	6503	150326132	SO:0001583	missense	126637				CCDS30857.1	1q21.3	2011-10-11	2004-10-05	2006-01-27	ENSG00000182898	ENSG00000182898		"""S100 calcium binding proteins"""	31796	protein-coding gene	gene with protein product			"""S100 calcium binding protein A17"""	S100A17, THHL1			Standard	NM_001008536		Approved		uc001ezo.1	Q5QJ38	OTTHUMG00000013058	ENST00000368806.1:c.650A>G	1.37:g.152059508T>C	ENSP00000357796:p.Lys217Arg		150326132	B2RPK8|Q5VTJ9	Missense_Mutation	SNP	ENST00000368806.1	37	CCDS30857.1	.	.	.	.	.	.	.	.	.	.	.	9.743	1.165333	0.21538	.	.	ENSG00000182898	ENST00000368806	T	0.21361	2.01	5.1	5.1	0.69264	.	0.666605	0.12399	N	0.472275	T	0.03564	0.0102	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37957	-0.9683	10	0.15499	T	0.54	0.1954	11.272	0.49144	0.0:0.0:0.0:1.0	.	217	Q5QJ38	TCHL1_HUMAN	R	217	ENSP00000357796:K217R	ENSP00000357796:K217R	K	-	2	0	TCHHL1	150326132	0.173000	0.23056	0.021000	0.16686	0.004000	0.04260	2.330000	0.43885	1.910000	0.55303	0.455000	0.32223	AAG		0.448	TCHHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036638.2	XM_060104	
FCRL4	83417	hgsc.bcm.edu	37	1	157559005	157559005	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:157559005A>G	ENST00000271532.1	-	3	431	c.296T>C	c.(295-297)cTc>cCc	p.L99P	FCRL4_ENST00000448509.2_5'UTR	NM_031282.2	NP_112572.1	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4	99					immune system process (GO:0002376)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L99R(1)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(20)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	40	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				TGAAGAAAAGAGCAAGCGCAC	0.493																																																	1	Substitution - Missense(1)	ovary(1)	1											63.0	68.0	66.0					1																	157559005		2203	4300	6503	155825629	SO:0001583	missense	83417			AF343661	CCDS1166.1	1q21	2013-01-14			ENSG00000163518	ENSG00000163518		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18507	protein-coding gene	gene with protein product		605876				11290337, 11493702	Standard	NM_031282		Approved	FCRH4, IRTA1, IGFP2, CD307d	uc001fqw.3	Q96PJ5	OTTHUMG00000035488	ENST00000271532.1:c.296T>C	1.37:g.157559005A>G	ENSP00000271532:p.Leu99Pro		155825629	Q96PJ3|Q96RE0	Missense_Mutation	SNP	ENST00000271532.1	37	CCDS1166.1	.	.	.	.	.	.	.	.	.	.	A	8.570	0.879827	0.17467	.	.	ENSG00000163518	ENST00000271532	T	0.19394	2.15	4.2	-8.41	0.00961	Immunoglobulin subtype (1);	4.121640	0.01047	N	0.004417	T	0.03305	0.0096	L	0.31664	0.95	0.09310	N	1	B	0.22800	0.075	B	0.25759	0.063	T	0.21415	-1.0246	10	0.30078	T	0.28	.	1.5384	0.02550	0.1751:0.115:0.3146:0.3954	.	99	Q96PJ5	FCRL4_HUMAN	P	99	ENSP00000271532:L99P	ENSP00000271532:L99P	L	-	2	0	FCRL4	155825629	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-2.190000	0.01247	-1.651000	0.01504	-0.410000	0.06199	CTC		0.493	FCRL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086180.1	NM_031282	
OR10J5	127385	hgsc.bcm.edu	37	1	159505349	159505349	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:159505349C>T	ENST00000334857.2	-	1	493	c.449G>A	c.(448-450)gGc>gAc	p.G150D		NM_001004469.1	NP_001004469.1	Q8NHC4	O10J5_HUMAN	olfactory receptor, family 10, subfamily J, member 5	150						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	22	all_hematologic(112;0.0429)					CAGACCAATGCCAAAGGACCC	0.512																																																	0			1											131.0	101.0	111.0					1																	159505349		2203	4300	6503	157771973	SO:0001583	missense	127385				CCDS30910.1	1q23.2	2012-08-09			ENSG00000184155	ENSG00000184155		"""GPCR / Class A : Olfactory receptors"""	14993	protein-coding gene	gene with protein product							Standard	NM_001004469		Approved		uc010piw.2	Q8NHC4	OTTHUMG00000022738	ENST00000334857.2:c.449G>A	1.37:g.159505349C>T	ENSP00000334441:p.Gly150Asp		157771973	B9EH35|Q6IFH2	Missense_Mutation	SNP	ENST00000334857.2	37	CCDS30910.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.763976	0.31228	.	.	ENSG00000184155	ENST00000334857	T	0.38240	1.15	4.17	2.19	0.27852	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.30696	0.0773	M	0.78637	2.42	0.29532	N	0.852742	P	0.37276	0.589	P	0.48770	0.589	T	0.23368	-1.0190	9	0.41790	T	0.15	.	6.5008	0.22168	0.1801:0.72:0.0:0.0999	.	150	Q8NHC4	O10J5_HUMAN	D	150	ENSP00000334441:G150D	ENSP00000334441:G150D	G	-	2	0	OR10J5	157771973	0.000000	0.05858	0.941000	0.38009	0.150000	0.21749	-0.351000	0.07711	0.448000	0.26722	0.467000	0.42956	GGC		0.512	OR10J5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059021.1	NM_001004469	
PRDX6	9588	hgsc.bcm.edu	37	1	173455445	173455445	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:173455445G>A	ENST00000340385.5	+	4	583	c.451G>A	c.(451-453)Gct>Act	p.A151T	PRDX6_ENST00000470017.1_3'UTR	NM_004905.2	NP_004896.1	P30041	PRDX6_HUMAN	peroxiredoxin 6	151	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				hydrogen peroxide catabolic process (GO:0042744)|phospholipid catabolic process (GO:0009395)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|membrane (GO:0016020)	antioxidant activity (GO:0016209)|glutathione peroxidase activity (GO:0004602)|peroxiredoxin activity (GO:0051920)|phospholipase A2 activity (GO:0004623)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	12						CCTCTACCCAGCTACCACTGG	0.448																																																	0			1											154.0	162.0	160.0					1																	173455445		2203	4300	6503	171722068	SO:0001583	missense	25824			D14662	CCDS1307.1	1q24.1	2008-02-05			ENSG00000117592	ENSG00000117592			16753	protein-coding gene	gene with protein product		602316				11233154	Standard	NM_004905		Approved	AOP2, KIAA0106, 1-Cys, NSGPx, PRX, aiPLA2, MGC46173, p29	uc001giy.1	P30041	OTTHUMG00000034804	ENST00000340385.5:c.451G>A	1.37:g.173455445G>A	ENSP00000342026:p.Ala151Thr		171722068	A8JZY7|P32077|Q5TAH4|Q5ZEZ8	Missense_Mutation	SNP	ENST00000340385.5	37	CCDS1307.1	.	.	.	.	.	.	.	.	.	.	G	35	5.429721	0.96131	.	.	ENSG00000117592	ENST00000340385	T	0.14022	2.54	5.63	5.63	0.86233	Thioredoxin-like fold (3);	0.000000	0.85682	D	0.000000	T	0.27241	0.0668	M	0.91972	3.26	0.80722	D	1	D	0.57899	0.981	P	0.48270	0.572	T	0.36040	-0.9764	10	0.72032	D	0.01	-10.3938	18.8049	0.92032	0.0:0.0:1.0:0.0	.	151	P30041	PRDX6_HUMAN	T	151	ENSP00000342026:A151T	ENSP00000342026:A151T	A	+	1	0	PRDX6	171722068	1.000000	0.71417	0.636000	0.29352	0.994000	0.84299	7.436000	0.80404	2.797000	0.96272	0.655000	0.94253	GCT		0.448	PRDX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084222.1	NM_004905	
ASTN1	460	hgsc.bcm.edu	37	1	176838003	176838003	+	Silent	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:176838003T>C	ENST00000367654.3	-	22	3859	c.3648A>G	c.(3646-3648)cgA>cgG	p.R1216R	ASTN1_ENST00000367657.3_Silent_p.R1208R|ASTN1_ENST00000424564.2_Silent_p.R1208R|ASTN1_ENST00000361833.2_Silent_p.R1208R	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	1216					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						CATCCTCACATCGCCAGGTGA	0.468																																																	0			1											118.0	116.0	117.0					1																	176838003		2203	4300	6503	175104626	SO:0001819	synonymous_variant	460			AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"""astrotactin"""	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.3648A>G	1.37:g.176838003T>C			175104626	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Silent	SNP	ENST00000367654.3	37																																																																																					0.468	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319	
ZBTB41	360023	hgsc.bcm.edu	37	1	197168857	197168857	+	Silent	SNP	G	G	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:197168857G>A	ENST00000367405.4	-	1	815	c.747C>T	c.(745-747)tcC>tcT	p.S249S	CRB1_ENST00000535699.1_5'Flank|ZBTB41_ENST00000467322.1_5'UTR	NM_194314.2	NP_919290.2	Q5SVQ8	ZBT41_HUMAN	zinc finger and BTB domain containing 41	249					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(11)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	40						ATCTTCTTGCGGAGAAACTTC	0.383																																																	0			1											43.0	46.0	45.0					1																	197168857		2195	4297	6492	195435480	SO:0001819	synonymous_variant	360023				CCDS30960.1	1q31.3	2013-01-08			ENSG00000177888	ENSG00000177888		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	24819	protein-coding gene	gene with protein product							Standard	NM_194314		Approved	FRBZ1, FLJ36199, DKFZp686C06120, ZNF924	uc001gtx.1	Q5SVQ8	OTTHUMG00000036275	ENST00000367405.4:c.747C>T	1.37:g.197168857G>A			195435480	A2RUA8|Q6MZT8|Q6ZR25|Q7Z4T1|Q8IZ99	Silent	SNP	ENST00000367405.4	37	CCDS30960.1																																																																																				0.383	ZBTB41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088249.2	NM_194314	
KIF14	9928	hgsc.bcm.edu	37	1	200524571	200524571	+	Silent	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:200524571T>C	ENST00000367350.4	-	28	4803	c.4365A>G	c.(4363-4365)gaA>gaG	p.E1455E		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	1455	Required for CIT-binding.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						TAGTTTTCATTTCTTTGGTAA	0.259																																																	0			1											54.0	58.0	57.0					1																	200524571		2199	4282	6481	198791194	SO:0001819	synonymous_variant	9928			D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"""Kinesins"""	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.4365A>G	1.37:g.200524571T>C			198791194	Q14CI8|Q4G0A5|Q5T1W3	Silent	SNP	ENST00000367350.4	37	CCDS30963.1																																																																																				0.259	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875	
OR2M5	127059	hgsc.bcm.edu	37	1	248308552	248308552	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:248308552T>C	ENST00000366476.1	+	1	103	c.103T>C	c.(103-105)Ttt>Ctt	p.F35L		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	35						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F35I(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)			CCTGGCCATCTTTTCAGTGGC	0.522																																																	1	Substitution - Missense(1)	ovary(1)	1											239.0	237.0	237.0					1																	248308552		2203	4296	6499	246375175	SO:0001583	missense	127059				CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"""GPCR / Class A : Olfactory receptors"""	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.103T>C	1.37:g.248308552T>C	ENSP00000355432:p.Phe35Leu		246375175		Missense_Mutation	SNP	ENST00000366476.1	37	CCDS31105.1	.	.	.	.	.	.	.	.	.	.	t	10.24	1.295534	0.23564	.	.	ENSG00000162727	ENST00000366476	T	0.00581	6.42	3.28	3.28	0.37604	.	0.250947	0.20653	U	0.088177	T	0.01092	0.0036	M	0.81497	2.545	0.09310	N	1	P	0.41546	0.754	B	0.39119	0.291	T	0.37731	-0.9693	10	0.72032	D	0.01	.	11.5465	0.50696	0.0:0.0:0.0:1.0	.	35	A3KFT3	OR2M5_HUMAN	L	35	ENSP00000355432:F35L	ENSP00000355432:F35L	F	+	1	0	OR2M5	246375175	0.022000	0.18835	0.140000	0.22221	0.115000	0.19883	2.033000	0.41136	1.250000	0.43966	0.403000	0.27427	TTT		0.522	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690	
BRSK2	9024	hgsc.bcm.edu	37	11	1466584	1466584	+	Silent	SNP	G	G	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr11:1466584G>A	ENST00000528841.1	+	10	1257	c.873G>A	c.(871-873)tcG>tcA	p.S291S	BRSK2_ENST00000308219.9_Silent_p.S291S|BRSK2_ENST00000531197.1_Silent_p.S291S|BRSK2_ENST00000528710.1_Silent_p.S231S|BRSK2_ENST00000308230.5_Silent_p.S291S|BRSK2_ENST00000526678.1_Silent_p.S291S|BRSK2_ENST00000544817.1_De_novo_Start_InFrame|BRSK2_ENST00000382179.1_Silent_p.S337S			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	291					actin cytoskeleton reorganization (GO:0031532)|axonogenesis (GO:0007409)|establishment of cell polarity (GO:0030010)|exocytosis (GO:0006887)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitotic nuclear division (GO:0007067)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(4)|large_intestine(1)|lung(5)	10		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		AGATCCGCTCGCTGCCCAGCC	0.652																																																	0			11											35.0	45.0	41.0					11																	1466584		2155	4255	6410	1423160	SO:0001819	synonymous_variant	9024			AF020089	CCDS41590.1, CCDS58106.1, CCDS58107.1, CCDS58108.1, CCDS60696.1	11p15.5	2008-02-05	2003-09-11	2005-01-27	ENSG00000174672	ENSG00000174672			11405	protein-coding gene	gene with protein product	"""serine/threonine kinase 29"""	609236	"""chromsosome 11 open reading frame 7"""	C11orf7, STK29		9852686, 9929968	Standard	NM_001256629		Approved	PEN11B	uc001ltm.4	Q8IWQ3	OTTHUMG00000167089	ENST00000528841.1:c.873G>A	11.37:g.1466584G>A			1423160	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	Silent	SNP	ENST00000528841.1	37	CCDS58107.1																																																																																				0.652	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393033.1	NM_003957	
STIM1	6786	hgsc.bcm.edu	37	11	4095835	4095835	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr11:4095835C>T	ENST00000300737.4	+	7	1464	c.895C>T	c.(895-897)Cgg>Tgg	p.R299W	STIM1_ENST00000533977.1_Missense_Mutation_p.R126W|STIM1_ENST00000527651.1_Missense_Mutation_p.R299W	NM_003156.3	NP_003147.2	Q13586	STIM1_HUMAN	stromal interaction molecule 1	299	Glu-rich.				activation of store-operated calcium channel activity (GO:0032237)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|regulation of calcium ion transport (GO:0051924)|regulation of store-operated calcium entry (GO:2001256)|store-operated calcium entry (GO:0002115)	cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of plasma membrane (GO:0005887)|microtubule (GO:0005874)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|microtubule plus-end binding (GO:0051010)|store-operated calcium channel activity (GO:0015279)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|liver(1)|lung(14)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)		GGAAGCCCAGCGGCTGAAGGA	0.572																																																	0			11											49.0	42.0	45.0					11																	4095835		2201	4298	6499	4052411	SO:0001583	missense	6786			BC021300, U52426	CCDS7749.1, CCDS60706.1, CCDS73247.1	11p15.5	2014-09-17			ENSG00000167323	ENSG00000167323		"""Sterile alpha motif (SAM) domain containing"""	11386	protein-coding gene	gene with protein product		605921				8921403, 11463338, 11983428	Standard	NM_003156		Approved	GOK, D11S4896E	uc021qco.1	Q13586	OTTHUMG00000133360	ENST00000300737.4:c.895C>T	11.37:g.4095835C>T	ENSP00000300737:p.Arg299Trp		4052411	E9PQJ4|Q8N382	Missense_Mutation	SNP	ENST00000300737.4	37	CCDS7749.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.089231	0.76756	.	.	ENSG00000167323	ENST00000300737;ENST00000527651;ENST00000533977	T;D;T	0.81659	-0.51;-1.52;-0.59	5.26	3.36	0.38483	.	0.057916	0.64402	D	0.000001	D	0.88738	0.6518	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.88996	0.3418	10	0.87932	D	0	-21.7865	13.1828	0.59663	0.2906:0.7094:0.0:0.0	.	299;299	E9PQJ4;Q13586	.;STIM1_HUMAN	W	299;299;126	ENSP00000300737:R299W;ENSP00000436208:R299W;ENSP00000434767:R126W	ENSP00000300737:R299W	R	+	1	2	STIM1	4052411	0.770000	0.28543	1.000000	0.80357	0.983000	0.72400	0.960000	0.29253	0.575000	0.29434	0.655000	0.94253	CGG		0.572	STIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257196.1	NM_003156	
OR2AG2	338755	hgsc.bcm.edu	37	11	6789691	6789691	+	Silent	SNP	G	G	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr11:6789691G>A	ENST00000338569.2	-	1	595	c.498C>T	c.(496-498)ctC>ctT	p.L166L		NM_001004490.1	NP_001004490.1	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG, member 2	166						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(13)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	28		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CACAGAAAGGGAGGTGCATAG	0.507																																																	0			11											118.0	96.0	103.0					11																	6789691		2201	4296	6497	6746267	SO:0001819	synonymous_variant	338755			AB065539	CCDS31413.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188124	ENSG00000188124		"""GPCR / Class A : Olfactory receptors"""	15143	protein-coding gene	gene with protein product				OR2AG2P			Standard	NM_001004490		Approved		uc001meq.1	A6NM03	OTTHUMG00000165868	ENST00000338569.2:c.498C>T	11.37:g.6789691G>A			6746267		Silent	SNP	ENST00000338569.2	37	CCDS31413.1																																																																																				0.507	OR2AG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386775.1	NM_001004490	
WT1	7490	hgsc.bcm.edu	37	11	32421544	32421544	+	Missense_Mutation	SNP	A	A	G	rs142059681	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr11:32421544A>G	ENST00000379079.2	-	6	685	c.412T>C	c.(412-414)Tgc>Cgc	p.C138R	WT1_ENST00000530998.1_Missense_Mutation_p.C121R|WT1_ENST00000332351.3_Missense_Mutation_p.C350R|WT1_ENST00000448076.3_Missense_Mutation_p.C350R	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1	282					adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.C282R(1)	EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			TGGGCTCCGCAGAGGATGGGC	0.577			"""D, Mis, N, F, S"""	EWSR1	"""Wilms, desmoplastic small round cell tumor"""	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome																														yes	Rec	yes	"""Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"""	11	11p13	7490	Wilms tumour 1 gene		O	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	11						A	ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS	1,4403	2.1+/-5.4	0,1,2201	299.0	249.0	266.0		997,412,361,1048,1048	6.0	1.0	11	dbSNP_134	266	7,8591	5.0+/-18.6	0,7,4292	yes	missense,missense,missense,missense,missense	WT1	NM_000378.4,NM_001198551.1,NM_001198552.1,NM_024424.3,NM_024426.4	180,180,180,180,180	0,8,6493	GG,GA,AA		0.0814,0.0227,0.0615	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	333/498,138/303,121/289,350/515,350/518	32421544	8,12994	2202	4299	6501	32378120	SO:0001583	missense	7490	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"""Zinc fingers, C2H2-type"""	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000379079.2:c.412T>C	11.37:g.32421544A>G	ENSP00000368370:p.Cys138Arg		32378120	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Missense_Mutation	SNP	ENST00000379079.2	37	CCDS55751.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.99|16.99	3.275255|3.275255	0.59649|0.59649	2.27E-4|2.27E-4	8.14E-4|8.14E-4	ENSG00000184937|ENSG00000184937	ENST00000379079;ENST00000332351;ENST00000530998;ENST00000452863;ENST00000448076;ENST00000527775|ENST00000527882	D;D;D;D;D;D|D	0.85955|0.87650	-2.05;-2.05;-2.05;-2.05;-2.05;-2.05|-2.28	5.98|5.98	5.98|5.98	0.97165|0.97165	Wilm&apos (1);s tumour protein, N-terminal (1);|.	0.000000|.	0.85682|.	U|.	0.000000|.	D|D	0.89801|0.89801	0.6820|0.6820	L|L	0.52905|0.52905	1.665|1.665	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.76494|.	0.999;0.998;0.999;0.993;0.984|.	D;D;D;D;D|.	0.74348|.	0.977;0.975;0.983;0.942;0.926|.	D|D	0.88980|0.88980	0.3407|0.3407	10|7	0.87932|0.41790	D|T	0|0.15	.|.	16.4781|16.4781	0.84144|0.84144	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	338;282;355;121;138|.	P19544-8;P19544;P19544-7;B3KSA5;P19544-6|.	.;WT1_HUMAN;.;.;.|.	R|P	138;350;121;333;350;101|40	ENSP00000368370:C138R;ENSP00000331327:C350R;ENSP00000435307:C121R;ENSP00000415516:C333R;ENSP00000413452:C350R;ENSP00000435351:C101R|ENSP00000435624:L40P	ENSP00000331327:C350R|ENSP00000435624:L40P	C|L	-|-	1|2	0|0	WT1|WT1	32378120|32378120	1.000000|1.000000	0.71417|0.71417	0.988000|0.988000	0.46212|0.46212	0.165000|0.165000	0.22458|0.22458	3.481000|3.481000	0.53179|0.53179	2.288000|2.288000	0.76882|0.76882	0.528000|0.528000	0.53228|0.53228	TGC|CTG		0.577	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000095434.1	NM_000378	
EIF3M	10480	hgsc.bcm.edu	37	11	32610203	32610203	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr11:32610203A>G	ENST00000531120.1	+	3	302	c.239A>G	c.(238-240)gAa>gGa	p.E80G	EIF3M_ENST00000524896.1_Intron|EIF3M_ENST00000532054.1_3'UTR	NM_006360.4	NP_006351.2			eukaryotic translation initiation factor 3, subunit M									p.E80G(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16	Breast(20;0.109)					GACAAGCAAGAAGCTTTGATT	0.418																																																	1	Substitution - Missense(1)	breast(1)	11											202.0	182.0	189.0					11																	32610203		2202	4299	6501	32566779	SO:0001583	missense	10480			AK131064	CCDS7880.1	11p13	2012-12-13	2007-07-27	2007-07-27	ENSG00000149100	ENSG00000149100			24460	protein-coding gene	gene with protein product	"""transport and golgi organization 7 homolog (Drosophila)"""	609641	"""PCI domain containing 1 (herpesvirus entry mediator)"""	PCID1		15919898, 15919899	Standard	NM_006360		Approved	hfl-B5, FLJ29030, GA17, eIF3m, TANGO7	uc001mtu.4	Q7L2H7	OTTHUMG00000166258	ENST00000531120.1:c.239A>G	11.37:g.32610203A>G	ENSP00000436049:p.Glu80Gly		32566779		Missense_Mutation	SNP	ENST00000531120.1	37	CCDS7880.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.935042	0.73442	.	.	ENSG00000149100	ENST00000531120;ENST00000323213;ENST00000533439	T;T	0.39592	1.07;1.07	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.44912	0.1316	M	0.71036	2.16	0.80722	D	1	B	0.14438	0.01	B	0.08055	0.003	T	0.31833	-0.9929	10	0.25751	T	0.34	-4.5193	16.5885	0.84745	1.0:0.0:0.0:0.0	.	80	Q7L2H7	EIF3M_HUMAN	G	80;17;17	ENSP00000436049:E80G;ENSP00000319910:E17G	ENSP00000319910:E17G	E	+	2	0	EIF3M	32566779	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.962000	0.93254	2.317000	0.78254	0.460000	0.39030	GAA		0.418	EIF3M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388762.2	NM_006360	
OR4S1	256148	hgsc.bcm.edu	37	11	48328541	48328541	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr11:48328541A>G	ENST00000319988.1	+	1	767	c.767A>G	c.(766-768)tAc>tGc	p.Y256C		NM_001004725.1	NP_001004725.1	Q8NGB4	OR4S1_HUMAN	olfactory receptor, family 4, subfamily S, member 1	256						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|skin(3)	21						ATGTTCATGTACATTCGTCCC	0.488																																																	0			11											241.0	218.0	226.0					11																	48328541		2201	4298	6499	48285117	SO:0001583	missense	256148			AB065908	CCDS31488.1	11p11.2	2012-08-09			ENSG00000176555	ENSG00000176555		"""GPCR / Class A : Olfactory receptors"""	14705	protein-coding gene	gene with protein product							Standard	NM_001004725		Approved		uc010rhu.2	Q8NGB4	OTTHUMG00000166578	ENST00000319988.1:c.767A>G	11.37:g.48328541A>G	ENSP00000321447:p.Tyr256Cys		48285117	Q6IFB4	Missense_Mutation	SNP	ENST00000319988.1	37	CCDS31488.1	.	.	.	.	.	.	.	.	.	.	A	16.90	3.249825	0.59212	.	.	ENSG00000176555	ENST00000319988	T	0.00295	8.25	5.02	5.02	0.67125	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01092	0.0036	H	0.95679	3.705	0.24266	N	0.995264	D	0.89917	1.0	D	0.97110	1.0	T	0.24154	-1.0168	9	0.87932	D	0	.	12.9764	0.58540	1.0:0.0:0.0:0.0	.	256	Q8NGB4	OR4S1_HUMAN	C	256	ENSP00000321447:Y256C	ENSP00000321447:Y256C	Y	+	2	0	OR4S1	48285117	1.000000	0.71417	0.543000	0.28128	0.888000	0.51559	6.013000	0.70776	2.020000	0.59435	0.533000	0.62120	TAC		0.488	OR4S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390556.1	NM_001004725	
OR5B2	390190	hgsc.bcm.edu	37	11	58189992	58189992	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr11:58189992A>G	ENST00000302581.2	-	1	794	c.743T>C	c.(742-744)gTc>gCc	p.V248A		NM_001005566.2	NP_001005566.1	Q96R09	OR5B2_HUMAN	olfactory receptor, family 5, subfamily B, member 2	248						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				CCCATAGAAGACGGAGACTGC	0.468																																																	0			11											126.0	115.0	119.0					11																	58189992		2201	4295	6496	57946568	SO:0001583	missense	390190			AB065852	CCDS31550.1	11q12.1	2012-08-09			ENSG00000172365	ENSG00000172365		"""GPCR / Class A : Olfactory receptors"""	8323	protein-coding gene	gene with protein product							Standard	NM_001005566		Approved	OST073	uc010rkg.2	Q96R09	OTTHUMG00000167517	ENST00000302581.2:c.743T>C	11.37:g.58189992A>G	ENSP00000303076:p.Val248Ala		57946568	B2RNJ6|B9EGY7|Q6IEV7|Q8NGF5	Missense_Mutation	SNP	ENST00000302581.2	37	CCDS31550.1	.	.	.	.	.	.	.	.	.	.	A	6.289	0.421467	0.11928	.	.	ENSG00000172365	ENST00000302581	T	0.00137	8.68	3.73	3.73	0.42828	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36167	U	0.002757	T	0.00144	0.0004	L	0.46157	1.445	0.09310	N	1	B	0.12013	0.005	B	0.22601	0.04	T	0.33624	-0.9861	10	0.87932	D	0	-5.8228	6.7921	0.23705	0.8895:0.0:0.1105:0.0	.	248	Q96R09	OR5B2_HUMAN	A	248	ENSP00000303076:V248A	ENSP00000303076:V248A	V	-	2	0	OR5B2	57946568	0.058000	0.20735	0.036000	0.18154	0.184000	0.23303	3.499000	0.53310	1.703000	0.51240	0.477000	0.44152	GTC		0.468	OR5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394887.2	NM_001005566	
MAML2	84441	hgsc.bcm.edu	37	11	95825623	95825623	+	Silent	SNP	C	C	A	rs373817562		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr11:95825623C>A	ENST00000524717.1	-	2	2856	c.1572G>T	c.(1570-1572)ggG>ggT	p.G524G		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	524					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				CATCTAGGTGCCCACCCTGGG	0.597			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid																																			Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	0			11											37.0	40.0	39.0					11																	95825623		1971	4144	6115	95465271	SO:0001819	synonymous_variant	84441			AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"""mastermind (Drosophila)-like 2"""			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1572G>T	11.37:g.95825623C>A			95465271	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																				0.597	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1		
SCGN	10590	hgsc.bcm.edu	37	6	25665247	25665247	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr6:25665247T>C	ENST00000377961.2	+	4	491	c.323T>C	c.(322-324)gTg>gCg	p.V108A	SCGN_ENST00000334979.6_3'UTR	NM_006998.3	NP_008929.2	O76038	SEGN_HUMAN	secretagogin, EF-hand calcium binding protein	108	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						GACAGCAGCGTGGAGTTTATG	0.493																																																	0			6											117.0	107.0	111.0					6																	25665247		2203	4300	6503	25773226	SO:0001583	missense	10590			BC000336	CCDS4561.1	6p22.3-p22.1	2013-01-10			ENSG00000079689	ENSG00000079689		"""EF-hand domain containing"""	16941	protein-coding gene	gene with protein product	"""calbindin-like"""	609202				10811645	Standard	NM_006998		Approved	SECRET, DJ501N12.8, SEGN, CALBL	uc003nfb.3	O76038	OTTHUMG00000014409	ENST00000377961.2:c.323T>C	6.37:g.25665247T>C	ENSP00000367197:p.Val108Ala		25773226	A8K0B2|Q5VV44|Q96QV7|Q9UJF6	Missense_Mutation	SNP	ENST00000377961.2	37	CCDS4561.1	.	.	.	.	.	.	.	.	.	.	T	12.91	2.080358	0.36662	.	.	ENSG00000079689	ENST00000377961	T	0.08720	3.06	5.09	5.09	0.68999	EF-hand-like domain (1);	0.056322	0.64402	D	0.000001	T	0.06188	0.0160	N	0.21583	0.68	0.80722	D	1	D	0.65815	0.995	P	0.56343	0.796	T	0.50285	-0.8846	10	0.25106	T	0.35	.	13.8698	0.63612	0.0:0.0:0.0:1.0	.	108	O76038	SEGN_HUMAN	A	108	ENSP00000367197:V108A	ENSP00000367197:V108A	V	+	2	0	SCGN	25773226	1.000000	0.71417	1.000000	0.80357	0.135000	0.20990	5.889000	0.69766	1.900000	0.55004	0.477000	0.44152	GTG		0.493	SCGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040067.1		
ZSCAN31	64288	hgsc.bcm.edu	37	6	28297345	28297345	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr6:28297345C>T	ENST00000414429.1	-	6	1019	c.116G>A	c.(115-117)cGa>cAa	p.R39Q	ZSCAN31_ENST00000481934.1_5'Flank|ZSCAN31_ENST00000396838.2_Missense_Mutation_p.R39Q|ZSCAN31_ENST00000446474.1_Intron|ZSCAN31_ENST00000439158.1_Missense_Mutation_p.R39Q|ZSCAN31_ENST00000344279.6_Missense_Mutation_p.R39Q			Q96LW9	ZSC31_HUMAN	zinc finger and SCAN domain containing 31	39	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										AAAAAGTTGTCGGGAGGCTTC	0.502																																																	0			6											96.0	103.0	101.0					6																	28297345		2203	4300	6503	28405324	SO:0001583	missense	64288				CCDS4649.1, CCDS59001.1	6p	2013-01-09	2013-01-08	2013-01-08	ENSG00000235109	ENSG00000235109		"""-"", ""Zinc fingers, C2H2-type"""	14097	protein-coding gene	gene with protein product		610794	"""zinc finger protein 310 pseudogene"", ""zinc finger protein 323"""	ZNF310P, ZNF323			Standard	NM_001135216		Approved		uc003nla.3	Q96LW9	OTTHUMG00000014518	ENST00000414429.1:c.116G>A	6.37:g.28297345C>T	ENSP00000390076:p.Arg39Gln		28405324	Q6P178|Q8WWS5	Missense_Mutation	SNP	ENST00000414429.1	37	CCDS4649.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.139596	0.77775	.	.	ENSG00000235109	ENST00000396838;ENST00000439158;ENST00000414429;ENST00000344279;ENST00000453745;ENST00000439636;ENST00000447021;ENST00000426756;ENST00000446222;ENST00000434036	T;T;T;T;T;T;T;T;T;T	0.07908	3.15;3.15;3.15;3.15;3.15;3.15;3.15;3.15;3.15;3.15	4.8	0.937	0.19494	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.05593	0.0147	M	0.90369	3.11	0.09310	N	1	P	0.42973	0.796	B	0.35813	0.211	T	0.15607	-1.0431	9	0.49607	T	0.09	.	9.2068	0.37293	0.0:0.6855:0.0:0.3145	.	39	Q96LW9	ZN323_HUMAN	Q	39	ENSP00000380050:R39Q;ENSP00000413705:R39Q;ENSP00000390076:R39Q;ENSP00000345339:R39Q;ENSP00000389479:R39Q;ENSP00000412519:R39Q;ENSP00000416108:R39Q;ENSP00000406376:R39Q;ENSP00000411033:R39Q;ENSP00000416225:R39Q	ENSP00000345339:R39Q	R	-	2	0	ZNF323	28405324	0.000000	0.05858	0.001000	0.08648	0.965000	0.64279	0.654000	0.24918	-0.053000	0.13289	0.563000	0.77884	CGA		0.502	ZSCAN31-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346804.1	NM_030899	
BAI3	577	hgsc.bcm.edu	37	6	69723982	69723982	+	Missense_Mutation	SNP	G	G	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr6:69723982G>T	ENST00000370598.1	+	12	2803	c.1982G>T	c.(1981-1983)tGg>tTg	p.W661L		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	661					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.W661L(1)		NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				AAGGAAAAATGGGAAGATGCA	0.289																																																	1	Substitution - Missense(1)	ovary(1)	6											64.0	67.0	66.0					6																	69723982		2203	4299	6502	69780703	SO:0001583	missense	577			AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"""-"", ""GPCR / Class B : Orphans"""	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.1982G>T	6.37:g.69723982G>T	ENSP00000359630:p.Trp661Leu		69780703	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.725729	0.89298	.	.	ENSG00000135298	ENST00000370598	T	0.81078	-1.45	5.76	5.76	0.90799	Domain of unknown function DUF3497 (1);	0.132166	0.53938	D	0.000042	D	0.88153	0.6360	M	0.69358	2.11	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88313	0.2957	10	0.87932	D	0	.	19.952	0.97200	0.0:0.0:1.0:0.0	.	661	O60242	BAI3_HUMAN	L	661	ENSP00000359630:W661L	ENSP00000359630:W661L	W	+	2	0	BAI3	69780703	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.781000	0.91805	2.728000	0.93425	0.655000	0.94253	TGG		0.289	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1		
NCOA7	135112	hgsc.bcm.edu	37	6	126236496	126236496	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr6:126236496C>T	ENST00000368357.3	+	12	2466	c.2114C>T	c.(2113-2115)aCa>aTa	p.T705I	NCOA7_ENST00000392477.2_Missense_Mutation_p.T705I|NCOA7_ENST00000229634.9_Missense_Mutation_p.T590I	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	705					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(2)	39				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		CATTTGTACACATTCTTTGTT	0.433																																																	0			6											219.0	184.0	196.0					6																	126236496		2203	4300	6503	126278189	SO:0001583	missense	135112			AJ420542	CCDS5132.1, CCDS56448.1	6q22.33	2013-03-14			ENSG00000111912	ENSG00000111912			21081	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 4"""	609752				11971969	Standard	NM_001199619		Approved	ERAP140, dJ187J11.3, TLDC4	uc003qai.3	Q8NI08	OTTHUMG00000015513	ENST00000368357.3:c.2114C>T	6.37:g.126236496C>T	ENSP00000357341:p.Thr705Ile		126278189	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	37	CCDS5132.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.402573	0.83230	.	.	ENSG00000111912	ENST00000368357;ENST00000392477;ENST00000229634;ENST00000433571;ENST00000368353	T;T;T;T	0.31510	2.68;2.68;2.69;1.49	5.67	5.67	0.87782	.	0.169666	0.53938	D	0.000058	T	0.25494	0.0620	L	0.43152	1.355	0.42549	D	0.993102	P;P;P	0.50617	0.895;0.937;0.895	B;P;B	0.49252	0.4;0.604;0.4	T	0.00728	-1.1591	10	0.45353	T	0.12	-5.4281	14.9088	0.70740	0.1432:0.8568:0.0:0.0	.	694;694;705	B3KXK4;Q8NI08-2;Q8NI08	.;.;NCOA7_HUMAN	I	705;705;590;15;15	ENSP00000357341:T705I;ENSP00000376269:T705I;ENSP00000229634:T590I;ENSP00000411002:T15I	ENSP00000229634:T590I	T	+	2	0	NCOA7	126278189	1.000000	0.71417	0.976000	0.42696	0.992000	0.81027	4.570000	0.60872	2.829000	0.97493	0.655000	0.94253	ACA		0.433	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748	
STXBP5	134957	hgsc.bcm.edu	37	6	147631344	147631344	+	Missense_Mutation	SNP	C	C	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr6:147631344C>G	ENST00000321680.6	+	10	1042	c.1042C>G	c.(1042-1044)Cta>Gta	p.L348V	STXBP5_ENST00000179882.6_Missense_Mutation_p.L19V|STXBP5_ENST00000367481.3_Missense_Mutation_p.L348V|STXBP5_ENST00000367480.3_Missense_Mutation_p.L348V	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)	348					exocytosis (GO:0006887)|negative regulation of exocytosis (GO:0045920)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|synapse (GO:0045202)	syntaxin-1 binding (GO:0017075)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	42		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		TGTTGATTTTCTAACGCTGTG	0.363																																																	0			6											108.0	109.0	109.0					6																	147631344		2203	4300	6503	147673037	SO:0001583	missense	134957			AK055484	CCDS5211.1, CCDS47499.1	6q24.3	2013-01-10			ENSG00000164506	ENSG00000164506		"""WD repeat domain containing"""	19665	protein-coding gene	gene with protein product		604586				9620695, 14767561	Standard	NM_139244		Approved	tomosyn, LLGL3	uc010khz.2	Q5T5C0	OTTHUMG00000015766	ENST00000321680.6:c.1042C>G	6.37:g.147631344C>G	ENSP00000321826:p.Leu348Val		147673037	Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Missense_Mutation	SNP	ENST00000321680.6	37	CCDS47499.1	.	.	.	.	.	.	.	.	.	.	C	11.25	1.584486	0.28268	.	.	ENSG00000164506	ENST00000367481;ENST00000321680;ENST00000367480;ENST00000179882	T;T;T;T	0.13196	2.62;2.61;2.73;3.31	5.64	4.77	0.60923	WD40 repeat-like-containing domain (1);Lethal giant larvae homologue 2 (1);	0.000000	0.85682	D	0.000000	T	0.10637	0.0260	N	0.11789	0.175	0.80722	D	1	D;D;D	0.76494	0.998;0.997;0.999	D;D;D	0.80764	0.99;0.962;0.994	T	0.35624	-0.9781	10	0.26408	T	0.33	.	14.4505	0.67382	0.0:0.9298:0.0:0.0702	.	348;348;19	Q5T5C0-2;Q5T5C0;B3KXX0	.;STXB5_HUMAN;.	V	348;348;348;19	ENSP00000356451:L348V;ENSP00000321826:L348V;ENSP00000356450:L348V;ENSP00000179882:L19V	ENSP00000179882:L19V	L	+	1	2	STXBP5	147673037	1.000000	0.71417	0.789000	0.31954	0.784000	0.44337	1.597000	0.36729	1.523000	0.49018	0.650000	0.86243	CTA		0.363	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1		
SYNE1	23345	hgsc.bcm.edu	37	6	152737559	152737559	+	Nonsense_Mutation	SNP	G	G	A	rs200119679		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr6:152737559G>A	ENST00000367255.5	-	41	6614	c.6013C>T	c.(6013-6015)Cga>Tga	p.R2005*	SYNE1_ENST00000341594.5_Nonsense_Mutation_p.R2042*|SYNE1_ENST00000448038.1_Nonsense_Mutation_p.R2012*|SYNE1_ENST00000423061.1_Nonsense_Mutation_p.R2012*|SYNE1_ENST00000265368.4_Nonsense_Mutation_p.R2005*	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2005					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCTTTCAATCGCTCTTTGTCA	0.428										HNSCC(10;0.0054)			G|||	1	0.000199681	0.0	0.0	5008	,	,		17029	0.0		0.001	False		,,,				2504	0.0																0			6											216.0	228.0	224.0					6																	152737559		2203	4300	6503	152779252	SO:0001587	stop_gained	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.6013C>T	6.37:g.152737559G>A	ENSP00000356224:p.Arg2005*		152779252	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Nonsense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	47	13.363140	0.99737	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	.	.	.	5.97	-2.23	0.06930	.	0.555045	0.16100	N	0.229637	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	.	5.3578	0.16071	0.0642:0.3916:0.1864:0.3578	.	.	.	.	X	2005;2012;2005;2012;2042	.	ENSP00000265368:R2005X	R	-	1	2	SYNE1	152779252	0.079000	0.21365	0.006000	0.13384	0.030000	0.12068	0.595000	0.24029	-0.130000	0.11599	-0.182000	0.12963	CGA		0.428	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
INPP5K	51763	hgsc.bcm.edu	37	17	1417206	1417206	+	Missense_Mutation	SNP	G	G	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr17:1417206G>T	ENST00000421807.2	-	2	500	c.112C>A	c.(112-114)Ctg>Atg	p.L38M	INPP5K_ENST00000406424.4_De_novo_Start_InFrame|INPP5K_ENST00000542125.1_Missense_Mutation_p.L38M|INPP5K_ENST00000320345.6_De_novo_Start_InFrame|INPP5K_ENST00000397335.3_Intron	NM_016532.3	NP_057616.2	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K	38	Catalytic. {ECO:0000255}.				actin cytoskeleton organization (GO:0030036)|cellular response to cAMP (GO:0071320)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hormone stimulus (GO:0032870)|cellular response to insulin stimulus (GO:0032869)|cellular response to tumor necrosis factor (GO:0071356)|dephosphorylation (GO:0016311)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inositol phosphate dephosphorylation (GO:0046855)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of dephosphorylation (GO:0035305)|negative regulation of glucose transport (GO:0010829)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of renal water transport (GO:2001153)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|protein targeting to plasma membrane (GO:0072661)|regulation of glycogen biosynthetic process (GO:0005979)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	inositol bisphosphate phosphatase activity (GO:0016312)|inositol trisphosphate phosphatase activity (GO:0046030)|inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|lipid phosphatase activity (GO:0042577)|phosphatidylinositol phosphate 5-phosphatase activity (GO:0034595)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)|vasopressin receptor activity (GO:0005000)			endometrium(1)|large_intestine(7)|lung(3)|skin(1)	12						CGGTTGTTCAGCTGAAGCAGG	0.552																																																	0			17											140.0	105.0	117.0					17																	1417206		2203	4300	6503	1363956	SO:0001583	missense	51763				CCDS11004.1, CCDS11005.1	17p13.3	2008-09-09			ENSG00000132376	ENSG00000132376			33882	protein-coding gene	gene with protein product	"""skeletal muscle and kidney enriched inositol phosphatase"""	607875				10753883, 12536145	Standard	NM_016532		Approved	SKIP	uc002fsr.3	Q9BT40	OTTHUMG00000150648	ENST00000421807.2:c.112C>A	17.37:g.1417206G>T	ENSP00000413937:p.Leu38Met		1363956	B2R6I2|B2R750|D3DTH8|Q15733|Q9NPJ5|Q9P2R5	Missense_Mutation	SNP	ENST00000421807.2	37	CCDS11004.1	.	.	.	.	.	.	.	.	.	.	G	19.39	3.818146	0.71028	.	.	ENSG00000132376	ENST00000350761;ENST00000542125	T	0.48836	0.8	5.4	4.43	0.53597	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.071765	0.56097	D	0.000022	T	0.67951	0.2948	M	0.83312	2.635	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.83275	0.996;0.988;0.984	T	0.71337	-0.4623	10	0.66056	D	0.02	-12.1724	9.6004	0.39601	0.159:0.0:0.841:0.0	.	38;38;38	F5GXZ0;B7Z8U3;Q9BT40	.;.;INP5K_HUMAN	M	38	ENSP00000440147:L38M	ENSP00000254712:L38M	L	-	1	2	INPP5K	1363956	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	4.976000	0.63785	1.413000	0.46997	0.462000	0.41574	CTG		0.552	INPP5K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319381.4		
TP53	7157	hgsc.bcm.edu	37	17	7577547	7577547	+	Missense_Mutation	SNP	C	C	T	rs121912656|rs397516437		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr17:7577547C>T	ENST00000269305.4	-	7	923	c.734G>A	c.(733-735)gGc>gAc	p.G245D	TP53_ENST00000445888.2_Missense_Mutation_p.G245D|TP53_ENST00000455263.2_Missense_Mutation_p.G245D|TP53_ENST00000413465.2_Missense_Mutation_p.G245D|TP53_ENST00000420246.2_Missense_Mutation_p.G245D|TP53_ENST00000359597.4_Missense_Mutation_p.G245D|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	245	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		G -> A (in sporadic cancers; somatic mutation).|G -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1978757}.|G -> D (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:2259385}.|G -> E (in a sporadic cancer; somatic mutation).|G -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|G -> L (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> N (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> R (in sporadic cancers; somatic mutation).|G -> S (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934575). {ECO:0000269|PubMed:8829627}.|G -> V (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:2263646}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.G245D(104)|p.G245V(66)|p.G245A(8)|p.0?(8)|p.?(5)|p.G152V(4)|p.G244_M246>V(3)|p.G152D(3)|p.G245N(2)|p.G245H(1)|p.G245L(1)|p.G244fs*17(1)|p.G245F(1)|p.G245E(1)|p.C242_M246>L(1)|p.G245fs*2(1)|p.S241_G245delSCMGG(1)|p.C242fs*98(1)|p.M243fs*18(1)|p.C238_M246delCNSSCMGGM(1)|p.G151_M153>V(1)|p.G245del(1)|p.G245fs*14(1)|p.G245fs*17(1)|p.G245fs*16(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CCGGTTCATGCCGCCCATGCA	0.582		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)		yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	219	Substitution - Missense(191)|Whole gene deletion(8)|Deletion - Frameshift(7)|Complex - deletion inframe(5)|Unknown(5)|Deletion - In frame(3)	large_intestine(37)|lung(32)|oesophagus(23)|breast(22)|ovary(18)|upper_aerodigestive_tract(16)|haematopoietic_and_lymphoid_tissue(15)|liver(9)|prostate(7)|stomach(6)|central_nervous_system(6)|skin(6)|biliary_tract(5)|urinary_tract(5)|bone(5)|pancreas(4)|cervix(1)|vulva(1)|endometrium(1)	17	GRCh37	CM010464|CM900209	TP53	M	rs121912656						151.0	113.0	126.0					17																	7577547		2203	4300	6503	7518272	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.734G>A	17.37:g.7577547C>T	ENSP00000269305:p.Gly245Asp		7518272	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.838149	0.91117	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99900	-7.62;-7.62;-7.62;-7.62;-7.62;-7.62;-7.62;-7.62	4.62	4.62	0.57501	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99898	0.9951	M	0.91920	3.255	0.80722	A	1	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	0.97110	0.999;0.999;1.0;0.999;1.0;1.0	D	0.96045	0.9027	9	0.87932	D	0	-19.4293	15.3618	0.74483	0.0:1.0:0.0:0.0	.	245;245;152;245;245;245	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	D	245;245;245;245;245;245;234;152;113;152	ENSP00000410739:G245D;ENSP00000352610:G245D;ENSP00000269305:G245D;ENSP00000398846:G245D;ENSP00000391127:G245D;ENSP00000391478:G245D;ENSP00000425104:G113D;ENSP00000423862:G152D	ENSP00000269305:G245D	G	-	2	0	TP53	7518272	1.000000	0.71417	0.997000	0.53966	0.973000	0.67179	7.609000	0.82925	2.564000	0.86499	0.462000	0.41574	GGC		0.582	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
TP53	7157	hgsc.bcm.edu	37	17	7578266	7578266	+	Missense_Mutation	SNP	T	T	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr17:7578266T>A	ENST00000269305.4	-	6	772	c.583A>T	c.(583-585)Atc>Ttc	p.I195F	TP53_ENST00000445888.2_Missense_Mutation_p.I195F|TP53_ENST00000455263.2_Missense_Mutation_p.I195F|TP53_ENST00000413465.2_Missense_Mutation_p.I195F|TP53_ENST00000420246.2_Missense_Mutation_p.I195F|TP53_ENST00000359597.4_Missense_Mutation_p.I195F|TP53_ENST00000574684.1_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	195	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		I -> F (in sporadic cancers; somatic mutation).|I -> L (in a sporadic cancer; somatic mutation).|I -> N (in sporadic cancers; somatic mutation).|I -> S (in sporadic cancers; somatic mutation).|I -> T (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:9450901}.|I -> V (in a sporadic cancer; somatic mutation).|I -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.I195F(20)|p.0?(8)|p.?(6)|p.I195fs*14(4)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.I102F(1)|p.I195fs*52(1)|p.L194fs*52(1)|p.I63fs*14(1)|p.I195fs*50(1)|p.I102fs*14(1)|p.P191fs*6(1)|p.I195_G199delIRVEG(1)|p.I195L(1)|p.P98_E105>Q(1)|p.I63F(1)|p.H193_I195delHLI(1)|p.P59_E66>Q(1)|p.H193_I195>AP(1)|p.I195fs*12(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCCACTCGGATAAGATGCTGA	0.557		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)		yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	60	Substitution - Missense(23)|Whole gene deletion(8)|Deletion - In frame(6)|Insertion - Frameshift(6)|Complex - deletion inframe(6)|Unknown(6)|Deletion - Frameshift(4)|Complex - frameshift(1)	upper_aerodigestive_tract(8)|breast(8)|large_intestine(6)|biliary_tract(5)|skin(5)|lung(5)|oesophagus(4)|bone(4)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(3)|ovary(3)|urinary_tract(2)|liver(2)|stomach(1)|soft_tissue(1)	17											99.0	89.0	92.0					17																	7578266		2203	4300	6503	7518991	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.583A>T	17.37:g.7578266T>A	ENSP00000269305:p.Ile195Phe		7518991	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	17.86	3.493726	0.64186	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99824	-6.96;-6.96;-6.96;-6.96;-6.96;-6.96;-6.96;-6.96	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.103171	0.64402	D	0.000004	D	0.99802	0.9915	M	0.85099	2.735	0.58432	D	0.999999	D;D;D;D;D;D;D	0.89917	1.0;0.999;0.998;0.998;0.997;0.998;1.0	D;D;D;D;D;D;D	0.91635	0.999;0.989;0.955;0.972;0.988;0.99;0.992	D	0.96806	0.9593	10	0.87932	D	0	-18.4587	13.709	0.62656	0.0:0.0:0.0:1.0	.	156;195;195;102;195;195;195	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	F	195;195;195;195;195;195;184;102;63;102;63	ENSP00000410739:I195F;ENSP00000352610:I195F;ENSP00000269305:I195F;ENSP00000398846:I195F;ENSP00000391127:I195F;ENSP00000391478:I195F;ENSP00000425104:I63F;ENSP00000423862:I102F	ENSP00000269305:I195F	I	-	1	0	TP53	7518991	1.000000	0.71417	0.895000	0.35142	0.030000	0.12068	6.159000	0.71856	2.183000	0.69458	0.533000	0.62120	ATC		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
SLFN13	146857	hgsc.bcm.edu	37	17	33772552	33772552	+	Missense_Mutation	SNP	C	C	T	rs7216628	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr17:33772552C>T	ENST00000285013.6	-	3	423	c.148G>A	c.(148-150)Gcg>Acg	p.A50T	SLFN13_ENST00000534689.1_Intron|SLFN13_ENST00000542635.1_Missense_Mutation_p.A50T|SLFN13_ENST00000533791.1_Missense_Mutation_p.A50T|SLFN13_ENST00000526861.1_Missense_Mutation_p.A50T|SLFN13_ENST00000360502.2_Intron	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	50			A -> T (in dbSNP:rs7216628).			intracellular (GO:0005622)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	31				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		AAAGCACACGCGGCCCGTATA	0.483													C|||	72	0.014377	0.0545	0.0	5008	,	,		16763	0.0		0.0	False		,,,				2504	0.0																0			17						C	THR/ALA	208,4198	128.6+/-165.4	8,192,2003	114.0	118.0	117.0		148	1.2	0.1	17	dbSNP_116	117	1,8599	2.2+/-6.3	0,1,4299	yes	missense	SLFN13	NM_144682.5	58	8,193,6302	TT,TC,CC		0.0116,4.7208,1.607	benign	50/898	33772552	209,12797	2203	4300	6503	30796665	SO:0001583	missense	146857			AL832726	CCDS32620.1	17q12	2006-04-05				ENSG00000154760			26481	protein-coding gene	gene with protein product		614957				9846487	Standard	NM_144682		Approved	FLJ31952	uc002hjl.2	Q68D06		ENST00000285013.6:c.148G>A	17.37:g.33772552C>T	ENSP00000285013:p.Ala50Thr		30796665	E1P645|Q658M1|Q6ZS51|Q96A81	Missense_Mutation	SNP	ENST00000285013.6	37	CCDS32620.1	31	0.014194139194139194	31	0.06300813008130081	0	0.0	0	0.0	0	0.0	C	3.929	-0.016561	0.07681	0.047208	1.16E-4	ENSG00000154760	ENST00000285013;ENST00000526861;ENST00000542635;ENST00000524511	T;T;T;T	0.23552	4.52;4.52;4.52;1.9	3.28	1.22	0.21188	.	0.225948	0.22432	U	0.060132	T	0.01387	0.0045	L	0.45352	1.415	0.09310	N	1	P	0.50943	0.94	B	0.35182	0.197	T	0.17776	-1.0358	10	0.30078	T	0.28	.	5.3892	0.16234	0.0:0.721:0.0:0.279	rs7216628;rs7216628	50	Q68D06	SLN13_HUMAN	T	50	ENSP00000285013:A50T;ENSP00000434439:A50T;ENSP00000444016:A50T;ENSP00000433181:A50T	ENSP00000285013:A50T	A	-	1	0	SLFN13	30796665	0.000000	0.05858	0.146000	0.22360	0.038000	0.13279	-0.209000	0.09358	0.213000	0.20722	0.205000	0.17691	GCG		0.483	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682	
CREBBP	1387	hgsc.bcm.edu	37	16	3779387	3779387	+	Silent	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr16:3779387T>C	ENST00000262367.5	-	31	6470	c.5661A>G	c.(5659-5661)tcA>tcG	p.S1887S	CREBBP_ENST00000382070.3_Silent_p.S1849S	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1887	Interaction with TRERF1.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CGGGCGGTGCTGAGGTAGGAG	0.687			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																																	Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	0			16											39.0	38.0	38.0					16																	3779387		2196	4299	6495	3719388	SO:0001819	synonymous_variant	1387			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.5661A>G	16.37:g.3779387T>C			3719388	D3DUC9|O00147|Q16376|Q4LE28	Silent	SNP	ENST00000262367.5	37	CCDS10509.1																																																																																				0.687	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
MYOM1	8736	hgsc.bcm.edu	37	18	3135700	3135700	+	Missense_Mutation	SNP	C	C	T	rs371246473		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr18:3135700C>T	ENST00000356443.4	-	15	2387	c.2054G>A	c.(2053-2055)cGa>cAa	p.R685Q	MYOM1_ENST00000400569.3_Missense_Mutation_p.R685Q|MYOM1_ENST00000261606.7_Missense_Mutation_p.R685Q	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	685	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CGTGTTCACTCGCTGCCAGTT	0.527																																																	0			18						C	GLN/ARG,GLN/ARG	0,3940		0,0,1970	42.0	47.0	45.0		2054,2054	4.9	1.0	18		45	1,8317		0,1,4158	no	missense,missense	MYOM1	NM_003803.3,NM_019856.1	43,43	0,1,6128	TT,TC,CC		0.012,0.0,0.0082	probably-damaging,probably-damaging	685/1686,685/1590	3135700	1,12257	1970	4159	6129	3125700	SO:0001583	missense	8736			AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.2054G>A	18.37:g.3135700C>T	ENSP00000348821:p.Arg685Gln		3125700	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.177441	0.78564	0.0	1.2E-4	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.56776	0.44;0.44;0.44	5.76	4.9	0.64082	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.66228	0.2768	L	0.52823	1.66	0.47094	D	0.999314	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.62383	-0.6866	10	0.20519	T	0.43	.	15.4097	0.74908	0.0:0.933:0.0:0.067	.	685;685	P52179-2;P52179	.;MYOM1_HUMAN	Q	685	ENSP00000348821:R685Q;ENSP00000383413:R685Q;ENSP00000261606:R685Q	ENSP00000261606:R685Q	R	-	2	0	MYOM1	3125700	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	4.934000	0.63491	1.578000	0.49821	0.650000	0.86243	CGA		0.527	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
MYOM1	8736	hgsc.bcm.edu	37	18	3188882	3188882	+	Missense_Mutation	SNP	C	C	T	rs200770047		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr18:3188882C>T	ENST00000356443.4	-	4	968	c.635G>A	c.(634-636)aGg>aAg	p.R212K	MYOM1_ENST00000400569.3_Missense_Mutation_p.R212K|MYOM1_ENST00000261606.7_Missense_Mutation_p.R212K|RP13-270P17.2_ENST00000580139.1_RNA	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	212	6 X 6 AA tandem repeats.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.R212K(1)		NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CGTGGACTGCCTGGATGCCGT	0.517																																																	1	Substitution - Missense(1)	endometrium(1)	18											260.0	242.0	248.0					18																	3188882		2044	4187	6231	3178882	SO:0001583	missense	8736			AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.635G>A	18.37:g.3188882C>T	ENSP00000348821:p.Arg212Lys		3178882	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	2.966	-0.213546	0.06140	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.45668	1.03;1.04;0.89	3.23	0.752	0.18398	.	0.084010	0.41097	N	0.000942	T	0.14830	0.0358	N	0.08118	0	0.09310	N	0.999995	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28808	-1.0032	10	0.05351	T	0.99	.	4.9448	0.13984	0.0:0.2653:0.0:0.7347	.	212;212	P52179-2;P52179	.;MYOM1_HUMAN	K	212	ENSP00000348821:R212K;ENSP00000383413:R212K;ENSP00000261606:R212K	ENSP00000261606:R212K	R	-	2	0	MYOM1	3178882	0.789000	0.28775	0.018000	0.16275	0.000000	0.00434	1.455000	0.35190	0.165000	0.19558	-1.097000	0.02148	AGG		0.517	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
SMAD4	4089	hgsc.bcm.edu	37	18	48593473	48593473	+	Missense_Mutation	SNP	T	T	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr18:48593473T>A	ENST00000342988.3	+	10	1762	c.1224T>A	c.(1222-1224)ttT>ttA	p.F408L	SMAD4_ENST00000588745.1_Missense_Mutation_p.F312L|SMAD4_ENST00000398417.2_Missense_Mutation_p.F408L	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	408	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		ACGCGGTCTTTGTACAGAGTT	0.433																																																	38	Whole gene deletion(36)|Unknown(2)	pancreas(26)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18											175.0	144.0	154.0					18																	48593473		2203	4300	6503	46847471	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"""SMADs"""	6770	protein-coding gene	gene with protein product		600993	"""MAD, mothers against decapentaplegic homolog 4 (Drosophila)"", ""SMAD, mothers against DPP homolog 4 (Drosophila)"""	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1224T>A	18.37:g.48593473T>A	ENSP00000341551:p.Phe408Leu		46847471	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.536060	0.85812	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.99194	-5.54;-5.54	5.49	4.3	0.51218	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.99266	0.9744	M	0.91300	3.195	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99529	1.0960	10	0.87932	D	0	.	8.2009	0.31424	0.0:0.1601:0.0:0.8399	.	408	Q13485	SMAD4_HUMAN	L	408	ENSP00000341551:F408L;ENSP00000381452:F408L	ENSP00000341551:F408L	F	+	3	2	SMAD4	46847471	0.996000	0.38824	1.000000	0.80357	0.989000	0.77384	0.379000	0.20585	0.870000	0.35726	0.455000	0.32223	TTT		0.433	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359	
DCC	1630	hgsc.bcm.edu	37	18	50683828	50683828	+	Missense_Mutation	SNP	C	C	T	rs145985306	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr18:50683828C>T	ENST00000442544.2	+	8	1980	c.1364C>T	c.(1363-1365)gCg>gTg	p.A455V	DCC_ENST00000412726.1_Missense_Mutation_p.A303V|DCC_ENST00000581580.1_Missense_Mutation_p.A110V	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	455	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		CCTGCAGAAGCGAAAGGGAAC	0.502																																																	0			18						C	VAL/ALA	8,4398	12.9+/-30.5	0,8,2195	119.0	107.0	111.0		1364	3.7	1.0	18	dbSNP_134	111	1,8599	1.2+/-3.3	0,1,4299	yes	missense	DCC	NM_005215.3	64	0,9,6494	TT,TC,CC		0.0116,0.1816,0.0692	benign	455/1448	50683828	9,12997	2203	4300	6503	48937826	SO:0001583	missense	1630			X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2701	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 1"""	120470	"""deleted in colorectal carcinoma"""			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.1364C>T	18.37:g.50683828C>T	ENSP00000389140:p.Ala455Val		48937826		Missense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.487223	0.44249	0.001816	1.16E-4	ENSG00000187323	ENST00000442544;ENST00000304775;ENST00000412726	T;T	0.56941	0.43;0.43	5.44	3.66	0.41972	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.248804	0.33438	N	0.004917	T	0.37210	0.0995	N	0.21324	0.655	0.30963	N	0.723433	B;B;B	0.17852	0.007;0.007;0.024	B;B;B	0.15052	0.004;0.004;0.012	T	0.41716	-0.9493	10	0.51188	T	0.08	.	10.701	0.45926	0.0:0.8431:0.0:0.1569	.	303;303;455	E7EQM8;B4DYX2;P43146	.;.;DCC_HUMAN	V	455;388;303	ENSP00000389140:A455V;ENSP00000397322:A303V	ENSP00000304146:A388V	A	+	2	0	DCC	48937826	0.996000	0.38824	1.000000	0.80357	0.930000	0.56654	3.414000	0.52693	1.326000	0.45319	-0.215000	0.12644	GCG		0.502	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
CNTN6	27255	hgsc.bcm.edu	37	3	1415428	1415428	+	Missense_Mutation	SNP	T	T	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:1415428T>A	ENST00000446702.2	+	15	2554	c.1927T>A	c.(1927-1929)Tgg>Agg	p.W643R	CNTN6_ENST00000539053.1_Missense_Mutation_p.W571R|CNTN6_ENST00000350110.2_Missense_Mutation_p.W643R			Q9UQ52	CNTN6_HUMAN	contactin 6	643	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		TTCTGTGGGTTGGCAGGCTGT	0.348																																																	0			3											66.0	68.0	67.0					3																	1415428		2203	4300	6503	1390428	SO:0001583	missense	27255			AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.1927T>A	3.37:g.1415428T>A	ENSP00000407822:p.Trp643Arg		1390428	Q2KHM2	Missense_Mutation	SNP	ENST00000446702.2	37	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.955981	0.73902	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	T;T;T	0.56275	0.47;0.47;0.47	4.77	4.77	0.60923	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.49916	D	0.000133	T	0.81814	0.4902	H	0.97758	4.07	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88499	0.3081	10	0.87932	D	0	.	14.5834	0.68308	0.0:0.0:0.0:1.0	.	643	Q9UQ52	CNTN6_HUMAN	R	643;571;643	ENSP00000407822:W643R;ENSP00000442791:W571R;ENSP00000341882:W643R	ENSP00000341882:W643R	W	+	1	0	CNTN6	1390428	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	5.850000	0.69473	1.896000	0.54893	0.482000	0.46254	TGG		0.348	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	
VHL	7428	hgsc.bcm.edu	37	3	10188291	10188291	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:10188291A>G	ENST00000256474.2	+	2	1274	c.434A>G	c.(433-435)cAg>cGg	p.Q145R	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	145	Involved in binding to CCT complex.		Q -> H (in VHLD).		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.Q145fs*12(1)|p.S139fs*12(1)|p.G144fs*19(1)|p.Q145fs*14(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GTTGACGGACAGCCTATTTTT	0.413		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	4	Deletion - Frameshift(4)	kidney(4)	3											216.0	199.0	205.0					3																	10188291		2203	4300	6503	10163291	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.434A>G	3.37:g.10188291A>G	ENSP00000256474:p.Gln145Arg		10163291	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	A	15.15	2.746540	0.49257	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99800	-6.8	5.07	5.07	0.68467	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.262110	0.33591	N	0.004751	D	0.99566	0.9844	L	0.59436	1.845	0.80722	D	1	P	0.50617	0.937	D	0.66847	0.947	D	0.97837	1.0266	10	0.45353	T	0.12	-29.4808	13.0886	0.59154	1.0:0.0:0.0:0.0	.	145	P40337	VHL_HUMAN	R	145;63	ENSP00000256474:Q145R	ENSP00000256474:Q145R	Q	+	2	0	VHL	10163291	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	3.644000	0.54381	2.047000	0.60756	0.460000	0.39030	CAG		0.413	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551	
HDAC11	79885	hgsc.bcm.edu	37	3	13542268	13542268	+	Silent	SNP	G	G	A	rs140627816		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:13542268G>A	ENST00000295757.3	+	6	651	c.468G>A	c.(466-468)gcG>gcA	p.A156A	HDAC11_ENST00000446613.2_Intron|HDAC11_ENST00000433119.1_Missense_Mutation_p.R114Q|HDAC11_ENST00000404548.1_Intron|HDAC11_ENST00000495099.2_Intron|HDAC11_ENST00000405025.1_Intron|HDAC11_ENST00000522202.1_Silent_p.A105A|HDAC11_ENST00000402259.1_Intron|HDAC11_ENST00000437379.2_Silent_p.A128A|HDAC11_ENST00000402271.1_Intron|HDAC11_ENST00000404040.1_Intron	NM_024827.3	NP_079103.2	Q96DB2	HDA11_HUMAN	histone deacetylase 11	156	Histone deacetylase.				chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|oligodendrocyte development (GO:0014003)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|transcription factor binding (GO:0008134)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(4)|prostate(3)	13						GTGCCTATGCGGACATCACGC	0.617											OREG0015412	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0.0	0.0	5008	,	,		16865	0.0		0.001	False		,,,				2504	0.0																0			3											32.0	27.0	29.0					3																	13542268		2202	4299	6501	13517268	SO:0001819	synonymous_variant	79885			AK025426	CCDS2615.1, CCDS46760.1	3p25.1	2008-07-18			ENSG00000163517	ENSG00000163517	3.5.1.98		19086	protein-coding gene	gene with protein product		607226				11948178	Standard	NM_001136041		Approved		uc003bxy.3	Q96DB2	OTTHUMG00000129800	ENST00000295757.3:c.468G>A	3.37:g.13542268G>A		688	13517268	B4DDK1|Q9H6I7|Q9H6X3|Q9NTC9	Silent	SNP	ENST00000295757.3	37	CCDS2615.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	11.58	1.679722	0.29783	.	.	ENSG00000163517	ENST00000433119;ENST00000434848	.	.	.	4.52	-7.93	0.01156	.	.	.	.	.	T	0.34600	0.0903	.	.	.	0.80722	D	1	B	0.17465	0.022	B	0.08055	0.003	T	0.13764	-1.0497	7	0.87932	D	0	-15.1823	0.9765	0.01426	0.4251:0.1941:0.1188:0.2621	.	114	Q658J9	.	Q	114;122	.	ENSP00000412514:R114Q	R	+	2	0	HDAC11	13517268	0.178000	0.23122	0.819000	0.32651	0.592000	0.36648	-0.720000	0.04969	-1.460000	0.01911	-0.345000	0.07892	CGG		0.617	HDAC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252028.5	NM_024827	
CLASP2	23122	hgsc.bcm.edu	37	3	33725898	33725898	+	Silent	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:33725898T>C	ENST00000468888.2	-	6	643	c.597A>G	c.(595-597)ggA>ggG	p.G199G	CLASP2_ENST00000399362.4_Silent_p.G199G|CLASP2_ENST00000359576.5_Silent_p.G199G|CLASP2_ENST00000307312.7_5'UTR			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1252					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						TCACTTTTTCTCCCACATGTC	0.318																																																	0			3											138.0	139.0	139.0					3																	33725898		1815	4079	5894	33700902	SO:0001819	synonymous_variant	23122			AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.597A>G	3.37:g.33725898T>C			33700902	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Silent	SNP	ENST00000468888.2	37																																																																																					0.318	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044	
SCAP	22937	hgsc.bcm.edu	37	3	47484371	47484371	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:47484371A>G	ENST00000265565.5	-	2	525	c.113T>C	c.(112-114)tTa>tCa	p.L38S	SCAP_ENST00000545718.1_5'UTR|SCAP_ENST00000441517.2_5'UTR	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	38					aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		CCAGCAGGCTAAGATGCAGAA	0.517																																					Pancreas(149;978 1908 29304 37806 46700)												0			3											139.0	120.0	126.0					3																	47484371		2203	4300	6503	47459375	SO:0001583	missense	22937			BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"""WD repeat domain containing"""	30634	protein-coding gene	gene with protein product	"""SREBP cleavage activating protein"""	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.113T>C	3.37:g.47484371A>G	ENSP00000265565:p.Leu38Ser		47459375	Q8N2E0|Q8WUA1	Missense_Mutation	SNP	ENST00000265565.5	37	CCDS2755.2	.	.	.	.	.	.	.	.	.	.	A	23.0	4.363554	0.82353	.	.	ENSG00000114650	ENST00000339815;ENST00000265565;ENST00000416847;ENST00000495603;ENST00000448217	D	0.87256	-2.23	4.75	4.75	0.60458	.	0.097415	0.39909	N	0.001240	D	0.90933	0.7150	M	0.74881	2.28	0.80722	D	1	P	0.40398	0.716	P	0.51866	0.682	D	0.92014	0.5620	10	0.72032	D	0.01	0.1046	14.0891	0.64977	1.0:0.0:0.0:0.0	.	38	Q12770	SCAP_HUMAN	S	38	ENSP00000265565:L38S	ENSP00000265565:L38S	L	-	2	0	SCAP	47459375	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.909000	0.92647	1.997000	0.58415	0.454000	0.30748	TTA		0.517	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235	
ADAMTS9	56999	hgsc.bcm.edu	37	3	64547349	64547349	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:64547349T>C	ENST00000498707.1	-	30	4945	c.4603A>G	c.(4603-4605)Acc>Gcc	p.T1535A	ADAMTS9-AS1_ENST00000493124.1_RNA|ADAMTS9-AS1_ENST00000492209.1_RNA|ADAMTS9-AS1_ENST00000480831.1_RNA|ADAMTS9-AS1_ENST00000601022.1_RNA|ADAMTS9-AS1_ENST00000470447.1_RNA|ADAMTS9-AS1_ENST00000474313.1_RNA|ADAMTS9_ENST00000295903.4_Missense_Mutation_p.T1507A|ADAMTS9-AS1_ENST00000594810.1_RNA	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	1535	TSP type-1 12. {ECO:0000255|PROSITE- ProRule:PRU00210}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		TTGCACTCGGTCTCTCTGGCT	0.562																																																	0			3											173.0	156.0	162.0					3																	64547349		2203	4300	6503	64522389	SO:0001583	missense	56999			AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	13202	protein-coding gene	gene with protein product		605421	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"""			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.4603A>G	3.37:g.64547349T>C	ENSP00000418735:p.Thr1535Ala		64522389	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Missense_Mutation	SNP	ENST00000498707.1	37	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	T	11.06	1.527095	0.27299	.	.	ENSG00000163638	ENST00000295903;ENST00000498707	T;T	0.60171	0.21;0.21	5.7	-1.56	0.08532	.	0.543603	0.18126	N	0.150893	T	0.27278	0.0669	N	0.12443	0.215	0.28668	N	0.905776	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.08166	-1.0735	10	0.19590	T	0.45	.	1.5841	0.02641	0.4191:0.1254:0.108:0.3475	.	1507;1535;1535	B7ZVX9;Q9P2N4-1;Q9P2N4	.;.;ATS9_HUMAN	A	1507;1535	ENSP00000295903:T1507A;ENSP00000418735:T1535A	ENSP00000295903:T1507A	T	-	1	0	ADAMTS9	64522389	0.837000	0.29446	0.101000	0.21167	0.785000	0.44390	0.155000	0.16362	-0.496000	0.06650	-0.480000	0.04831	ACC		0.562	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1		
ROBO2	6092	hgsc.bcm.edu	37	3	77651633	77651633	+	Missense_Mutation	SNP	G	G	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:77651633G>C	ENST00000461745.1	+	20	4027	c.3127G>C	c.(3127-3129)Ggt>Cgt	p.G1043R	ROBO2_ENST00000487694.3_Missense_Mutation_p.G1059R|ROBO2_ENST00000332191.8_Missense_Mutation_p.G1043R	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	1043					apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		TCAGAACAAAGGTAACAATGG	0.378																																																	0			3											100.0	94.0	96.0					3																	77651633		1925	4133	6058	77734323	SO:0001583	missense	6092			AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10250	protein-coding gene	gene with protein product		602431	"""roundabout (axon guidance receptor, Drosophila) homolog 2"""			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.3127G>C	3.37:g.77651633G>C	ENSP00000417164:p.Gly1043Arg		77734323	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	37	CCDS43109.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	15.35|15.35|15.35	2.806096|2.806096|2.806096	0.50421|0.50421|0.50421	.|.|.	.|.|.	ENSG00000185008|ENSG00000185008|ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191|ENST00000490991|ENST00000471893	T;T;T|T|.	0.62639|0.66280|.	0.01;0.04;0.07|-0.2|.	5.84|5.84|5.84	5.84|5.84|5.84	0.93424|0.93424|0.93424	.|.|.	0.000000|.|.	0.46758|.|.	D|.|.	0.000263|.|.	T|T|T	0.69387|0.69387|0.69387	0.3105|0.3105|0.3105	L|L|L	0.43923|0.43923|0.43923	1.385|1.385|1.385	.|.|.	.|.|.	.|.|.	P;P;P|.|.	0.46457|.|.	0.766;0.878;0.766|.|.	B;P;B|.|.	0.46825|.|.	0.243;0.528;0.243|.|.	T|T|T	0.63175|0.63175|0.63175	-0.6696|-0.6696|-0.6696	9|6|4	0.25751|0.59425|.	T|D|.	0.34|0.04|.	.|.|.	20.1432|20.1432|20.1432	0.98067|0.98067|0.98067	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	1059;1043;1043|.|.	Q19AB5;F8W703;Q9HCK4|.|.	.;.;ROBO2_HUMAN|.|.	R|N|T	1059;1059;1063;1043;1043|199|117	ENSP00000417335:G1059R;ENSP00000417164:G1043R;ENSP00000327536:G1043R|ENSP00000418344:K199N|.	ENSP00000327536:G1043R|ENSP00000418344:K199N|.	G|K|R	+|+|+	1|3|2	0|2|0	ROBO2|ROBO2|ROBO2	77734323|77734323|77734323	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.979000|0.979000|0.979000	0.70002|0.70002|0.70002	6.564000|6.564000|6.564000	0.73969|0.73969|0.73969	2.769000|2.769000|2.769000	0.95229|0.95229|0.95229	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	GGT|AAG|AGG		0.378	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246	
MYH15	22989	hgsc.bcm.edu	37	3	108195349	108195349	+	Silent	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:108195349A>G	ENST00000273353.3	-	13	1244	c.1188T>C	c.(1186-1188)gcT>gcC	p.A396A		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	396	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.A396A(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TGAGGAAAGCAGCTTTGTCAG	0.403																																																	1	Substitution - coding silent(1)	ovary(1)	3											69.0	63.0	65.0					3																	108195349		1908	4127	6035	109678039	SO:0001819	synonymous_variant	22989			AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.1188T>C	3.37:g.108195349A>G			109678039		Silent	SNP	ENST00000273353.3	37	CCDS43127.1																																																																																				0.403	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
PARP14	54625	hgsc.bcm.edu	37	3	122437033	122437033	+	Silent	SNP	G	G	T	rs201050912		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:122437033G>T	ENST00000474629.2	+	13	4382	c.4116G>T	c.(4114-4116)ctG>ctT	p.L1372L		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1372	Macro 3. {ECO:0000255|PROSITE- ProRule:PRU00490}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.L1209L(1)		NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		TTATCTTTCTGCCTCAAGTAC	0.408																																																	1	Substitution - coding silent(1)	ovary(1)	3											105.0	97.0	99.0					3																	122437033		1868	4112	5980	123919723	SO:0001819	synonymous_variant	54625			AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.4116G>T	3.37:g.122437033G>T			123919723	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Silent	SNP	ENST00000474629.2	37	CCDS46894.1																																																																																				0.408	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
TOPBP1	11073	hgsc.bcm.edu	37	3	133327386	133327386	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:133327386A>G	ENST00000260810.5	-	27	4549	c.4418T>C	c.(4417-4419)cTc>cCc	p.L1473P		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1473	BRCT 8. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						AACCTGCATGAGATAATCAGC	0.403								Other conserved DNA damage response genes																													Ovarian(21;193 658 4424 15423 17362)												0			3											142.0	134.0	136.0					3																	133327386		1909	4125	6034	134810076	SO:0001583	missense	11073			AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.4418T>C	3.37:g.133327386A>G	ENSP00000260810:p.Leu1473Pro		134810076	B7Z7W8|Q7LGC1|Q9UEB9	Missense_Mutation	SNP	ENST00000260810.5	37	CCDS46919.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.273732	0.80580	.	.	ENSG00000163781	ENST00000260810	T	0.28895	1.59	5.31	5.31	0.75309	.	0.054132	0.85682	D	0.000000	T	0.58566	0.2131	M	0.80982	2.52	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.64964	-0.6283	10	0.87932	D	0	.	15.2583	0.73601	1.0:0.0:0.0:0.0	.	1473	Q92547	TOPB1_HUMAN	P	1473	ENSP00000260810:L1473P	ENSP00000260810:L1473P	L	-	2	0	TOPBP1	134810076	1.000000	0.71417	0.973000	0.42090	0.976000	0.68499	9.289000	0.96061	1.991000	0.58162	0.533000	0.62120	CTC		0.403	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027	
EPHB1	2047	hgsc.bcm.edu	37	3	134911606	134911606	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:134911606C>T	ENST00000398015.3	+	11	2441	c.2071C>T	c.(2071-2073)Cgg>Tgg	p.R691W	EPHB1_ENST00000493838.1_Missense_Mutation_p.R252W	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	691	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						CACCAAGAGTCGGCCTGTCAT	0.527																																																	0			3											105.0	104.0	104.0					3																	134911606		2198	4298	6496	136394296	SO:0001583	missense	2047			L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3392	protein-coding gene	gene with protein product		600600	"""EphB1"""	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.2071C>T	3.37:g.134911606C>T	ENSP00000381097:p.Arg691Trp		136394296	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	37	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.940438	0.73557	.	.	ENSG00000154928	ENST00000398015;ENST00000493838	T;T	0.62941	-0.01;-0.01	5.44	3.49	0.39957	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.76421	0.3985	M	0.73372	2.23	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	T	0.79468	-0.1791	10	0.87932	D	0	.	12.9402	0.58337	0.4179:0.5821:0.0:0.0	.	691	P54762	EPHB1_HUMAN	W	691;252	ENSP00000381097:R691W;ENSP00000419574:R252W	ENSP00000381097:R691W	R	+	1	2	EPHB1	136394296	1.000000	0.71417	0.937000	0.37676	0.989000	0.77384	2.392000	0.44433	1.257000	0.44085	0.561000	0.74099	CGG		0.527	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441	
RSRC1	51319	hgsc.bcm.edu	37	3	157839989	157839989	+	Missense_Mutation	SNP	T	T	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:157839989T>A	ENST00000295930.3	+	2	258	c.96T>A	c.(94-96)agT>agA	p.S32R	RSRC1_ENST00000480820.1_Missense_Mutation_p.S32R|RSRC1_ENST00000475278.2_Missense_Mutation_p.S32R|RSRC1_ENST00000464171.1_Missense_Mutation_p.S32R|RSRC1_ENST00000312179.6_Missense_Mutation_p.S32R	NM_001271838.1|NM_016625.2	NP_001258767.1|NP_057709.2	Q96IZ7	RSRC1_HUMAN	arginine/serine-rich coiled-coil 1	32	Arg/Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)|nucleocytoplasmic transport (GO:0006913)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)				cervix(1)|endometrium(2)|large_intestine(3)|lung(11)|upper_aerodigestive_tract(1)	18			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)			CTTCAGATAGTAGAACATACA	0.428																																																	0			3											97.0	93.0	94.0					3																	157839989		2203	4300	6503	159322683	SO:0001583	missense	51319			AF208853	CCDS3181.1, CCDS63822.1	3q25.32	2009-09-09			ENSG00000174891	ENSG00000174891			24152	protein-coding gene	gene with protein product	"""splicing factor, arginine/serine-rich 21"""	613352				15798186, 19065146	Standard	NM_001271838		Approved	MGC12197, BM-011, SRrp53, SFRS21	uc003fbu.2	Q96IZ7	OTTHUMG00000158758	ENST00000295930.3:c.96T>A	3.37:g.157839989T>A	ENSP00000295930:p.Ser32Arg		159322683	A8K2R9|Q96QK2|Q9NZE5	Missense_Mutation	SNP	ENST00000295930.3	37	CCDS3181.1	.	.	.	.	.	.	.	.	.	.	T	16.27	3.075802	0.55646	.	.	ENSG00000174891	ENST00000480820;ENST00000494002;ENST00000295930;ENST00000471994;ENST00000464171;ENST00000312179;ENST00000475278;ENST00000476899	.	.	.	5.41	-3.41	0.04839	.	0.432573	0.29616	N	0.011643	T	0.44456	0.1294	L	0.43152	1.355	0.43657	D	0.996071	B;B;B	0.33238	0.275;0.275;0.403	B;B;B	0.30179	0.112;0.112;0.112	T	0.40040	-0.9584	9	0.72032	D	0.01	.	14.1363	0.65289	0.0:0.5696:0.0:0.4304	.	32;32;32	B4DTW0;Q96IZ7-2;Q96IZ7	.;.;RSRC1_HUMAN	R	32	.	ENSP00000295930:S32R	S	+	3	2	RSRC1	159322683	0.926000	0.31397	0.974000	0.42286	0.962000	0.63368	-0.215000	0.09279	-0.491000	0.06697	0.454000	0.30748	AGT		0.428	RSRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352063.2	NM_016625	
SKIL	6498	hgsc.bcm.edu	37	3	170078891	170078891	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:170078891A>G	ENST00000458537.3	+	1	1481	c.772A>G	c.(772-774)Act>Gct	p.T258A	SKIL_ENST00000413427.2_Missense_Mutation_p.T258A|SKIL_ENST00000259119.4_Missense_Mutation_p.T258A|SKIL_ENST00000426052.2_Missense_Mutation_p.T238A	NM_001145097.2|NM_001248008.1|NM_005414.4	NP_001138569.1|NP_001234937.1|NP_005405.2	P12757	SKIL_HUMAN	SKI-like proto-oncogene	258					blastocyst formation (GO:0001825)|cell cycle arrest (GO:0007050)|gene expression (GO:0010467)|lens fiber cell differentiation (GO:0070306)|lymphocyte homeostasis (GO:0002260)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of axonogenesis (GO:0050772)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|protein heterotrimerization (GO:0070208)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|response to antibiotic (GO:0046677)|response to cytokine (GO:0034097)|response to growth factor (GO:0070848)|skeletal muscle tissue development (GO:0007519)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	25	all_cancers(22;7.13e-23)|all_epithelial(15;9.95e-28)|all_lung(20;1.23e-16)|Lung NSC(18;5.15e-16)|Ovarian(172;0.000337)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			GTTAAAGGAAACTGGCAGTGC	0.438																																																	0			3											138.0	121.0	127.0					3																	170078891		2203	4300	6503	171561585	SO:0001583	missense	6498			X15217	CCDS33890.1, CCDS46953.1, CCDS46954.1	3q26	2014-06-25	2014-06-25		ENSG00000136603	ENSG00000136603		"""SKI transcriptional corepressors"""	10897	protein-coding gene	gene with protein product		165340	"""SKI-like oncogene"""			2762147	Standard	NM_005414		Approved	SNO, SnoN, SnoA	uc003fgw.3	P12757	OTTHUMG00000158831	ENST00000458537.3:c.772A>G	3.37:g.170078891A>G	ENSP00000415243:p.Thr258Ala		171561585	A6NGT1|B4DT50|O00464|P12756|Q07501	Missense_Mutation	SNP	ENST00000458537.3	37	CCDS33890.1	.	.	.	.	.	.	.	.	.	.	A	15.53	2.862122	0.51482	.	.	ENSG00000136603	ENST00000259119;ENST00000426052;ENST00000413427;ENST00000458537	D;D;D;D	0.91351	-2.83;-2.82;-2.81;-2.83	5.51	5.51	0.81932	.	0.044394	0.85682	D	0.000000	D	0.85805	0.5782	L	0.34521	1.04	0.38568	D	0.949875	P;P	0.38729	0.644;0.563	B;B	0.38985	0.287;0.214	D	0.87440	0.2394	10	0.56958	D	0.05	-15.4577	11.432	0.50047	0.865:0.0:0.0:0.135	.	258;258	P12757-3;P12757	.;SKIL_HUMAN	A	258;238;258;258	ENSP00000259119:T258A;ENSP00000406520:T238A;ENSP00000400193:T258A;ENSP00000415243:T258A	ENSP00000259119:T258A	T	+	1	0	SKIL	171561585	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.902000	0.56310	2.111000	0.64477	0.524000	0.50904	ACT		0.438	SKIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352351.4	NM_005414	
PIK3CA	5290	hgsc.bcm.edu	37	3	178952005	178952005	+	Silent	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:178952005A>G	ENST00000263967.3	+	21	3217	c.3060A>G	c.(3058-3060)gcA>gcG	p.A1020A	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1020	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	ATGACATTGCATACATTCGAA	0.393		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)			Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	0			3											106.0	94.0	98.0					3																	178952005		1877	4119	5996	180434699	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3060A>G	3.37:g.178952005A>G			180434699	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				0.393	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
PIK3CA	5290	hgsc.bcm.edu	37	3	178952099	178952099	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:178952099A>G	ENST00000263967.3	+	21	3311	c.3154A>G	c.(3154-3156)Aca>Gca	p.T1052A	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1052	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		T -> K (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.T1052A(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TGGTGGCTGGACAACAAAAAT	0.393		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)			Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	1	Substitution - Missense(1)	breast(1)	3											97.0	87.0	90.0					3																	178952099		1916	4131	6047	180434793	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3154A>G	3.37:g.178952099A>G	ENSP00000263967:p.Thr1052Ala		180434793	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	15.43	2.830182	0.50845	.	.	ENSG00000121879	ENST00000263967	D	0.82803	-1.65	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.78960	0.4366	L	0.47078	1.49	0.80722	D	1	P	0.35433	0.501	B	0.34452	0.183	T	0.76476	-0.2945	10	0.27785	T	0.31	-14.979	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1052	P42336	PK3CA_HUMAN	A	1052	ENSP00000263967:T1052A	ENSP00000263967:T1052A	T	+	1	0	PIK3CA	180434793	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	ACA		0.393	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
EPHB3	2049	hgsc.bcm.edu	37	3	184298232	184298232	+	Silent	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:184298232T>C	ENST00000330394.2	+	12	2667	c.2215T>C	c.(2215-2217)Ttg>Ctg	p.L739L	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	739	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			GGTGGGCATGTTGCGGGGCAT	0.597																																																	0			3											142.0	129.0	134.0					3																	184298232		2203	4300	6503	185780926	SO:0001819	synonymous_variant	2049			X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3394	protein-coding gene	gene with protein product		601839	"""EphB3"""	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.2215T>C	3.37:g.184298232T>C			185780926	Q7Z740	Silent	SNP	ENST00000330394.2	37	CCDS3268.1																																																																																				0.597	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443	
EHHADH	1962	hgsc.bcm.edu	37	3	184910747	184910747	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr3:184910747A>G	ENST00000231887.3	-	7	1514	c.1439T>C	c.(1438-1440)gTg>gCg	p.V480A	EHHADH_ENST00000456310.1_Missense_Mutation_p.V384A|EHHADH-AS1_ENST00000417720.1_RNA	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	480	3-hydroxyacyl-CoA dehydrogenase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			TCGATTCCCCACAAATCCAAA	0.418																																																	0			3											108.0	109.0	108.0					3																	184910747		2203	4300	6503	186393441	SO:0001583	missense	1962			L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"""enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"""	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.1439T>C	3.37:g.184910747A>G	ENSP00000231887:p.Val480Ala		186393441	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	37	CCDS33901.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.703750	0.68501	.	.	ENSG00000113790	ENST00000231887;ENST00000456310	D;D	0.91124	-2.79;-2.79	5.91	5.91	0.95273	3-hydroxyacyl-CoA dehydrogenase, C-terminal (1);3-hydroxyacyl-CoA dehydrogenase, conserved site (1);Dehydrogenase, multihelical (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.117554	0.56097	D	0.000023	D	0.93897	0.8047	L	0.61387	1.9	0.80722	D	1	D	0.67145	0.996	D	0.65010	0.931	D	0.93489	0.6834	10	0.44086	T	0.13	-29.7634	16.3483	0.83171	1.0:0.0:0.0:0.0	.	480	Q08426	ECHP_HUMAN	A	480;384	ENSP00000231887:V480A;ENSP00000387746:V384A	ENSP00000231887:V480A	V	-	2	0	EHHADH	186393441	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.845000	0.69437	2.254000	0.74563	0.533000	0.62120	GTG		0.418	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1		
ZNF384	171017	hgsc.bcm.edu	37	12	6777072	6777072	+	Silent	SNP	C	C	T	rs78573212|rs72393318|rs544124628|rs3835029	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr12:6777072C>T	ENST00000396801.3	-	11	1749	c.1542G>A	c.(1540-1542)caG>caA	p.Q514Q	ZNF384_ENST00000361959.3_Silent_p.Q514Q|RP4-761J14.8_ENST00000586338.1_RNA|ZNF384_ENST00000319770.3_Silent_p.Q437Q|ZNF384_ENST00000396795.1_Silent_p.Q453Q|ZNF384_ENST00000396799.2_Silent_p.Q453Q|RP4-761J14.8_ENST00000589924.1_RNA|ZNF384_ENST00000355772.4_Silent_p.Q398Q	NM_001135734.2	NP_001129206.1	Q8TF68	ZN384_HUMAN	zinc finger protein 384	514	Gln-rich.				nucleocytoplasmic transport (GO:0006913)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	focal adhesion (GO:0005925)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)	p.L139delL(6)|p.Q455delQ(3)|p.Q516delQ(3)	EWSR1/ZNF384(4)	breast(3)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(1)	18						GTGgctgttgctgctgctgct	0.667			T	"""EWSR1, TAF15 """	ALL																																			Dom	yes		12	12p13	171017	zinc finger protein 384 (CIZ/NMP4)		L	12	Deletion - In frame(12)	breast(12)	12											18.0	21.0	20.0					12																	6777072		2203	4296	6499	6647333	SO:0001819	synonymous_variant	171017			U80738	CCDS8557.1, CCDS31732.1, CCDS44817.1	12p12	2013-01-08	2002-05-23	2002-05-24		ENSG00000126746		"""Zinc fingers, C2H2-type"""	11955	protein-coding gene	gene with protein product		609951	"""trinucleotide repeat containing 1"""	TNRC1		9225980, 11149472	Standard	NM_001135734		Approved	CAGH1A, CIZ, NMP4, NP	uc010sfh.2	Q8TF68		ENST00000396801.3:c.1542G>A	12.37:g.6777072C>T			6647333	O15407|Q7Z722|Q8N938	Silent	SNP	ENST00000396801.3	37	CCDS44817.1																																																																																				0.667	ZNF384-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400712.1		
KRAS	3845	hgsc.bcm.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)			Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91.0	81.0	85.0					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
ABCD2	225	hgsc.bcm.edu	37	12	40013006	40013006	+	Missense_Mutation	SNP	T	T	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr12:40013006T>G	ENST00000308666.3	-	1	547	c.412A>C	c.(412-414)Aag>Cag	p.K138Q		NM_005164.3	NP_005155.1	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D (ALD), member 2	138	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.|Interaction with PEX19.				fatty acid beta-oxidation (GO:0006635)|positive regulation of fatty acid beta-oxidation (GO:0032000)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(24)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	52						CGAGGCTTCTTTTCCACAATG	0.438																																																	0			12											92.0	91.0	91.0					12																	40013006		2203	4300	6503	38299273	SO:0001583	missense	225			U28150	CCDS8734.1	12q12	2012-05-16			ENSG00000173208	ENSG00000173208		"""ATP binding cassette transporters / subfamily D"""	66	protein-coding gene	gene with protein product		601081		ALDL1		8577752	Standard	NM_005164		Approved	ALDR, ALDRP	uc001rmb.2	Q9UBJ2	OTTHUMG00000169337	ENST00000308666.3:c.412A>C	12.37:g.40013006T>G	ENSP00000310688:p.Lys138Gln		38299273	B2RAM3|Q13210|Q2M3H9	Missense_Mutation	SNP	ENST00000308666.3	37	CCDS8734.1	.	.	.	.	.	.	.	.	.	.	T	17.41	3.383031	0.61845	.	.	ENSG00000173208	ENST00000308666	D	0.91843	-2.92	4.58	4.58	0.56647	ABC transporter, N-terminal (1);ABC transporter, integral membrane type 1 (1);	0.000000	0.85682	D	0.000000	D	0.94876	0.8344	M	0.67625	2.065	0.58432	D	0.999993	D	0.67145	0.996	D	0.73380	0.98	D	0.94565	0.7766	9	.	.	.	-10.0656	14.1471	0.65357	0.0:0.0:0.0:1.0	.	138	Q9UBJ2	ABCD2_HUMAN	Q	138	ENSP00000310688:K138Q	.	K	-	1	0	ABCD2	38299273	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.384000	0.79751	1.927000	0.55829	0.460000	0.39030	AAG		0.438	ABCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403591.1	NM_005164	
DDN	23109	hgsc.bcm.edu	37	12	49391847	49391847	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr12:49391847T>C	ENST00000421952.2	-	2	833	c.812A>G	c.(811-813)aAg>aGg	p.K271R	RP11-386G11.5_ENST00000552284.1_RNA|RP11-386G11.3_ENST00000549516.1_RNA|RP11-386G11.5_ENST00000547395.1_RNA|RP11-386G11.5_ENST00000547866.1_RNA|RP11-386G11.5_ENST00000552933.1_RNA	NM_015086.1	NP_055901.2	O94850	DEND_HUMAN	dendrin	271						cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	8						ATCCAGCCTCTTCTTTGTGCG	0.652																																																	0			12											50.0	58.0	55.0					12																	49391847		2203	4297	6500	47678114	SO:0001583	missense	23109			AB018292	CCDS31791.2	12q13	2008-02-05			ENSG00000181418	ENSG00000181418			24458	protein-coding gene	gene with protein product		610588					Standard	NM_015086		Approved	KIAA0749	uc001rsv.1	O94850	OTTHUMG00000156183	ENST00000421952.2:c.812A>G	12.37:g.49391847T>C	ENSP00000390590:p.Lys271Arg		47678114		Missense_Mutation	SNP	ENST00000421952.2	37	CCDS31791.2	.	.	.	.	.	.	.	.	.	.	T	17.46	3.396422	0.62177	.	.	ENSG00000181418	ENST00000421952	T	0.57273	0.41	3.89	3.89	0.44902	.	0.000000	0.48286	D	0.000198	T	0.34164	0.0888	L	0.27053	0.805	0.32752	N	0.506301	P	0.46142	0.873	B	0.40009	0.316	T	0.46789	-0.9166	10	0.38643	T	0.18	-19.3521	6.0274	0.19662	0.0:0.1126:0.0:0.8874	.	271	O94850	DEND_HUMAN	R	271	ENSP00000390590:K271R	ENSP00000390590:K271R	K	-	2	0	DDN	47678114	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.354000	0.44098	2.004000	0.58718	0.459000	0.35465	AAG		0.652	DDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343335.1		
DCN	1634	hgsc.bcm.edu	37	12	91550854	91550854	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr12:91550854T>C	ENST00000052754.5	-	5	1151	c.650A>G	c.(649-651)cAa>cGa	p.Q217R	DCN_ENST00000547568.2_Intron|DCN_ENST00000303320.3_Intron|DCN_ENST00000420120.2_Missense_Mutation_p.Q108R|DCN_ENST00000456569.2_Intron|DCN_ENST00000228329.5_Missense_Mutation_p.Q108R|DCN_ENST00000393155.1_Missense_Mutation_p.Q217R|DCN_ENST00000441303.2_Intron|DCN_ENST00000552962.1_Missense_Mutation_p.Q217R|DCN_ENST00000425043.1_Intron	NM_001920.3	NP_001911.1	P07585	PGS2_HUMAN	decorin	217					aging (GO:0007568)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|kidney development (GO:0001822)|organ morphogenesis (GO:0009887)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|placenta development (GO:0001890)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|skeletal muscle tissue development (GO:0007519)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	collagen type VI trimer (GO:0005589)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|glycosaminoglycan binding (GO:0005539)|poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|skin(1)	20						TCTATCACCTTGAGGAATGCT	0.368																																																	0			12											103.0	99.0	100.0					12																	91550854		2203	4300	6503	90074985	SO:0001583	missense	1634			AF138300	CCDS9039.1, CCDS9040.1, CCDS9041.1, CCDS9042.1, CCDS44951.1	12q21.33	2014-04-16			ENSG00000011465	ENSG00000011465		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	2705	protein-coding gene	gene with protein product	"""decorin proteoglycan"""	125255				8432526	Standard	NM_133507		Approved	DSPG2, SLRR1B	uc001tbt.3	P07585	OTTHUMG00000169998	ENST00000052754.5:c.650A>G	12.37:g.91550854T>C	ENSP00000052754:p.Gln217Arg		90074985	Q9P0Z0|Q9P0Z1|Q9Y5N8|Q9Y5N9	Missense_Mutation	SNP	ENST00000052754.5	37	CCDS9039.1	.	.	.	.	.	.	.	.	.	.	T	12.65	2.002247	0.35320	.	.	ENSG00000011465	ENST00000052754;ENST00000228329;ENST00000393155;ENST00000552962;ENST00000420120	T;T;T;T;T	0.04317	3.65;3.65;3.65;3.65;3.65	5.69	0.295	0.15752	.	0.140299	0.64402	D	0.000006	T	0.02848	0.0085	N	0.11698	0.16	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.48175	-0.9058	10	0.56958	D	0.05	.	9.0489	0.36363	0.0:0.0627:0.3505:0.5868	.	217;108	P07585;P07585-2	PGS2_HUMAN;.	R	217;108;217;217;108	ENSP00000052754:Q217R;ENSP00000228329:Q108R;ENSP00000376862:Q217R;ENSP00000447654:Q217R;ENSP00000413723:Q108R	ENSP00000052754:Q217R	Q	-	2	0	DCN	90074985	1.000000	0.71417	1.000000	0.80357	0.580000	0.36256	1.519000	0.35888	0.061000	0.16311	0.477000	0.44152	CAA		0.368	DCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406799.3	NM_133507	
CUX2	23316	hgsc.bcm.edu	37	12	111729259	111729259	+	Silent	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr12:111729259C>T	ENST00000261726.6	+	5	493	c.339C>T	c.(337-339)gaC>gaT	p.D113D		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	113					cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						GCAGCCTAGACGACAGACTGC	0.637																																																	0			12											56.0	63.0	61.0					12																	111729259		1991	4155	6146	110213642	SO:0001819	synonymous_variant	23316			AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"""Homeoboxes / CUT class"""	19347	protein-coding gene	gene with protein product		610648	"""cut-like 2 (Drosophila)"""	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.339C>T	12.37:g.111729259C>T			110213642	A7E2Y4	Silent	SNP	ENST00000261726.6	37	CCDS41837.1																																																																																				0.637	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267	
SBNO1	55206	hgsc.bcm.edu	37	12	123818625	123818625	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr12:123818625A>G	ENST00000602398.1	-	7	1011	c.884T>C	c.(883-885)cTt>cCt	p.L295P	SBNO1_ENST00000420886.2_Missense_Mutation_p.L295P|SBNO1_ENST00000267176.4_Missense_Mutation_p.L294P|SBNO1_ENST00000602750.1_Missense_Mutation_p.L294P			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	295					regulation of transcription, DNA-templated (GO:0006355)			p.L294H(1)		NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		AATTGCCTCAAGCTGCAATGC	0.348																																																	1	Substitution - Missense(1)	kidney(1)	12											67.0	62.0	64.0					12																	123818625		2203	4300	6503	122384578	SO:0001583	missense	55206			AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"""sno, strawberry notch homolog 1 (Drosophila)"""				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.884T>C	12.37:g.123818625A>G	ENSP00000473665:p.Leu295Pro		122384578	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	37	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.533445	0.85812	.	.	ENSG00000139697	ENST00000420886;ENST00000267176;ENST00000442601	D;D	0.94376	-3.41;-3.41	5.73	5.73	0.89815	Helicase/UvrB domain (1);	0.000000	0.64402	D	0.000001	D	0.97760	0.9265	H	0.95328	3.655	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.999;0.998	D	0.98997	1.0810	10	0.87932	D	0	-20.3217	16.0337	0.80603	1.0:0.0:0.0:0.0	.	295;294;293	A3KN83;A3KN83-2;A3KN83-3	SBNO1_HUMAN;.;.	P	295;294;294	ENSP00000387361:L295P;ENSP00000267176:L294P	ENSP00000267176:L294P	L	-	2	0	SBNO1	122384578	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	9.228000	0.95250	2.189000	0.69895	0.528000	0.53228	CTT		0.348	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183	
TMEM132B	114795	hgsc.bcm.edu	37	12	125834830	125834830	+	Silent	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr12:125834830C>T	ENST00000299308.3	+	2	893	c.885C>T	c.(883-885)gaC>gaT	p.D295D		NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	295						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		GGGAAGGGGACACGGCCACCT	0.537																																																	0			12											199.0	190.0	193.0					12																	125834830		1970	4138	6108	124400783	SO:0001819	synonymous_variant	114795			AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.885C>T	12.37:g.125834830C>T			124400783	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Silent	SNP	ENST00000299308.3	37	CCDS41859.1																																																																																				0.537	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907	
PGAM5	192111	hgsc.bcm.edu	37	12	133294357	133294357	+	Silent	SNP	C	C	T	rs371236067		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr12:133294357C>T	ENST00000498926.2	+	4	616	c.558C>T	c.(556-558)ccC>ccT	p.P186P	PGAM5_ENST00000543955.1_Silent_p.P37P|PGAM5_ENST00000454808.2_Silent_p.P37P|PGAM5_ENST00000317555.2_Silent_p.P186P|PXMP2_ENST00000545677.1_3'UTR	NM_001170543.1|NM_001170544.1	NP_001164014.1|NP_001164015.1	Q96HS1	PGAM5_HUMAN	phosphoglycerate mutase family member 5	186					dephosphorylation (GO:0016311)|necroptotic process (GO:0070266)|positive regulation of GTPase activity (GO:0043547)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|protein complex binding (GO:0032403)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.89e-08)|Epithelial(86;1.14e-07)|all cancers(50;3.57e-06)		CAGACCCGCCCGTGTCTCATT	0.662																																																	0			12						C	,,	0,4350		0,0,2175	21.0	27.0	25.0		558,558,558	-7.6	0.2	12		25	1,8559		0,1,4279	no	coding-synonymous,coding-synonymous,coding-synonymous	PGAM5	NM_001170543.1,NM_001170544.1,NM_138575.3	,,	0,1,6454	TT,TC,CC		0.0117,0.0,0.0077	,,	186/290,186/289,186/256	133294357	1,12909	2175	4280	6455	131804430	SO:0001819	synonymous_variant	192111			BC008196	CCDS9280.1, CCDS53845.1	12q24.33	2011-07-28			ENSG00000247077	ENSG00000247077			28763	protein-coding gene	gene with protein product		614939				11283018	Standard	NM_001170543		Approved	MGC5352, BXLBv68	uc009zyv.3	Q96HS1	OTTHUMG00000168021	ENST00000498926.2:c.558C>T	12.37:g.133294357C>T			131804430	A9LN06|C9IZY7|Q96JB0	Silent	SNP	ENST00000498926.2	37	CCDS53845.1																																																																																				0.662	PGAM5-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397562.1	NM_138575	
MEIS2	4212	hgsc.bcm.edu	37	15	37329088	37329088	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr15:37329088C>T	ENST00000561208.1	-	8	1245	c.827G>A	c.(826-828)cGc>cAc	p.R276H	MEIS2_ENST00000382766.2_Missense_Mutation_p.R276H|MEIS2_ENST00000397624.3_Missense_Mutation_p.R188H|MEIS2_ENST00000397620.2_Missense_Mutation_p.R188H|MEIS2_ENST00000444725.1_Missense_Mutation_p.R276H|MEIS2_ENST00000340545.5_Missense_Mutation_p.R263H|MEIS2_ENST00000559085.1_Missense_Mutation_p.R263H|MEIS2_ENST00000338564.5_Missense_Mutation_p.R276H|MEIS2_ENST00000557796.2_Missense_Mutation_p.R263H|MEIS2_ENST00000424352.2_Missense_Mutation_p.R276H|MEIS2_ENST00000219869.9_Missense_Mutation_p.R130H|MEIS2_ENST00000559561.1_Missense_Mutation_p.R276H			O14770	MEIS2_HUMAN	Meis homeobox 2	276					eye development (GO:0001654)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas development (GO:0031016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	36		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)		TTTCTTCTGGCGTTTTTTGTC	0.393																																																	0			15											216.0	185.0	196.0					15																	37329088		2201	4297	6498	35116380	SO:0001583	missense	4212			AF017418	CCDS10044.1, CCDS10045.1, CCDS42014.1, CCDS45217.1, CCDS45218.1, CCDS45219.1, CCDS45220.1	15q14	2011-06-20	2007-02-15		ENSG00000134138	ENSG00000134138		"""Homeoboxes / TALE class"""	7001	protein-coding gene	gene with protein product		601740	"""Meis (mouse) homolog 2"", ""Meis1, myeloid ecotropic viral integration site 1 homolog 2 (mouse)"""			9383298	Standard	NM_172315		Approved	MRG1, HsT18361	uc001zjr.4	O14770	OTTHUMG00000129781	ENST00000561208.1:c.827G>A	15.37:g.37329088C>T	ENSP00000453793:p.Arg276His		35116380	A6NJI5|A8MWD5|B3KP98|B3KPQ6|Q96DI2|Q96KI4|Q96KI5|Q9NRS1|Q9NRS2|Q9NRS3	Missense_Mutation	SNP	ENST00000561208.1	37	CCDS10044.1	.	.	.	.	.	.	.	.	.	.	C	13.34	2.207426	0.39003	.	.	ENSG00000134138	ENST00000314177;ENST00000338564;ENST00000382766;ENST00000424352;ENST00000444725;ENST00000340545;ENST00000397624;ENST00000397620;ENST00000219869	T;D;D;D;D;D;D;D	0.84442	1.88;-1.85;-1.85;-1.85;-1.85;-1.85;-1.85;-1.85	5.14	4.2	0.49525	Homeodomain-related (1);Homeobox (2);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.85199	0.5642	L	0.35644	1.08	0.80722	D	1	B;B;B;B;D;B;B;B	0.64830	0.016;0.083;0.063;0.006;0.994;0.007;0.002;0.013	B;B;B;B;P;B;B;B	0.57152	0.009;0.046;0.005;0.021;0.814;0.004;0.001;0.009	D	0.84217	0.0459	10	0.39692	T	0.17	-5.1959	13.3746	0.60730	0.0:0.9238:0.0:0.0762	.	263;276;276;276;276;130;188;263	Q96DI2;O14770-4;O14770;O14770-3;O14770-2;B3KP81;B3KPQ6;B3KP98	.;.;MEIS2_HUMAN;.;.;.;.;.	H	276;276;276;276;276;263;263;188;130	ENSP00000326296:R276H;ENSP00000341400:R276H;ENSP00000372216:R276H;ENSP00000404185:R276H;ENSP00000391887:R276H;ENSP00000339549:R263H;ENSP00000380745:R188H;ENSP00000219869:R130H	ENSP00000219869:R130H	R	-	2	0	MEIS2	35116380	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.042000	0.70996	2.556000	0.86216	0.650000	0.86243	CGC		0.393	MEIS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252003.2	NM_170677	
C15orf56	644809	hgsc.bcm.edu	37	15	40544943	40544943	+	Silent	SNP	A	A	G	rs369720850	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr15:40544943A>G	ENST00000319503.3	-	1	168	c.147T>C	c.(145-147)gtT>gtC	p.V49V	PAK6_ENST00000560346.1_Intron|C15orf56_ENST00000559727.1_Silent_p.V49V|PAK6_ENST00000260404.4_Intron|PAK6_ENST00000542403.2_5'Flank|PAK6_ENST00000455577.2_Intron|PAK6_ENST00000453867.1_Intron|PAK6_ENST00000441369.1_Intron|RP11-133K1.2_ENST00000558658.1_Intron	NM_001039905.1	NP_001034994.1	Q8N910	CO056_HUMAN	chromosome 15 open reading frame 56	49										lung(1)	1		all_cancers(109;1.62e-14)|all_epithelial(112;7.09e-12)|Lung NSC(122;3.4e-09)|all_lung(180;6.88e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.28e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0503)		CGGGCCTCCCAACACGCGCAG	0.741													A|||	6	0.00119808	0.0008	0.0014	5008	,	,		11887	0.001		0.002	False		,,,				2504	0.001																0			15						A	,,,	5,3987		0,5,1991	4.0	5.0	5.0		147,,,	0.6	0.0	15		5	39,7921		0,39,3941	no	coding-synonymous,intron,intron,intron	PAK6,C15orf56	NM_001039905.1,NM_001128628.1,NM_001128629.1,NM_020168.4	,,,	0,44,5932	GG,GA,AA		0.4899,0.1253,0.3681	,,,	49/162,,,	40544943	44,11908	1996	3980	5976	38332235	SO:0001819	synonymous_variant	644809				CCDS32197.1	15q15.1	2012-05-30			ENSG00000176753	ENSG00000176753			33868	protein-coding gene	gene with protein product							Standard	NM_001039905		Approved	FLJ38596	uc001zla.2	Q8N910	OTTHUMG00000172399	ENST00000319503.3:c.147T>C	15.37:g.40544943A>G			38332235		Silent	SNP	ENST00000319503.3	37	CCDS32197.1																																																																																				0.741	C15orf56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418370.2	NM_001039905	
BAHD1	22893	hgsc.bcm.edu	37	15	40751659	40751659	+	Silent	SNP	C	C	T	rs534764286		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr15:40751659C>T	ENST00000416165.1	+	2	1067	c.996C>T	c.(994-996)ggC>ggT	p.G332G	BAHD1_ENST00000561234.1_Silent_p.G332G|BAHD1_ENST00000560846.1_Silent_p.G332G	NM_014952.3	NP_055767.3	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	332	Pro-rich.				heterochromatin assembly (GO:0031507)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)	chromatin binding (GO:0003682)			NS(1)|endometrium(6)|kidney(3)|large_intestine(3)|lung(10)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	28		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)		GGCGCCCAGGCGAGGAGTCAC	0.672													c|||	1	0.000199681	0.0008	0.0	5008	,	,		17317	0.0		0.0	False		,,,				2504	0.0																0			15											38.0	46.0	43.0					15																	40751659		2203	4300	6503	38538951	SO:0001819	synonymous_variant	22893			AL833923	CCDS10058.1, CCDS73705.1	15q14	2005-11-10			ENSG00000140320	ENSG00000140320			29153	protein-coding gene	gene with protein product		613880				10231032	Standard	XM_005254229		Approved	KIAA0945	uc001zlu.2	Q8TBE0	OTTHUMG00000129982	ENST00000416165.1:c.996C>T	15.37:g.40751659C>T			38538951	Q8NDF7|Q9Y2F4	Silent	SNP	ENST00000416165.1	37	CCDS10058.1																																																																																				0.672	BAHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252248.1	NM_014952	
TGM7	116179	hgsc.bcm.edu	37	15	43572000	43572000	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr15:43572000C>T	ENST00000452443.2	-	10	1505	c.1501G>A	c.(1501-1503)Gag>Aag	p.E501K		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	501					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	TGGCCCCACTCGGGTATCCTG	0.647																																																	0			15											36.0	43.0	41.0					15																	43572000		2202	4298	6500	41359292	SO:0001583	missense	116179			AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"""Transglutaminases"""	30790	protein-coding gene	gene with protein product	"""transglutaminase Z"""	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.1501G>A	15.37:g.43572000C>T	ENSP00000389466:p.Glu501Lys		41359292		Missense_Mutation	SNP	ENST00000452443.2	37	CCDS32213.1	.	.	.	.	.	.	.	.	.	.	C	0.017	-1.500546	0.01001	.	.	ENSG00000159495	ENST00000452443	T	0.28255	1.62	4.55	-0.762	0.11034	Transglutaminase, C-terminal (1);Immunoglobulin-like fold (1);	0.848314	0.10531	N	0.663871	T	0.12732	0.0309	L	0.27053	0.805	0.09310	N	1	B	0.31837	0.342	B	0.20184	0.028	T	0.26608	-1.0098	10	0.05959	T	0.93	-3.5654	4.0428	0.09760	0.0:0.3907:0.1775:0.4318	.	501	Q96PF1	TGM7_HUMAN	K	501	ENSP00000389466:E501K	ENSP00000389466:E501K	E	-	1	0	TGM7	41359292	0.001000	0.12720	0.003000	0.11579	0.062000	0.15995	-0.386000	0.07370	-0.334000	0.08463	-0.126000	0.14955	GAG		0.647	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955	
VPS33B	26276	hgsc.bcm.edu	37	15	91542927	91542927	+	Missense_Mutation	SNP	C	C	T	rs147814686		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr15:91542927C>T	ENST00000333371.3	-	22	2107	c.1754G>A	c.(1753-1755)cGg>cAg	p.R585Q	VPS33B_ENST00000535906.1_Missense_Mutation_p.R558Q|VPS33B_ENST00000535843.1_Missense_Mutation_p.R494Q	NM_018668.3	NP_061138.3	Q9H267	VP33B_HUMAN	vacuolar protein sorting 33 homolog B (yeast)	585					lysosome localization (GO:0032418)|melanosome localization (GO:0032400)|membrane fusion (GO:0061025)|platelet alpha granule organization (GO:0070889)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule (GO:0031091)				central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|stomach(2)	16	Lung NSC(78;0.0987)|all_lung(78;0.175)					GCCCAGGAACCGGAGGGCTGA	0.507																																																	0			15						C	GLN/ARG	0,4396		0,0,2198	222.0	228.0	226.0		1754	5.9	1.0	15	dbSNP_134	226	1,8595	1.2+/-3.3	0,1,4297	no	missense	VPS33B	NM_018668.3	43	0,1,6495	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	585/618	91542927	1,12991	2198	4298	6496	89343931	SO:0001583	missense	26276			AF201694	CCDS10369.1, CCDS73783.1	15q26.1	2006-12-19	2006-12-19		ENSG00000184056	ENSG00000184056			12712	protein-coding gene	gene with protein product		608552	"""vacuolar protein sorting 33B (yeast homolog)"""			8996080	Standard	XM_005254887		Approved	FLJ14848	uc002bqp.1	Q9H267	OTTHUMG00000149835	ENST00000333371.3:c.1754G>A	15.37:g.91542927C>T	ENSP00000327650:p.Arg585Gln		89343931	B3KQF6|Q96K14|Q9NRP6|Q9NSF3	Missense_Mutation	SNP	ENST00000333371.3	37	CCDS10369.1	.	.	.	.	.	.	.	.	.	.	C	36	5.838613	0.97009	0.0	1.16E-4	ENSG00000184056	ENST00000333371;ENST00000535906;ENST00000535843;ENST00000537510	T;T;T	0.75704	-0.96;-0.96;-0.96	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	D	0.87947	0.6306	M	0.85859	2.78	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.992;0.993	D	0.88511	0.3089	10	0.62326	D	0.03	-32.8143	18.1584	0.89701	0.0:1.0:0.0:0.0	.	558;585	F5H008;Q9H267	.;VP33B_HUMAN	Q	585;558;494;540	ENSP00000327650:R585Q;ENSP00000444053:R558Q;ENSP00000446267:R494Q	ENSP00000327650:R585Q	R	-	2	0	VPS33B	89343931	1.000000	0.71417	0.992000	0.48379	0.997000	0.91878	6.396000	0.73234	2.825000	0.97269	0.655000	0.94253	CGG		0.507	VPS33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313496.1	NM_018668	
LINS	55180	hgsc.bcm.edu	37	15	101109902	101109902	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr15:101109902C>T	ENST00000314742.8	-	7	2037	c.1815G>A	c.(1813-1815)atG>atA	p.M605I	LINS_ENST00000559149.1_5'Flank	NM_001040616.2	NP_001035706	Q8NG48	LINES_HUMAN	lines homolog (Drosophila)	605										central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(4)	21						CCCCCTTGGACATCACAGCTT	0.537																																																	0			15											69.0	66.0	67.0					15																	101109902		2203	4300	6503	98927425	SO:0001583	missense	0			AK095448	CCDS10385.1	15q26.3	2010-09-08	2010-09-08	2010-09-08	ENSG00000140471	ENSG00000140471			30922	protein-coding gene	gene with protein product		610350	"""lines homolog 1 (Drosophila)"""	LINS1		12119551, 8889548	Standard	NM_001040616		Approved	WINS1	uc002bwg.3	Q8NG48	OTTHUMG00000149865	ENST00000314742.8:c.1815G>A	15.37:g.101109902C>T	ENSP00000318423:p.Met605Ile		98927425	Q96FW2|Q9NVQ3	Missense_Mutation	SNP	ENST00000314742.8	37	CCDS10385.1	.	.	.	.	.	.	.	.	.	.	C	8.935	0.964408	0.18583	.	.	ENSG00000140471	ENST00000314742	T	0.09723	2.95	4.85	-2.02	0.07388	.	0.807412	0.11487	N	0.559142	T	0.06050	0.0157	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.37888	-0.9686	10	0.32370	T	0.25	-0.9308	2.4109	0.04424	0.1225:0.3085:0.3576:0.2114	.	605	Q8NG48	LINES_HUMAN	I	605	ENSP00000318423:M605I	ENSP00000318423:M605I	M	-	3	0	LINS	98927425	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.464000	0.06688	-0.801000	0.04427	-1.211000	0.01629	ATG		0.537	LINS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313592.1	NM_018148	
PRRG1	5638	hgsc.bcm.edu	37	X	37312702	37312702	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chrX:37312702G>A	ENST00000542554.1	+	5	757	c.485G>A	c.(484-486)cGc>cAc	p.R162H	TM4SF2_ENST00000465127.1_Intron|PRRG1_ENST00000491253.1_3'UTR|PRRG1_ENST00000449135.2_Missense_Mutation_p.R162H|PRRG1_ENST00000543642.1_Missense_Mutation_p.R162H|PRRG1_ENST00000378628.4_Missense_Mutation_p.R162H	NM_001173489.1	NP_001166960.1	O14668	TMG1_HUMAN	proline rich Gla (G-carboxyglutamic acid) 1	162						extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	15						GTCTCTACTCGCCTGTCCAAT	0.547																																																	0			X											87.0	73.0	78.0					X																	37312702		2202	4300	6502	37197623	SO:0001583	missense	5638			AF009242	CCDS14239.1, CCDS55397.1	Xp21.1	2010-08-13	2004-05-27		ENSG00000130962	ENSG00000130962			9469	protein-coding gene	gene with protein product		604428	"""proline-rich Gla (G-carboxyglutamic acid) polypeptide 1"""			9256434	Standard	NM_000950		Approved	PRGP1	uc004ddo.3	O14668	OTTHUMG00000021360	ENST00000542554.1:c.485G>A	X.37:g.37312702G>A	ENSP00000444278:p.Arg162His		37197623	B2R7A3|C9JXL7|D3DWA9|Q5JT66	Missense_Mutation	SNP	ENST00000542554.1	37	CCDS14239.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.450550	0.84101	.	.	ENSG00000130962	ENST00000378628;ENST00000542554;ENST00000543642;ENST00000449135	D;D;D;D	0.99121	-5.45;-5.45;-5.45;-5.45	5.96	5.96	0.96718	.	0.047968	0.85682	D	0.000000	D	0.98043	0.9355	L	0.55481	1.735	0.45403	D	0.99838	D	0.54047	0.964	P	0.44477	0.451	D	0.98691	1.0696	10	0.56958	D	0.05	-12.5273	17.7889	0.88547	0.0:0.0:1.0:0.0	.	162	O14668	TMG1_HUMAN	H	162	ENSP00000367894:R162H;ENSP00000444278:R162H;ENSP00000443271:R162H;ENSP00000390332:R162H	ENSP00000367894:R162H	R	+	2	0	PRRG1	37197623	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.463000	0.60128	2.524000	0.85096	0.600000	0.82982	CGC		0.547	PRRG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056228.2	NM_000950	
ZNF81	347344	hgsc.bcm.edu	37	X	47775003	47775003	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chrX:47775003T>C	ENST00000376954.1	+	6	1326	c.958T>C	c.(958-960)Tat>Cat	p.Y320H	ZNF81_ENST00000338637.7_Missense_Mutation_p.Y320H			P51508	ZNF81_HUMAN	zinc finger protein 81	320					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(1)|lung(1)|skin(1)	4		all_lung(315;0.0973)				ACTCAGTATATATCTGAGAGT	0.343																																																	0			X											30.0	28.0	29.0					X																	47775003		1853	4096	5949	47659947	SO:0001583	missense	347344			AK126949	CCDS43933.1	Xp11.23	2013-01-08	2006-05-12		ENSG00000197779	ENSG00000197779		"""Zinc fingers, C2H2-type"", ""-"""	13156	protein-coding gene	gene with protein product		314998	"""zinc finger protein 81 (HFZ20)"", ""mental retardation, X-linked 45"""	MRX45		8507979, 15121780	Standard	NM_007137		Approved	HFZ20	uc022bvq.1	P51508	OTTHUMG00000021462	ENST00000376954.1:c.958T>C	X.37:g.47775003T>C	ENSP00000366153:p.Tyr320His		47659947	Q6RX22|Q96QH6	Missense_Mutation	SNP	ENST00000376954.1	37	CCDS43933.1	.	.	.	.	.	.	.	.	.	.	T	4.652	0.121137	0.08881	.	.	ENSG00000197779	ENST00000376954;ENST00000338637	T;T	0.04502	3.61;3.61	4.16	4.16	0.48862	.	0.000000	0.36932	N	0.002325	T	0.00608	0.0020	N	0.00009	-3.09	0.26395	N	0.976514	B	0.13594	0.008	B	0.17433	0.018	T	0.42932	-0.9422	10	0.02654	T	1	.	5.4493	0.16554	0.0:0.1228:0.0:0.8772	.	320	P51508	ZNF81_HUMAN	H	320	ENSP00000366153:Y320H;ENSP00000341151:Y320H	ENSP00000341151:Y320H	Y	+	1	0	ZNF81	47659947	0.986000	0.35501	1.000000	0.80357	0.996000	0.88848	2.980000	0.49321	1.853000	0.53794	0.486000	0.48141	TAT		0.343	ZNF81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056455.2	NM_007137	
DLG3	1741	hgsc.bcm.edu	37	X	69711975	69711975	+	Silent	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chrX:69711975T>C	ENST00000374360.3	+	11	1772	c.1539T>C	c.(1537-1539)gaT>gaC	p.D513D	DLG3_ENST00000194900.4_Silent_p.D531D|DLG3_ENST00000542398.1_Silent_p.D30D|DLG3_ENST00000374355.3_Silent_p.D176D	NM_021120.3	NP_066943.2	Q92796	DLG3_HUMAN	discs, large homolog 3 (Drosophila)	513	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				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)			endometrium(4)|kidney(1)|large_intestine(10)|lung(5)|pancreas(1)|urinary_tract(1)	22	Renal(35;0.156)					TTGATTATGATCGGACTCGGG	0.502																																																	0			X											56.0	31.0	39.0					X																	69711975		2202	4291	6493	69628700	SO:0001819	synonymous_variant	4356			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.1539T>C	X.37:g.69711975T>C			69628700	B4E0H1|D3DVU5|Q5JUW6|Q5JUW7|Q9ULI8	Silent	SNP	ENST00000374360.3	37	CCDS14403.1																																																																																				0.502	DLG3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057074.2	NM_021120	
MED12	9968	hgsc.bcm.edu	37	X	70339907	70339907	+	Missense_Mutation	SNP	C	C	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chrX:70339907C>G	ENST00000374080.3	+	4	472	c.440C>G	c.(439-441)gCc>gGc	p.A147G	MED12_ENST00000374102.1_Missense_Mutation_p.A147G|MED12_ENST00000333646.6_Missense_Mutation_p.A147G			Q93074	MED12_HUMAN	mediator complex subunit 12	147					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					GGGTACTTAGCCAAATACACA	0.473			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome																																	Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	0			X											120.0	113.0	115.0					X																	70339907		1974	4152	6126	70256632	SO:0001583	missense	9968			U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"""trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)"", ""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)"", ""FG syndrome 1"""	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.440C>G	X.37:g.70339907C>G	ENSP00000363193:p.Ala147Gly		70256632	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	37	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	.	20.6	4.010856	0.75046	.	.	ENSG00000184634	ENST00000333646;ENST00000536756;ENST00000374102;ENST00000374080;ENST00000430072	T;T;T;T	0.59638	0.26;0.26;0.26;0.25	5.16	5.16	0.70880	Mediator complex, subunit Med12 (1);	0.000000	0.85682	D	0.000000	T	0.61640	0.2363	L	0.40543	1.245	0.58432	D	0.999998	P;D;P	0.54772	0.486;0.968;0.772	B;P;B	0.54270	0.185;0.747;0.407	T	0.60362	-0.7278	10	0.38643	T	0.18	-13.1395	15.953	0.79859	0.0:1.0:0.0:0.0	.	147;147;147	F5H3Y1;Q93074-3;Q93074	.;.;MED12_HUMAN	G	147;147;147;147;115	ENSP00000333125:A147G;ENSP00000363215:A147G;ENSP00000363193:A147G;ENSP00000414203:A115G	ENSP00000333125:A147G	A	+	2	0	MED12	70256632	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.431000	0.80335	2.391000	0.81399	0.600000	0.82982	GCC		0.473	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120	
PCDH11X	27328	hgsc.bcm.edu	37	X	91133863	91133863	+	Missense_Mutation	SNP	A	A	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chrX:91133863A>C	ENST00000373094.1	+	2	3469	c.2624A>C	c.(2623-2625)aAg>aCg	p.K875T	PCDH11X_ENST00000373097.1_Missense_Mutation_p.K875T|PCDH11X_ENST00000361724.1_Missense_Mutation_p.K875T|PCDH11X_ENST00000361655.2_Missense_Mutation_p.K875T|PCDH11X_ENST00000504220.2_Missense_Mutation_p.K875T|PCDH11X_ENST00000298274.8_Missense_Mutation_p.K875T|PCDH11X_ENST00000395337.2_Missense_Mutation_p.K875T|PCDH11X_ENST00000406881.1_Missense_Mutation_p.K875T|PCDH11X_ENST00000373088.1_Missense_Mutation_p.K875T	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	875	Poly-Lys.				homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						aagaagaagaagCATTCCCCT	0.398																																					NSCLC(38;925 1092 2571 38200 45895)												0			X											82.0	75.0	77.0					X																	91133863		2203	4300	6503	91020519	SO:0001583	missense	83259			AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"""Cadherins / Protocadherins : Non-clustered"""	8656	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 119"""	300246	"""protocadherin 11"""	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.2624A>C	X.37:g.91133863A>C	ENSP00000362186:p.Lys875Thr		91020519	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	37	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	A	11.06	1.527234	0.27299	.	.	ENSG00000102290	ENST00000395337;ENST00000373094;ENST00000373097;ENST00000361724;ENST00000373088;ENST00000504220;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	T;T;T;T;T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4;1.4;1.4;1.4;1.4	4.44	4.44	0.53790	Protocadherin (1);	0.090591	0.56097	D	0.000033	T	0.39332	0.1074	M	0.71581	2.175	0.40946	D	0.984508	B;B;B;B;B;B;B;B	0.28026	0.016;0.165;0.165;0.165;0.165;0.198;0.009;0.009	B;B;B;B;B;B;B;B	0.28011	0.03;0.051;0.051;0.051;0.051;0.085;0.012;0.012	T	0.44862	-0.9300	10	0.72032	D	0.01	.	12.5269	0.56091	1.0:0.0:0.0:0.0	.	875;875;875;875;875;875;875;875	Q9BZA7-6;Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7;Q9BZA7-7;Q9BZA7-2	.;.;.;.;.;PC11X_HUMAN;.;.	T	875	ENSP00000378746:K875T;ENSP00000362186:K875T;ENSP00000362189:K875T;ENSP00000355040:K875T;ENSP00000362180:K875T;ENSP00000423762:K875T;ENSP00000355105:K875T;ENSP00000384758:K875T;ENSP00000298274:K875T	ENSP00000298274:K875T	K	+	2	0	PCDH11X	91020519	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	4.566000	0.60843	1.706000	0.51276	0.486000	0.48141	AAG		0.398	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969	
CRMP1	1400	hgsc.bcm.edu	37	4	5827225	5827225	+	Missense_Mutation	SNP	T	T	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:5827225T>G	ENST00000397890.2	-	13	1837	c.1623A>C	c.(1621-1623)ttA>ttC	p.L541F	CRMP1_ENST00000512574.1_Missense_Mutation_p.L539F|CRMP1_ENST00000324989.7_Missense_Mutation_p.L655F|EVC_ENST00000382674.2_Intron|CRMP1_ENST00000511535.1_5'UTR	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	541					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		TCCTACCTGATAAGCTGAAGT	0.547																																																	0			4											148.0	146.0	147.0					4																	5827225		2203	4300	6503	5878126	SO:0001583	missense	1400			D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.1623A>C	4.37:g.5827225T>G	ENSP00000380987:p.Leu541Phe		5878126	A0EJG6|Q13024|Q4W5F1|Q96TC8	Missense_Mutation	SNP	ENST00000397890.2	37	CCDS43207.1	.	.	.	.	.	.	.	.	.	.	T	17.67	3.447033	0.63178	.	.	ENSG00000072832	ENST00000324989;ENST00000397890;ENST00000534845;ENST00000512574	D;D;D	0.90385	-2.66;-2.48;-2.48	4.13	-3.64	0.04515	.	0.000000	0.64402	D	0.000003	D	0.93572	0.7948	M	0.82193	2.58	0.58432	D	0.99999	D;B;B;D	0.76494	0.999;0.105;0.377;0.992	D;B;B;D	0.76575	0.988;0.068;0.295;0.938	D	0.91387	0.5132	10	0.87932	D	0	-14.4329	10.1534	0.42807	0.0:0.3865:0.0:0.6135	.	655;539;541;478	A0EJG6;E9PD68;Q14194;B3KT07	.;.;DPYL1_HUMAN;.	F	655;541;541;539	ENSP00000321606:L655F;ENSP00000380987:L541F;ENSP00000425742:L539F	ENSP00000321606:L655F	L	-	3	2	CRMP1	5878126	0.797000	0.28877	0.938000	0.37757	0.992000	0.81027	-0.172000	0.09868	-0.815000	0.04346	0.459000	0.35465	TTA		0.547	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313	
CRMP1	1400	hgsc.bcm.edu	37	4	5827227	5827227	+	Missense_Mutation	SNP	A	A	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:5827227A>T	ENST00000397890.2	-	13	1835	c.1621T>A	c.(1621-1623)Tta>Ata	p.L541I	CRMP1_ENST00000512574.1_Missense_Mutation_p.L539I|CRMP1_ENST00000324989.7_Missense_Mutation_p.L655I|EVC_ENST00000382674.2_Intron|CRMP1_ENST00000511535.1_5'UTR	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	541					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		CTACCTGATAAGCTGAAGTTG	0.547																																																	0			4											151.0	148.0	149.0					4																	5827227		2203	4300	6503	5878128	SO:0001583	missense	1400			D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.1621T>A	4.37:g.5827227A>T	ENSP00000380987:p.Leu541Ile		5878128	A0EJG6|Q13024|Q4W5F1|Q96TC8	Missense_Mutation	SNP	ENST00000397890.2	37	CCDS43207.1	.	.	.	.	.	.	.	.	.	.	A	18.10	3.549020	0.65311	.	.	ENSG00000072832	ENST00000324989;ENST00000397890;ENST00000534845;ENST00000512574	D;D;D	0.89485	-2.52;-2.33;-2.32	4.13	1.69	0.24217	.	0.000000	0.64402	D	0.000003	D	0.89385	0.6700	L	0.58810	1.83	0.58432	D	0.999991	D;B;P;P	0.62365	0.991;0.172;0.517;0.894	P;B;B;P	0.58970	0.849;0.077;0.323;0.573	D	0.85083	0.0947	10	0.35671	T	0.21	-14.4329	6.6721	0.23074	0.7218:0.0:0.2782:0.0	.	655;539;541;478	A0EJG6;E9PD68;Q14194;B3KT07	.;.;DPYL1_HUMAN;.	I	655;541;541;539	ENSP00000321606:L655I;ENSP00000380987:L541I;ENSP00000425742:L539I	ENSP00000321606:L655I	L	-	1	2	CRMP1	5878128	1.000000	0.71417	0.953000	0.39169	0.995000	0.86356	3.136000	0.50554	0.270000	0.21984	0.459000	0.35465	TTA		0.547	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313	
SORCS2	57537	hgsc.bcm.edu	37	4	7715969	7715969	+	Silent	SNP	C	C	T	rs540252369	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:7715969C>T	ENST00000507866.2	+	16	2101	c.1992C>T	c.(1990-1992)ggC>ggT	p.G664G	SORCS2_ENST00000329016.9_Silent_p.G492G	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	664					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						TGCTGCAGGGCGACCGCTGTA	0.602													C|||	2	0.000399361	0.0	0.0029	5008	,	,		20055	0.0		0.0	False		,,,				2504	0.0																0			4											34.0	37.0	36.0					4																	7715969		2078	4214	6292	7766869	SO:0001819	synonymous_variant	57537			AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.1992C>T	4.37:g.7715969C>T			7766869	Q9P2L7	Silent	SNP	ENST00000507866.2	37	CCDS47008.1																																																																																				0.602	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777	
BST1	683	hgsc.bcm.edu	37	4	15707179	15707179	+	Missense_Mutation	SNP	C	C	T	rs2302466		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:15707179C>T	ENST00000265016.4	+	2	425	c.230C>T	c.(229-231)gCg>gTg	p.A77V	BST1_ENST00000382346.3_Missense_Mutation_p.A92V	NM_004334.2	NP_004325.2	Q10588	BST1_HUMAN	bone marrow stromal cell antigen 1	77			A -> V (in dbSNP:rs2302466).		humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|transferase activity (GO:0016740)			central_nervous_system(1)|large_intestine(1)|lung(2)|stomach(3)|urinary_tract(1)	8						TTTAAAGTGGCGCTGGACAAG	0.468													C|||	1	0.000199681	0.0	0.0	5008	,	,		20677	0.001		0.0	False		,,,				2504	0.0																0			4						C	VAL/ALA	0,4406		0,0,2203	139.0	125.0	130.0		230	4.4	1.0	4	dbSNP_100	130	1,8599	1.2+/-3.3	0,1,4299	yes	missense	BST1	NM_004334.2	64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	77/319	15707179	1,13005	2203	4300	6503	15316277	SO:0001583	missense	683			D21878	CCDS3416.1	4p15	2010-05-04			ENSG00000109743	ENSG00000109743	3.2.2.5	"""CD molecules"""	1118	protein-coding gene	gene with protein product	"""NAD(+) nucleosidase"", ""ADP-ribosyl cyclase 2"""	600387				8202488	Standard	NM_004334		Approved	CD157	uc003goh.4	Q10588	OTTHUMG00000097739	ENST00000265016.4:c.230C>T	4.37:g.15707179C>T	ENSP00000265016:p.Ala77Val		15316277	B2R6A2|Q1XII0|Q5U0K0|Q96EN3	Missense_Mutation	SNP	ENST00000265016.4	37	CCDS3416.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	8.909	0.958139	0.18507	0.0	1.16E-4	ENSG00000109743	ENST00000265016;ENST00000382346	T;T	0.24908	1.83;1.83	5.72	4.45	0.53987	.	0.128393	0.51477	N	0.000090	T	0.05456	0.0144	N	0.00142	-2.005	0.26652	N	0.972072	B	0.14438	0.01	B	0.04013	0.001	T	0.26710	-1.0095	10	0.22706	T	0.39	-15.4407	8.4747	0.33005	0.0:0.0897:0.0:0.9103	rs2302466;rs2302466	77	Q10588	BST1_HUMAN	V	77;92	ENSP00000265016:A77V;ENSP00000371783:A92V	ENSP00000265016:A77V	A	+	2	0	BST1	15316277	0.980000	0.34600	0.994000	0.49952	0.245000	0.25701	1.889000	0.39718	0.995000	0.38917	-0.303000	0.09236	GCG		0.468	BST1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214968.2	NM_004334	
TMPRSS11A	339967	hgsc.bcm.edu	37	4	68795672	68795672	+	Missense_Mutation	SNP	A	A	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:68795672A>T	ENST00000334830.7	-	5	1162	c.416T>A	c.(415-417)aTc>aAc	p.I139N	TMPRSS11A_ENST00000508048.1_Missense_Mutation_p.I135N|TMPRSS11A_ENST00000396188.2_Missense_Mutation_p.I136N|UBA6-AS1_ENST00000500538.2_RNA			Q6ZMR5	TM11A_HUMAN	transmembrane protease, serine 11A	139	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|cervix(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	29						GATGCTTTGGATTTTCTTCTC	0.403																																					NSCLC(26;2 894 10941 14480 22546)												0			4											189.0	169.0	176.0					4																	68795672		2203	4300	6503	68478267	SO:0001583	missense	339967			AF071882	CCDS3519.1	4q13.2	2010-04-13			ENSG00000187054	ENSG00000187054		"""Serine peptidases / Transmembrane"""	27954	protein-coding gene	gene with protein product		611704				15328353	Standard	NM_182606		Approved	ECRG1	uc003hdr.1	Q6ZMR5	OTTHUMG00000129303	ENST00000334830.7:c.416T>A	4.37:g.68795672A>T	ENSP00000334611:p.Ile139Asn		68478267	J3KNQ8|Q2NKI9|Q6JE90|Q7RTY4|Q86TK8	Missense_Mutation	SNP	ENST00000334830.7	37	CCDS3519.1	.	.	.	.	.	.	.	.	.	.	A	12.35	1.912354	0.33721	.	.	ENSG00000187054	ENST00000508048;ENST00000334830;ENST00000396188;ENST00000513536	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	6.07	4.87	0.63330	SEA (1);	0.350049	0.24206	N	0.040580	T	0.44664	0.1304	M	0.76002	2.32	0.22620	N	0.99892	P;P	0.50369	0.934;0.934	P;P	0.47528	0.549;0.549	T	0.47045	-0.9147	10	0.87932	D	0	.	9.2693	0.37661	0.8339:0.0:0.0:0.1661	.	136;139	B5MDI9;Q6ZMR5	.;TM11A_HUMAN	N	135;139;136;116	ENSP00000426911:I135N;ENSP00000334611:I139N;ENSP00000379491:I136N;ENSP00000427621:I116N	ENSP00000334611:I139N	I	-	2	0	TMPRSS11A	68478267	0.997000	0.39634	0.066000	0.19879	0.048000	0.14542	1.224000	0.32539	1.073000	0.40885	0.533000	0.62120	ATC		0.403	TMPRSS11A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251433.3	NM_182606	
FRAS1	80144	hgsc.bcm.edu	37	4	79158685	79158685	+	Missense_Mutation	SNP	G	G	A	rs568676550		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:79158685G>A	ENST00000325942.6	+	3	570	c.130G>A	c.(130-132)Gat>Aat	p.D44N	FRAS1_ENST00000264895.6_Missense_Mutation_p.D44N|FRAS1_ENST00000264899.6_Missense_Mutation_p.D44N	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	44	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)	p.D44N(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						TTGGAAGCCCGATTCATGCCA	0.448													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19895	0.0		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	ovary(1)	4											80.0	79.0	79.0					4																	79158685		1983	4160	6143	79377709	SO:0001583	missense	80144			AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.130G>A	4.37:g.79158685G>A	ENSP00000326330:p.Asp44Asn		79377709	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	37	CCDS54772.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.772688	0.90108	.	.	ENSG00000138759	ENST00000325942;ENST00000264895;ENST00000264899;ENST00000380674	T;T;T	0.68903	-0.36;-0.36;-0.36	5.14	5.14	0.70334	.	0.133258	0.49305	D	0.000154	T	0.81456	0.4826	M	0.71920	2.185	0.50632	D	0.999887	D;D	0.89917	1.0;1.0	D;D	0.83275	0.951;0.996	T	0.83078	-0.0139	10	0.66056	D	0.02	.	17.7499	0.88430	0.0:0.0:1.0:0.0	.	44;44	E9PHH6;A2RRR8	.;.	N	44	ENSP00000326330:D44N;ENSP00000264895:D44N;ENSP00000264899:D44N	ENSP00000264895:D44N	D	+	1	0	FRAS1	79377709	1.000000	0.71417	0.993000	0.49108	0.997000	0.91878	4.876000	0.63079	2.560000	0.86352	0.467000	0.42956	GAT		0.448	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
PTPN13	5783	hgsc.bcm.edu	37	4	87731014	87731014	+	Missense_Mutation	SNP	C	C	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:87731014C>G	ENST00000411767.2	+	46	7239	c.7176C>G	c.(7174-7176)atC>atG	p.I2392M	PTPN13_ENST00000427191.2_Missense_Mutation_p.I2373M|PTPN13_ENST00000316707.6_Missense_Mutation_p.I2201M|PTPN13_ENST00000511467.1_Missense_Mutation_p.I2397M|PTPN13_ENST00000436978.1_Missense_Mutation_p.I2397M			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	2392	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TTACTTTTATCTCCTACATGA	0.473																																																	0			4											168.0	153.0	158.0					4																	87731014		1971	4155	6126	87950038	SO:0001583	missense	5783				CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.7176C>G	4.37:g.87731014C>G	ENSP00000407249:p.Ile2392Met		87950038	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.213074	0.58452	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	D;D;D;D;D	0.85013	-1.93;-1.93;-1.93;-1.93;-1.93	5.38	4.52	0.55395	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.52532	D	0.000070	D	0.89921	0.6855	M	0.64170	1.965	0.46654	D	0.999142	D;D;D;D	0.89917	0.997;0.999;1.0;0.999	D;D;D;D	0.97110	0.988;0.999;1.0;1.0	D	0.89986	0.4104	10	0.87932	D	0	.	10.0341	0.42118	0.1371:0.7905:0.0:0.0724	.	2201;2373;2392;2397	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	M	2373;2397;2201;2392;2397;2341	ENSP00000408368:I2373M;ENSP00000394794:I2397M;ENSP00000322675:I2201M;ENSP00000407249:I2392M;ENSP00000426626:I2397M	ENSP00000322675:I2201M	I	+	3	3	PTPN13	87950038	0.999000	0.42202	0.995000	0.50966	0.933000	0.57130	0.680000	0.25306	1.236000	0.43740	0.655000	0.94253	ATC		0.473	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
TRPC3	7222	hgsc.bcm.edu	37	4	122824123	122824123	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:122824123C>T	ENST00000379645.3	-	9	2420	c.2347G>A	c.(2347-2349)Gtt>Att	p.V783I	TRPC3_ENST00000513531.1_Missense_Mutation_p.V655I|TRPC3_ENST00000264811.5_Missense_Mutation_p.V710I	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	698	Binds to IP3R3.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						GGACTAGGAACTAGACTGAAA	0.378																																																	0			4											113.0	110.0	111.0					4																	122824123		2203	4300	6503	123043573	SO:0001583	missense	7222			Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.2347G>A	4.37:g.122824123C>T	ENSP00000368966:p.Val783Ile		123043573	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Missense_Mutation	SNP	ENST00000379645.3	37	CCDS47130.1	.	.	.	.	.	.	.	.	.	.	C	13.95	2.391188	0.42410	.	.	ENSG00000138741	ENST00000264811;ENST00000379645;ENST00000513531	D;D;D	0.83163	-1.69;-1.69;-1.69	5.77	5.77	0.91146	.	0.000000	0.64402	D	0.000002	T	0.68833	0.3044	N	0.11364	0.135	0.58432	D	0.999999	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.17979	0.003;0.005;0.02	T	0.65524	-0.6147	10	0.02654	T	1	-11.259	19.9944	0.97379	0.0:1.0:0.0:0.0	.	698;655;783	Q13507;E9PCJ9;Q5G1L5	TRPC3_HUMAN;.;.	I	710;783;655	ENSP00000264811:V710I;ENSP00000368966:V783I;ENSP00000426899:V655I	ENSP00000264811:V710I	V	-	1	0	TRPC3	123043573	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.855000	0.62925	2.720000	0.93068	0.557000	0.71058	GTT		0.378	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305	
SPOCK3	50859	hgsc.bcm.edu	37	4	167656168	167656168	+	Silent	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:167656168T>C	ENST00000357154.3	-	12	1352	c.1215A>G	c.(1213-1215)gaA>gaG	p.E405E	SPOCK3_ENST00000535728.1_Silent_p.E273E|SPOCK3_ENST00000504953.1_Silent_p.E402E|SPOCK3_ENST00000541354.1_Silent_p.E285E|SPOCK3_ENST00000511531.1_Silent_p.E405E|SPOCK3_ENST00000511269.1_Silent_p.E402E|SPOCK3_ENST00000541637.1_Silent_p.E307E|SPOCK3_ENST00000510741.1_Silent_p.E362E|SPOCK3_ENST00000502330.1_Silent_p.E405E|SPOCK3_ENST00000357545.4_Silent_p.E402E|SPOCK3_ENST00000506886.1_Silent_p.E405E|SPOCK3_ENST00000534949.1_Silent_p.E309E|SPOCK3_ENST00000421836.2_Silent_p.E354E|SPOCK3_ENST00000512681.1_Silent_p.E307E|SPOCK3_ENST00000507137.1_5'UTR	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	405	Asp-rich.			E -> G (in Ref. 4; BAG58265). {ECO:0000305}.	negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		taatatcgtcttcatcatcct	0.353																																																	0			4											193.0	179.0	184.0					4																	167656168		2203	4299	6502	167892743	SO:0001819	synonymous_variant	50859			AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.1215A>G	4.37:g.167656168T>C			167892743	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Silent	SNP	ENST00000357154.3	37	CCDS54817.1																																																																																				0.353	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1		
NEK1	4750	hgsc.bcm.edu	37	4	170523707	170523707	+	Silent	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:170523707T>C	ENST00000439128.2	-	2	715	c.75A>G	c.(73-75)gaA>gaG	p.E25E	NEK1_ENST00000512193.1_Silent_p.E25E|NEK1_ENST00000511633.1_Silent_p.E25E|NEK1_ENST00000510533.1_Silent_p.E25E|NEK1_ENST00000507142.1_Silent_p.E25E	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	25	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> K (in a lung large cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		GTCTGCCATCTTCTGTAGATT	0.323																																																	0			4											148.0	144.0	145.0					4																	170523707		1813	4073	5886	170760282	SO:0001819	synonymous_variant	4750			AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"""NIMA (never in mitosis gene a)-related kinase 1"""			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.75A>G	4.37:g.170523707T>C			170760282	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Silent	SNP	ENST00000439128.2	37	CCDS47162.1																																																																																				0.323	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3		
APOB	338	hgsc.bcm.edu	37	2	21233814	21233814	+	Missense_Mutation	SNP	C	C	T	rs267599184		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:21233814C>T	ENST00000233242.1	-	26	6053	c.5926G>A	c.(5926-5928)Gag>Aag	p.E1976K		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1976					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.E1976*(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCTGTCTGCTCAGCTGGAGTA	0.453																																																	1	Substitution - Nonsense(1)	skin(1)	2											146.0	136.0	140.0					2																	21233814		2203	4300	6503	21087319	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.5926G>A	2.37:g.21233814C>T	ENSP00000233242:p.Glu1976Lys		21087319	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	C	18.27	3.585906	0.66105	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.01240	5.12	5.46	5.46	0.80206	.	0.000000	0.56097	D	0.000023	T	0.09335	0.0230	M	0.79475	2.455	0.80722	D	1	D	0.76494	0.999	D	0.68192	0.956	T	0.00549	-1.1676	10	0.72032	D	0.01	.	19.2954	0.94119	0.0:1.0:0.0:0.0	.	1976	P04114	APOB_HUMAN	K	1976	ENSP00000233242:E1976K	ENSP00000233242:E1976K	E	-	1	0	APOB	21087319	0.938000	0.31826	0.995000	0.50966	0.942000	0.58702	2.074000	0.41529	2.554000	0.86153	0.555000	0.69702	GAG		0.453	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
APOB	338	hgsc.bcm.edu	37	2	21238336	21238336	+	Silent	SNP	G	G	A	rs140456702		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:21238336G>A	ENST00000233242.1	-	22	3541	c.3414C>T	c.(3412-3414)ctC>ctT	p.L1138L		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1138					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACCAGTGGGCGAGGATCTCAC	0.463																																																	0			2						G		1,4405	2.1+/-5.4	0,1,2202	144.0	131.0	135.0		3414	-3.4	0.0	2	dbSNP_134	135	0,8600		0,0,4300	no	coding-synonymous	APOB	NM_000384.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1138/4564	21238336	1,13005	2203	4300	6503	21091841	SO:0001819	synonymous_variant	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.3414C>T	2.37:g.21238336G>A			21091841	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																				0.463	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
DPP10	57628	hgsc.bcm.edu	37	2	116534842	116534842	+	Missense_Mutation	SNP	A	A	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:116534842A>T	ENST00000410059.1	+	14	1760	c.1280A>T	c.(1279-1281)aAg>aTg	p.K427M	DPP10_ENST00000393147.2_Missense_Mutation_p.K431M|DPP10_ENST00000409163.1_Missense_Mutation_p.K377M|DPP10_ENST00000310323.8_Missense_Mutation_p.K420M	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	427						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						GAAGTGATAAAGATCTTGGCA	0.363																																																	0			2											119.0	114.0	116.0					2																	116534842		2203	4299	6502	116251312	SO:0001583	missense	57628			AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"""dipeptidylpeptidase 10"", ""dipeptidyl-peptidase 10"""			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.1280A>T	2.37:g.116534842A>T	ENSP00000386565:p.Lys427Met		116251312	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	37	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	A	15.54	2.862491	0.51482	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323;ENST00000476155	T;T;T;T	0.32272	1.46;1.46;1.46;1.46	4.97	2.63	0.31362	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.160378	0.53938	D	0.000047	T	0.43722	0.1260	M	0.80746	2.51	0.38323	D	0.943576	B;P;B;B	0.50943	0.165;0.94;0.198;0.198	B;P;B;B	0.52386	0.217;0.697;0.239;0.324	T	0.47824	-0.9087	10	0.72032	D	0.01	-11.4582	7.2268	0.26020	0.8099:0.0:0.1901:0.0	.	420;431;423;427	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	M	427;377;431;420;377	ENSP00000386565:K427M;ENSP00000387038:K377M;ENSP00000376855:K431M;ENSP00000309066:K420M	ENSP00000309066:K420M	K	+	2	0	DPP10	116251312	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.099000	0.50267	0.477000	0.27464	0.533000	0.62120	AAG		0.363	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868	
LRP1B	53353	hgsc.bcm.edu	37	2	141643869	141643869	+	Missense_Mutation	SNP	G	G	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:141643869G>C	ENST00000389484.3	-	24	4773	c.3802C>G	c.(3802-3804)Cat>Gat	p.H1268D		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1268					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CTGATCTCATGACGAATAGAA	0.313										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)												0			2											71.0	71.0	71.0					2																	141643869		2203	4300	6503	141360339	SO:0001583	missense	53353			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.3802C>G	2.37:g.141643869G>C	ENSP00000374135:p.His1268Asp		141360339	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	19.51	3.841985	0.71488	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.90676	-2.71;-2.71	5.78	5.78	0.91487	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.95284	0.8470	M	0.75884	2.315	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.78314	0.978;0.991	D	0.94421	0.7641	10	0.48119	T	0.1	.	20.0175	0.97485	0.0:0.0:1.0:0.0	.	451;1268	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	D	1268;1206;413	ENSP00000374135:H1268D;ENSP00000413239:H413D	ENSP00000374135:H1268D	H	-	1	0	LRP1B	141360339	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.805000	0.86005	2.730000	0.93505	0.650000	0.86243	CAT		0.313	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
NEB	4703	hgsc.bcm.edu	37	2	152359931	152359931	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:152359931T>C	ENST00000172853.10	-	138	18811	c.18664A>G	c.(18664-18666)Aca>Gca	p.T6222A	NEB_ENST00000427231.2_Missense_Mutation_p.T7923A|NEB_ENST00000509223.2_Missense_Mutation_p.T53A|NEB_ENST00000603639.1_Missense_Mutation_p.T7923A|NEB_ENST00000498015.2_Intron|NEB_ENST00000397345.3_Missense_Mutation_p.T7923A|NEB_ENST00000409198.1_Missense_Mutation_p.T6222A|NEB_ENST00000397336.2_5'UTR|NEB_ENST00000604864.1_Missense_Mutation_p.T7923A			P20929	NEBU_HUMAN	nebulin	6222					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GGAATGCCTGTTCCCAAGTTT	0.363																																																	0			2											90.0	86.0	87.0					2																	152359931		1833	4091	5924	152068177	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.18664A>G	2.37:g.152359931T>C	ENSP00000172853:p.Thr6222Ala		152068177	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.26|14.26	2.482567|2.482567	0.44147|0.44147	.|.	.|.	ENSG00000183091|ENSG00000183091	ENST00000421461|ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853;ENST00000509223;ENST00000424585	.|T;T;T;T;T;T;T	.|0.09911	.|3.38;3.37;3.38;3.31;3.38;4.18;2.93	5.38|5.38	5.38|5.38	0.77491|0.77491	.|.	.|0.667376	.|0.16500	.|N	.|0.211717	T|T	0.19208|0.19208	0.0461|0.0461	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	.|B;B;B;B;D;B	.|0.58268	.|0.004;0.002;0.015;0.288;0.982;0.039	.|B;B;B;B;D;B	.|0.67548	.|0.017;0.003;0.041;0.137;0.952;0.127	T|T	0.03354|0.03354	-1.1045|-1.1045	5|10	.|0.23891	.|T	.|0.37	.|.	12.2413|12.2413	0.54544|0.54544	0.0:0.0:0.1419:0.8581|0.0:0.0:0.1419:0.8581	.|.	.|53;53;6222;7923;2653;7923	.|B7Z6B9;B7Z6P9;P20929;F8WCP0;Q14215;F8WCL5	.|.;.;NEBU_HUMAN;.;.;.	S|A	99|6222;7923;7923;2271;2653;6222;53;150	.|ENSP00000386259:T6222A;ENSP00000380505:T7923A;ENSP00000416578:T7923A;ENSP00000410961:T2653A;ENSP00000172853:T6222A;ENSP00000427083:T53A;ENSP00000404876:T150A	.|ENSP00000172853:T6222A	N|T	-|-	2|1	0|0	NEB|NEB	152068177|152068177	0.996000|0.996000	0.38824|0.38824	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.579000|1.579000	0.36536|0.36536	2.169000|2.169000	0.68431|0.68431	0.528000|0.528000	0.53228|0.53228	AAC|ACA		0.363	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
NEB	4703	hgsc.bcm.edu	37	2	152406166	152406166	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:152406166C>T	ENST00000172853.10	-	102	15077	c.14930G>A	c.(14929-14931)cGt>cAt	p.R4977H	NEB_ENST00000427231.2_Missense_Mutation_p.R6678H|NEB_ENST00000603639.1_Missense_Mutation_p.R6678H|NEB_ENST00000397345.3_Missense_Mutation_p.R6678H|NEB_ENST00000409198.1_Missense_Mutation_p.R4977H|NEB_ENST00000604864.1_Missense_Mutation_p.R6678H			P20929	NEBU_HUMAN	nebulin	4977					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GCTCATGTAACGGGTGTCCTT	0.478																																																	0			2											124.0	121.0	122.0					2																	152406166		1954	4168	6122	152114412	SO:0001583	missense	4703			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.14930G>A	2.37:g.152406166C>T	ENSP00000172853:p.Arg4977His		152114412	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	16.88	3.243729	0.58995	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853	T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87	6.16	4.16	0.48862	.	0.358373	0.32687	N	0.005765	T	0.50480	0.1618	L	0.47716	1.5	0.58432	D	0.999999	P;D	0.76494	0.87;0.999	P;D	0.78314	0.667;0.991	T	0.51419	-0.8708	10	0.51188	T	0.08	.	4.9222	0.13876	0.0:0.6757:0.0:0.3243	.	4977;1408	P20929;Q14215	NEBU_HUMAN;.	H	4977;6678;6678;1026;1408;4977	ENSP00000386259:R4977H;ENSP00000380505:R6678H;ENSP00000416578:R6678H;ENSP00000410961:R1408H;ENSP00000172853:R4977H	ENSP00000172853:R4977H	R	-	2	0	NEB	152114412	0.951000	0.32395	0.188000	0.23233	0.384000	0.30261	1.892000	0.39748	1.623000	0.50342	0.650000	0.86243	CGT		0.478	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
ITGB6	3694	hgsc.bcm.edu	37	2	161051889	161051889	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:161051889T>C	ENST00000283249.2	-	4	821	c.584A>G	c.(583-585)aAc>aGc	p.N195S	ITGB6_ENST00000428609.2_Missense_Mutation_p.N153S|ITGB6_ENST00000409872.1_Missense_Mutation_p.N195S|ITGB6_ENST00000409967.2_Missense_Mutation_p.N195S|ITGB6_ENST00000485635.1_5'UTR	NM_001282353.1|NM_001282354.1|NM_001282388.1	NP_001269282.1|NP_001269283.1|NP_001269317.1	P18564	ITB6_HUMAN	integrin, beta 6	195	VWFA.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|multicellular organismal development (GO:0007275)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23						CCTGCAAGGGTTGGCAATTTC	0.443																																																	0			2											93.0	99.0	97.0					2																	161051889		2203	4300	6503	160760135	SO:0001583	missense	3694				CCDS2212.1, CCDS63040.1, CCDS74596.1, CCDS74597.1	2q24.2	2010-03-23			ENSG00000115221	ENSG00000115221		"""Integrins"""	6161	protein-coding gene	gene with protein product		147558				1729173, 8120056	Standard	NM_001282353		Approved		uc002ubh.2	P18564	OTTHUMG00000132026	ENST00000283249.2:c.584A>G	2.37:g.161051889T>C	ENSP00000283249:p.Asn195Ser		160760135	B2R9W5|C9JA97|Q0VA95|Q16500|Q53RG5|Q53RR6	Missense_Mutation	SNP	ENST00000283249.2	37	CCDS2212.1	.	.	.	.	.	.	.	.	.	.	T	14.73	2.622898	0.46840	.	.	ENSG00000115221	ENST00000283249;ENST00000428609;ENST00000409967;ENST00000409872	D;D;D;D	0.97941	-4.62;-4.62;-4.62;-4.62	6.05	6.05	0.98169	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.000000	0.85682	D	0.000000	D	0.96719	0.8929	M	0.70275	2.135	0.51233	D	0.999915	B;B	0.19445	0.036;0.036	B;B	0.16722	0.016;0.016	D	0.94631	0.7822	10	0.39692	T	0.17	.	16.5932	0.84781	0.0:0.0:0.0:1.0	.	153;195	E9PEE8;P18564	.;ITB6_HUMAN	S	195;153;195;195	ENSP00000283249:N195S;ENSP00000408024:N153S;ENSP00000386828:N195S;ENSP00000386367:N195S	ENSP00000283249:N195S	N	-	2	0	ITGB6	160760135	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	7.991000	0.88244	2.320000	0.78422	0.528000	0.53228	AAC		0.443	ITGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255036.1	NM_000888	
FIGN	55137	hgsc.bcm.edu	37	2	164466675	164466675	+	Missense_Mutation	SNP	A	A	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:164466675A>T	ENST00000333129.3	-	3	1981	c.1667T>A	c.(1666-1668)gTc>gAc	p.V556D	FIGN_ENST00000482917.1_5'Flank|FIGN_ENST00000409634.1_Intron	NM_018086.2	NP_060556.2	Q5HY92	FIGN_HUMAN	fidgetin	556					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)			breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(1)|prostate(2)|skin(1)	47						CCACTTGGCGACTAGTCCAGA	0.483																																																	0			2											57.0	56.0	56.0					2																	164466675		1925	4125	6050	164174921	SO:0001583	missense	55137			AK001267	CCDS2221.2	2q24	2010-04-21			ENSG00000182263	ENSG00000182263		"""ATPases / AAA-type"""	13285	protein-coding gene	gene with protein product		605295				11017077	Standard	XM_005246661		Approved		uc002uck.1	Q5HY92	OTTHUMG00000074059	ENST00000333129.3:c.1667T>A	2.37:g.164466675A>T	ENSP00000333836:p.Val556Asp		164174921	B3KWM0|Q9H6M5|Q9NVZ9	Missense_Mutation	SNP	ENST00000333129.3	37	CCDS2221.2	.	.	.	.	.	.	.	.	.	.	A	15.19	2.760674	0.49468	.	.	ENSG00000182263	ENST00000333129	D	0.95447	-3.71	5.36	5.36	0.76844	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.059606	0.64402	D	0.000003	D	0.96710	0.8926	L	0.50993	1.605	0.80722	D	1	D	0.69078	0.997	D	0.79784	0.993	D	0.97421	1.0009	10	0.87932	D	0	-7.8026	15.6507	0.77091	1.0:0.0:0.0:0.0	.	556	Q5HY92	FIGN_HUMAN	D	556	ENSP00000333836:V556D	ENSP00000333836:V556D	V	-	2	0	FIGN	164174921	1.000000	0.71417	0.098000	0.21074	0.962000	0.63368	7.468000	0.80943	2.163000	0.67991	0.460000	0.39030	GTC		0.483	FIGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157220.2	NM_018086	
DUSP19	142679	hgsc.bcm.edu	37	2	183960266	183960266	+	Silent	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:183960266T>C	ENST00000354221.4	+	4	709	c.534T>C	c.(532-534)tcT>tcC	p.S178S	AC064871.3_ENST00000444562.1_RNA|DUSP19_ENST00000469344.1_3'UTR|AC064871.3_ENST00000413954.1_RNA|DUSP19_ENST00000342619.6_Silent_p.S127S	NM_080876.3	NP_543152.1	Q8WTR2	DUS19_HUMAN	dual specificity phosphatase 19	178	Tyrosine-protein phosphatase.				inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase activity (GO:0045860)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	JUN kinase phosphatase activity (GO:0008579)|MAP-kinase scaffold activity (GO:0005078)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase activator activity (GO:0030295)|protein kinase inhibitor activity (GO:0004860)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/threonine phosphatase activity (GO:0008330)			breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(4)|pancreas(1)	17						GTGCTTTTTCTTTGGTGAAAA	0.408																																																	0			2											135.0	138.0	137.0					2																	183960266		2203	4300	6503	183668511	SO:0001819	synonymous_variant	142679			AB038770	CCDS2289.1, CCDS46469.1	2q32.1	2011-06-09			ENSG00000162999	ENSG00000162999		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	18894	protein-coding gene	gene with protein product		611437					Standard	NM_080876		Approved	SKRP1, DUSP17	uc002upd.3	Q8WTR2	OTTHUMG00000132622	ENST00000354221.4:c.534T>C	2.37:g.183960266T>C			183668511	B2RA79|Q547H4|Q8WYN4	Silent	SNP	ENST00000354221.4	37	CCDS2289.1																																																																																				0.408	DUSP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255866.1		
ALPI	248	hgsc.bcm.edu	37	2	233321912	233321912	+	Silent	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr2:233321912C>T	ENST00000295463.3	+	5	605	c.528C>T	c.(526-528)gcC>gcT	p.A176A		NM_001631.3	NP_001622.2	P09923	PPBI_HUMAN	alkaline phosphatase, intestinal	176					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(2)|upper_aerodigestive_tract(1)	24		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)		CCTCGCCAGCCGGCACCTACG	0.622																																																	0			2											68.0	68.0	68.0					2																	233321912		2203	4300	6503	233030156	SO:0001819	synonymous_variant	248			M15694	CCDS2492.1	2q37.1	2008-02-05			ENSG00000163295	ENSG00000163295	3.1.3.1		437	protein-coding gene	gene with protein product		171740				3468508, 3469665	Standard	NM_001631		Approved		uc002vst.4	P09923	OTTHUMG00000133258	ENST00000295463.3:c.528C>T	2.37:g.233321912C>T			233030156	B2R7Y4|Q53S80|Q9UBV5|Q9UCL2	Silent	SNP	ENST00000295463.3	37	CCDS2492.1																																																																																				0.622	ALPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257035.2	NM_001631	
JAK2	3717	hgsc.bcm.edu	37	9	5070026	5070026	+	Missense_Mutation	SNP	A	A	G	rs121912473		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr9:5070026A>G	ENST00000381652.3	+	12	2109	c.1615A>G	c.(1615-1617)Aaa>Gaa	p.K539E	JAK2_ENST00000544510.1_Missense_Mutation_p.K390E|JAK2_ENST00000539801.1_Missense_Mutation_p.K539E	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	539			FHK -> L (in myeloproliferative disorder with erythrocytosis). {ECO:0000269|PubMed:17267906}.|HK -> QL (in myeloproliferative disorder with erythrocytosis).|K -> L (in myeloproliferative disorder with erythrocytosis; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:17267906}.		actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)	p.K539L(15)|p.F537_K539>L(13)|p.H538_K539>L(10)|p.H538_K539>QL(4)|p.H538_K539>F(1)|p.H538_K539del(1)|p.H538_K539>I(1)|p.K539E(1)|p.F537_K539>R(1)	BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	GGTGTTTCACAAAATCAGAAA	0.323		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial																															Dom	yes		9	9p24	3717	Janus kinase 2		L	47	Complex - deletion inframe(26)|Substitution - Missense(16)|Complex - compound substitution(4)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(47)	9											86.0	81.0	83.0					9																	5070026		2202	4300	6502	5060026	SO:0001583	missense	3717	Familial Cancer Database			CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"""SH2 domain containing"""	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1615A>G	9.37:g.5070026A>G	ENSP00000371067:p.Lys539Glu		5060026	O14636|O75297	Missense_Mutation	SNP	ENST00000381652.3	37	CCDS6457.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.502094	0.85176	.	.	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	T;T;T	0.23552	1.9;1.9;1.9	5.07	5.07	0.68467	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.42359	0.1199	M	0.77103	2.36	0.80722	D	1	D	0.58620	0.983	P	0.51101	0.659	T	0.48747	-0.9008	10	0.66056	D	0.02	-24.3061	14.4823	0.67592	1.0:0.0:0.0:0.0	.	539	O60674	JAK2_HUMAN	E	539;539;390	ENSP00000440387:K539E;ENSP00000371067:K539E;ENSP00000443103:K390E	ENSP00000371067:K539E	K	+	1	0	JAK2	5060026	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.912000	0.92726	1.892000	0.54788	0.455000	0.32223	AAA		0.323	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1		
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18777556	18777556	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr9:18777556G>A	ENST00000380548.4	+	19	3668	c.3329G>A	c.(3328-3330)cGc>cAc	p.R1110H		NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	1110						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		GAGATCTTCCGCAGCCACCTG	0.647																																																	0			9											19.0	23.0	22.0					9																	18777556		2053	4188	6241	18767556	SO:0001583	missense	92949			AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"""Immunoglobulin superfamily / I-set domain containing"""	14632	protein-coding gene	gene with protein product	"""punctin"""	609198	"""chromosome 9 open reading frame 94"""	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.3329G>A	9.37:g.18777556G>A	ENSP00000369921:p.Arg1110His		18767556	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Missense_Mutation	SNP	ENST00000380548.4	37	CCDS47954.1	.	.	.	.	.	.	.	.	.	.	G	16.73	3.204596	0.58234	.	.	ENSG00000178031	ENST00000380548	T	0.63744	-0.06	5.88	4.99	0.66335	.	0.063246	0.08080	U	1.000000	T	0.47746	0.1462	N	0.14661	0.345	0.80722	D	1	B	0.14438	0.01	B	0.06405	0.002	T	0.31392	-0.9945	10	0.66056	D	0.02	.	9.7332	0.40374	0.1962:0.0:0.8038:0.0	.	1110	Q8N6G6	ATL1_HUMAN	H	1110	ENSP00000369921:R1110H	ENSP00000369921:R1110H	R	+	2	0	ADAMTSL1	18767556	0.999000	0.42202	1.000000	0.80357	0.813000	0.45954	0.469000	0.22067	1.502000	0.48669	0.557000	0.71058	CGC		0.647	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		
TAF1L	138474	hgsc.bcm.edu	37	9	32630107	32630107	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr9:32630107T>C	ENST00000242310.4	-	1	5560	c.5471A>G	c.(5470-5472)cAc>cGc	p.H1824R		NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1824			H -> Q (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TCATTTTCCGTGCCCATCCTT	0.498																																																	0			9											191.0	138.0	156.0					9																	32630107		2203	4300	6503	32620107	SO:0001583	missense	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.5471A>G	9.37:g.32630107T>C	ENSP00000418379:p.His1824Arg		32620107	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	T	7.702	0.693292	0.15039	.	.	ENSG00000122728	ENST00000242310	T	0.06933	3.24	0.479	0.479	0.16796	.	0.268520	0.39341	N	0.001400	T	0.03178	0.0093	N	0.08118	0	0.20307	N	0.999911	B	0.24186	0.099	B	0.12156	0.007	T	0.41910	-0.9482	10	0.28530	T	0.3	.	5.1959	0.15236	0.0:1.0E-4:0.0:0.9999	.	1824	Q8IZX4	TAF1L_HUMAN	R	1824	ENSP00000418379:H1824R	ENSP00000418379:H1824R	H	-	2	0	TAF1L	32620107	1.000000	0.71417	0.981000	0.43875	0.135000	0.20990	0.972000	0.29409	0.426000	0.26116	0.164000	0.16699	CAC		0.498	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
RNF38	152006	hgsc.bcm.edu	37	9	36356448	36356448	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr9:36356448T>C	ENST00000259605.6	-	6	868	c.761A>G	c.(760-762)cAg>cGg	p.Q254R	RNF38_ENST00000377885.2_Missense_Mutation_p.Q171R|RNF38_ENST00000377877.4_Missense_Mutation_p.Q178R|RNF38_ENST00000491349.1_5'UTR|RNF38_ENST00000357058.3_Missense_Mutation_p.Q171R|RNF38_ENST00000350199.4_Missense_Mutation_p.Q171R|RNF38_ENST00000353739.4_Missense_Mutation_p.Q204R	NM_022781.4	NP_073618.3	Q9H0F5	RNF38_HUMAN	ring finger protein 38	254	Pro-rich.				male gonad development (GO:0008584)|protein ubiquitination (GO:0016567)	nucleus (GO:0005634)|sperm flagellum (GO:0036126)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.Q254L(1)		breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|liver(1)|lung(3)|stomach(1)	11			STAD - Stomach adenocarcinoma(86;0.228)			TGGTAAGTGCTGAACTGAACA	0.368																																																	1	Substitution - Missense(1)	central_nervous_system(1)	9											176.0	163.0	167.0					9																	36356448		2203	4300	6503	36346448	SO:0001583	missense	152006				CCDS6603.1, CCDS6604.1	9p	2013-01-09			ENSG00000137075	ENSG00000137075		"""RING-type (C3HC4) zinc fingers"""	18052	protein-coding gene	gene with protein product		612488					Standard	XM_005251364		Approved		uc003zzh.3	Q9H0F5	OTTHUMG00000019905	ENST00000259605.6:c.761A>G	9.37:g.36356448T>C	ENSP00000259605:p.Gln254Arg		36346448	A6PVP9|B1AM81|B1AM82|B3KSG4|E7EVL3|Q7LB33|Q8N0Y0|Q9H748	Missense_Mutation	SNP	ENST00000259605.6	37	CCDS6603.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.741990	0.89573	.	.	ENSG00000137075	ENST00000259605;ENST00000353739;ENST00000377885;ENST00000357058;ENST00000350199;ENST00000377876;ENST00000377870;ENST00000377877	T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.62768	0.2455	M	0.68593	2.085	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.998	D;D;D	0.85130	0.993;0.997;0.993	T	0.64287	-0.6443	10	0.54805	T	0.06	-4.6694	14.3198	0.66479	0.0:0.0:0.0:1.0	.	178;204;254	B1AM81;Q9H0F5-2;Q9H0F5	.;.;RNF38_HUMAN	R	254;204;171;171;171;71;178;178	ENSP00000259605:Q254R;ENSP00000335239:Q204R;ENSP00000367117:Q171R;ENSP00000349566:Q171R;ENSP00000343947:Q171R;ENSP00000367109:Q178R	ENSP00000259605:Q254R	Q	-	2	0	RNF38	36346448	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.655000	0.83696	2.254000	0.74563	0.528000	0.53228	CAG		0.368	RNF38-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052422.3	NM_022781	
PTCH1	5727	hgsc.bcm.edu	37	9	98229638	98229638	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr9:98229638C>T	ENST00000331920.6	-	15	2619	c.2320G>A	c.(2320-2322)Ggg>Agg	p.G774R	PTCH1_ENST00000418258.1_Missense_Mutation_p.G623R|PTCH1_ENST00000421141.1_Missense_Mutation_p.G623R|PTCH1_ENST00000430669.2_Missense_Mutation_p.G708R|PTCH1_ENST00000437951.1_Missense_Mutation_p.G708R|PTCH1_ENST00000375274.2_Missense_Mutation_p.G773R|PTCH1_ENST00000429896.2_Missense_Mutation_p.G623R	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	774					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.G774R(2)|p.G773R(2)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				AGGTCCAGCCCGTCTCTCACT	0.478																																																	4	Substitution - Missense(4)	lung(4)	9	GRCh37	CM064176	PTCH1	M							90.0	90.0	90.0					9																	98229638		2203	4300	6503	97269459	SO:0001583	missense	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.2320G>A	9.37:g.98229638C>T	ENSP00000332353:p.Gly774Arg		97269459	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	C	33	5.284695	0.95517	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000375275;ENST00000430669;ENST00000429896;ENST00000375274	D;D;D;D;D;D;D	0.96587	-4.03;-4.01;-4.02;-4.02;-4.01;-4.02;-4.06	5.82	5.82	0.92795	.	0.047110	0.85682	D	0.000000	D	0.98157	0.9391	M	0.78801	2.425	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.98630	1.0671	10	0.87932	D	0	-23.8555	20.1013	0.97878	0.0:1.0:0.0:0.0	.	708;773;774	Q13635-3;Q13635-2;Q13635	.;.;PTC1_HUMAN	R	774;708;623;623;210;708;623;773	ENSP00000332353:G774R;ENSP00000389744:G708R;ENSP00000399981:G623R;ENSP00000396135:G623R;ENSP00000410287:G708R;ENSP00000414823:G623R;ENSP00000364423:G773R	ENSP00000332353:G774R	G	-	1	0	PTCH1	97269459	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	7.487000	0.81328	2.748000	0.94277	0.655000	0.94253	GGG		0.478	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
RB1	5925	hgsc.bcm.edu	37	13	48955572	48955572	+	Missense_Mutation	SNP	G	G	T	rs587778863		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr13:48955572G>T	ENST00000267163.4	+	17	1826	c.1688G>T	c.(1687-1689)tGg>tTg	p.W563L		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	563	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	TCCCTTGCATGGCTCTCAGTA	0.343		6	"""D, Mis, N, F, S"""		"""retinoblastoma, sarcoma, breast, small cell lung"""	"""retinoblastoma, sarcoma, breast, small cell lung"""			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																													yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"""L, E, M, O"""	23	Whole gene deletion(15)|Unknown(8)	bone(11)|breast(5)|central_nervous_system(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	13	GRCh37	CM004729|CM040263	RB1	M							67.0	63.0	64.0					13																	48955572		2203	4300	6503	47853573	SO:0001583	missense	5925	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"""Endogenous ligands"""	9884	protein-coding gene	gene with protein product	"""prepro-retinoblastoma-associated protein"", ""protein phosphatase 1, regulatory subunit 130"""	614041	"""osteosarcoma"""	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1688G>T	13.37:g.48955572G>T	ENSP00000267163:p.Trp563Leu		47853573	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.795609	0.90453	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.96587	-4.06	5.34	5.34	0.76211	Retinoblastoma-associated protein, A-box (1);Cyclin-like (2);	0.000000	0.85682	D	0.000000	D	0.98308	0.9439	M	0.84846	2.72	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99293	1.0899	10	0.87932	D	0	.	19.0281	0.92941	0.0:0.0:1.0:0.0	.	563	P06400	RB_HUMAN	L	542;563	ENSP00000267163:W563L	ENSP00000267163:W563L	W	+	2	0	RB1	47853573	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.471000	0.97696	2.488000	0.83962	0.650000	0.86243	TGG		0.343	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		
PCDH20	64881	hgsc.bcm.edu	37	13	61986435	61986435	+	Silent	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr13:61986435T>C	ENST00000409186.1	-	5	3902	c.1797A>G	c.(1795-1797)cgA>cgG	p.R599R	PCDH20_ENST00000409204.4_Silent_p.R599R			Q8N6Y1	PCD20_HUMAN	protocadherin 20	599	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		CTTTCTCTTCTCGGTCCAGCT	0.453																																																	0			13											115.0	112.0	113.0					13																	61986435		2203	4300	6503	60884436	SO:0001819	synonymous_variant	64881			AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"""Cadherins / Protocadherins : Non-clustered"""	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.1797A>G	13.37:g.61986435T>C			60884436	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Silent	SNP	ENST00000409186.1	37	CCDS9442.2																																																																																				0.453	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843	
FAM155A	728215	hgsc.bcm.edu	37	13	107822990	107822990	+	Missense_Mutation	SNP	C	C	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr13:107822990C>G	ENST00000375915.2	-	3	1370	c.1232G>C	c.(1231-1233)aGa>aCa	p.R411T		NM_001080396.2	NP_001073865.1	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A	411						integral component of membrane (GO:0016021)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						GTTGCACAGTCTTGTTGCTGA	0.493																																																	0			13											272.0	189.0	217.0					13																	107822990		2203	4300	6503	106620991	SO:0001583	missense	728215			L10374	CCDS32006.1	13q33.3	2008-04-15			ENSG00000204442	ENSG00000204442			33877	protein-coding gene	gene with protein product							Standard	NM_001080396		Approved		uc001vql.3	B1AL88	OTTHUMG00000017326	ENST00000375915.2:c.1232G>C	13.37:g.107822990C>G	ENSP00000365080:p.Arg411Thr		106620991	B2RUV1|B7Z334	Missense_Mutation	SNP	ENST00000375915.2	37	CCDS32006.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.865952	0.91511	.	.	ENSG00000204442	ENST00000375915	.	.	.	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.76364	0.3977	L	0.49778	1.585	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.77305	-0.2637	9	0.87932	D	0	.	19.0063	0.92852	0.0:1.0:0.0:0.0	.	411	B1AL88	F155A_HUMAN	T	411	.	ENSP00000365080:R411T	R	-	2	0	FAM155A	106620991	1.000000	0.71417	0.984000	0.44739	0.986000	0.74619	7.135000	0.77276	2.723000	0.93209	0.638000	0.83543	AGA		0.493	FAM155A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045736.2	NM_001080396	
ARHGEF7	8874	hgsc.bcm.edu	37	13	111896589	111896589	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr13:111896589G>A	ENST00000375741.2	+	9	1211	c.961G>A	c.(961-963)Gaa>Aaa	p.E321K	ARHGEF7_ENST00000375739.2_Missense_Mutation_p.E271K|ARHGEF7_ENST00000375723.1_Missense_Mutation_p.E143K|ARHGEF7_ENST00000375736.4_Missense_Mutation_p.E143K|ARHGEF7_ENST00000478679.1_Missense_Mutation_p.E65K|ARHGEF7_ENST00000375737.5_Missense_Mutation_p.E218K|ARHGEF7_ENST00000544132.1_Intron|ARHGEF7_ENST00000483189.1_3'UTR|ARHGEF7_ENST00000218789.5_Missense_Mutation_p.E143K|ARHGEF7_ENST00000426073.2_Missense_Mutation_p.E143K|ARHGEF7_ENST00000317133.5_Missense_Mutation_p.E300K|ARHGEF7_ENST00000370623.3_Missense_Mutation_p.E228K	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	321	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			AAATCTAGAAGAAATATGTTC	0.308																																																	0			13											62.0	66.0	65.0					13																	111896589		2202	4294	6496	110694590	SO:0001583	missense	8874			D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	15607	protein-coding gene	gene with protein product	"""SH3 domain-containing proline-rich protein"", ""PAK-interacting exchange factor beta"", ""rho"", ""guanine nucleotide exchange factor 7"""	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.961G>A	13.37:g.111896589G>A	ENSP00000364893:p.Glu321Lys		110694590	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Missense_Mutation	SNP	ENST00000375741.2	37	CCDS45068.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.555991	0.86231	.	.	ENSG00000102606	ENST00000317133;ENST00000375741;ENST00000375739;ENST00000370623;ENST00000545635;ENST00000466143;ENST00000218789;ENST00000375736;ENST00000426073;ENST00000375737;ENST00000375723;ENST00000478679	T;T;T;T;T;T;T;T;T;T;T	0.20069	2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1	5.04	5.04	0.67666	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.46483	0.1395	M	0.66297	2.02	0.80722	D	1	B;P;B;D;D;D	0.69078	0.348;0.904;0.348;0.973;0.994;0.997	P;P;P;P;D;D	0.75484	0.564;0.861;0.564;0.908;0.986;0.968	T	0.43988	-0.9357	10	0.56958	D	0.05	.	18.0048	0.89207	0.0:0.0:1.0:0.0	.	65;218;65;271;321;300	E9PDQ5;B7Z6G2;B7Z344;Q14155-2;Q14155;Q14155-3	.;.;.;.;ARHG7_HUMAN;.	K	300;321;271;228;298;143;143;143;143;218;143;65	ENSP00000325994:E300K;ENSP00000364893:E321K;ENSP00000364891:E271K;ENSP00000359657:E228K;ENSP00000418067:E143K;ENSP00000218789:E143K;ENSP00000364888:E143K;ENSP00000397068:E143K;ENSP00000364889:E218K;ENSP00000364875:E143K;ENSP00000417596:E65K	ENSP00000218789:E143K	E	+	1	0	ARHGEF7	110694590	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.084000	0.89516	2.325000	0.78763	0.563000	0.77884	GAA		0.308	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511	
SKIDA1	387640	hgsc.bcm.edu	37	10	21806618	21806618	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr10:21806618A>G	ENST00000449193.2	-	4	2386	c.134T>C	c.(133-135)gTg>gCg	p.V45A	SKIDA1_ENST00000487107.1_5'Flank|SKIDA1_ENST00000444772.3_Missense_Mutation_p.V45A	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	45						nucleus (GO:0005634)											GCGCTTGTGCACGGTCGTCCT	0.527																																																	0			10											87.0	84.0	85.0					10																	21806618		2069	4215	6284	21846624	SO:0001583	missense	387640			AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 140"""	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.134T>C	10.37:g.21806618A>G	ENSP00000410041:p.Val45Ala		21846624	B1ANA5|Q6ZMX4|Q8N3C3	Missense_Mutation	SNP	ENST00000449193.2	37	CCDS44363.1	.	.	.	.	.	.	.	.	.	.	A	15.08	2.726890	0.48833	.	.	ENSG00000180592	ENST00000449193;ENST00000444772	D;D	0.86432	-2.12;-2.12	4.96	4.96	0.65561	DNA binding domain, putative (1);Transforming protein Ski (2);	0.000000	0.64402	D	0.000002	D	0.90957	0.7157	L	0.46157	1.445	0.53688	D	0.999979	D;D	0.89917	0.999;1.0	D;D	0.87578	0.997;0.998	D	0.92002	0.5611	10	0.87932	D	0	0.3012	14.6105	0.68512	1.0:0.0:0.0:0.0	.	45;45	Q1XH10;E9PAX1	DLN1_HUMAN;.	A	45	ENSP00000410041:V45A;ENSP00000442432:V45A	ENSP00000442432:V45A	V	-	2	0	C10orf140	21846624	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.249000	0.95470	1.857000	0.53885	0.260000	0.18958	GTG		0.527	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286950.2	NM_207371	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37454053	37454053	+	Missense_Mutation	SNP	G	G	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr10:37454053G>T	ENST00000602533.1	+	18	1965	c.1866G>T	c.(1864-1866)aaG>aaT	p.K622N	ANKRD30A_ENST00000374660.1_Missense_Mutation_p.K622N|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.K622N			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	678					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						CCAAACAAAAGGACTATGAAG	0.294																																																	0			10											129.0	124.0	126.0					10																	37454053		1811	4062	5873	37494059	SO:0001583	missense	91074			AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"""Ankyrin repeat domain containing"""	17234	protein-coding gene	gene with protein product	"""breast cancer antigen NY-BR-1"""	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.1866G>T	10.37:g.37454053G>T	ENSP00000473551:p.Lys622Asn		37494059	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		.	.	.	.	.	.	.	.	.	.	.	4.341	0.062630	0.08388	.	.	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.08282	3.11;3.11	1.01	-0.0617	0.13784	.	.	.	.	.	T	0.11793	0.0287	L	0.36672	1.1	0.09310	N	1	P	0.45126	0.851	P	0.55391	0.775	T	0.22730	-1.0208	9	0.51188	T	0.08	.	4.0394	0.09745	0.0:0.0:0.5907:0.4093	.	678	Q9BXX3	AN30A_HUMAN	N	622	ENSP00000354432:K622N;ENSP00000363792:K622N	ENSP00000354432:K622N	K	+	3	2	ANKRD30A	37494059	0.070000	0.21116	0.001000	0.08648	0.021000	0.10359	0.834000	0.27518	-0.020000	0.14032	0.391000	0.25812	AAG		0.294	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
KAT6B	23522	hgsc.bcm.edu	37	10	76789171	76789171	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr10:76789171G>A	ENST00000287239.4	+	18	5078	c.4589G>A	c.(4588-4590)gGa>gAa	p.G1530E	KAT6B_ENST00000372714.1_Missense_Mutation_p.G1238E|KAT6B_ENST00000372724.1_Missense_Mutation_p.G1238E|KAT6B_ENST00000372711.1_Missense_Mutation_p.G1347E|KAT6B_ENST00000372725.1_Missense_Mutation_p.G1238E	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1530					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.G1530E(1)									TTCAAAGAGGGAAACCCAGCA	0.537																																																	1	Substitution - Missense(1)	central_nervous_system(1)	10											114.0	114.0	114.0					10																	76789171		2203	4300	6503	76459177	SO:0001583	missense	23522			AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	17582	protein-coding gene	gene with protein product	"""MOZ-related factor"""	605880	"""MYST histone acetyltransferase (monocytic leukemia) 4"""	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.4589G>A	10.37:g.76789171G>A	ENSP00000287239:p.Gly1530Glu		76459177	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	37	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	G	3.070	-0.191418	0.06299	.	.	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	T;T;T;T;T	0.74106	-0.81;-0.81;-0.81;-0.81;-0.81	4.77	-0.229	0.13094	.	0.620256	0.14149	N	0.338149	T	0.30727	0.0774	N	0.00413	-1.525	0.20196	N	0.999928	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.43621	-0.9380	10	0.02654	T	1	1.0449	5.8686	0.18791	0.2365:0.4408:0.3227:0.0	.	1347;1238;1530	Q8WYB5-2;Q8WYB5-3;Q8WYB5	.;.;KAT6B_HUMAN	E	1238;1238;1530;1238;1347	ENSP00000361810:G1238E;ENSP00000361809:G1238E;ENSP00000287239:G1530E;ENSP00000361799:G1238E;ENSP00000361796:G1347E	ENSP00000287239:G1530E	G	+	2	0	KAT6B	76459177	0.983000	0.35010	0.106000	0.21319	0.902000	0.53008	2.263000	0.43293	0.057000	0.16193	0.563000	0.77884	GGA		0.537	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330	
PTEN	5728	hgsc.bcm.edu	37	10	89720709	89720709	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr10:89720709C>T	ENST00000371953.3	+	8	2217	c.860C>T	c.(859-861)tCa>tTa	p.S287L	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	287	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.S287fs*8(1)|p.W274_F341del(1)|p.S287fs*1(1)|p.S287*(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		GAGGAAACCTCAGAAAAAGTA	0.313		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																													yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	53	Whole gene deletion(37)|Deletion - Frameshift(11)|Deletion - In frame(2)|Unknown(2)|Substitution - Nonsense(1)	prostate(16)|central_nervous_system(12)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|endometrium(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	10											53.0	57.0	56.0					10																	89720709		2201	4295	6496	89710689	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.860C>T	10.37:g.89720709C>T	ENSP00000361021:p.Ser287Leu		89710689	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	C	17.79	3.476338	0.63737	.	.	ENSG00000171862	ENST00000371953	D	0.84944	-1.92	5.13	5.13	0.70059	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.313296	0.30602	N	0.009272	T	0.80507	0.4636	L	0.40543	1.245	0.47123	D	0.999321	B	0.06786	0.001	B	0.08055	0.003	T	0.74636	-0.3599	9	.	.	.	-7.973	18.5632	0.91108	0.0:1.0:0.0:0.0	.	287	P60484	PTEN_HUMAN	L	287	ENSP00000361021:S287L	.	S	+	2	0	PTEN	89710689	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.976000	0.49289	2.399000	0.81585	0.591000	0.81541	TCA		0.313	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
PTEN	5728	hgsc.bcm.edu	37	10	89720769	89720769	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr10:89720769A>G	ENST00000371953.3	+	8	2277	c.920A>G	c.(919-921)gAg>gGg	p.E307G	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	307	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.W274_F341del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TGCAGTATAGAGCGTGCAGAT	0.348		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																													yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	50	Whole gene deletion(37)|Deletion - Frameshift(9)|Deletion - In frame(2)|Unknown(2)	prostate(16)|central_nervous_system(12)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	10											104.0	101.0	102.0					10																	89720769		2203	4298	6501	89710749	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.920A>G	10.37:g.89720769A>G	ENSP00000361021:p.Glu307Gly		89710749	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	14.04	2.415677	0.42817	.	.	ENSG00000171862	ENST00000371953	D	0.94758	-3.51	5.13	5.13	0.70059	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.181618	0.46758	D	0.000280	D	0.89121	0.6625	N	0.22421	0.69	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	D	0.84991	0.0894	9	.	.	.	-11.7975	14.9228	0.70854	1.0:0.0:0.0:0.0	.	307	P60484	PTEN_HUMAN	G	307	ENSP00000361021:E307G	.	E	+	2	0	PTEN	89710749	1.000000	0.71417	0.997000	0.53966	0.971000	0.66376	8.050000	0.89445	1.942000	0.56320	0.482000	0.46254	GAG		0.348	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
CFAP43	80217	hgsc.bcm.edu	37	10	105990458	105990458	+	Missense_Mutation	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr10:105990458A>G	ENST00000357060.3	-	2	324	c.209T>C	c.(208-210)gTc>gCc	p.V70A	WDR96_ENST00000428666.1_Missense_Mutation_p.V70A|WDR96_ENST00000369720.1_5'UTR|WDR96_ENST00000369719.1_5'UTR|WDR96_ENST00000278064.2_5'UTR	NM_025145.5	NP_079421.5														NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						AGTTGCCATGACGCCCACAAT	0.413																																																	0			10											144.0	132.0	136.0					10																	105990458		2203	4300	6503	105980448	SO:0001583	missense	80217																														ENST00000357060.3:c.209T>C	10.37:g.105990458A>G	ENSP00000349568:p.Val70Ala		105980448		Missense_Mutation	SNP	ENST00000357060.3	37	CCDS31281.1	.	.	.	.	.	.	.	.	.	.	A	5.632	0.301352	0.10678	.	.	ENSG00000197748	ENST00000357060;ENST00000428666	T;T	0.17528	2.27;2.27	4.83	3.7	0.42460	.	0.291378	0.18676	N	0.134302	T	0.05547	0.0146	N	0.03324	-0.35	0.33001	D	0.526233	B;B;B	0.13145	0.007;0.003;0.007	B;B;B	0.13407	0.003;0.009;0.007	T	0.23332	-1.0191	10	0.13108	T	0.6	.	3.074	0.06240	0.5736:0.0:0.4264:0.0	.	70;70;70	Q8NDM7-5;B4DHB6;Q8NDM7	.;.;WDR96_HUMAN	A	70	ENSP00000349568:V70A;ENSP00000400289:V70A	ENSP00000349568:V70A	V	-	2	0	WDR96	105980448	1.000000	0.71417	0.998000	0.56505	0.928000	0.56348	6.531000	0.73820	1.813000	0.52934	0.402000	0.26972	GTC		0.413	WDR96-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PDZD8	118987	hgsc.bcm.edu	37	10	119044524	119044524	+	Missense_Mutation	SNP	C	C	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr10:119044524C>A	ENST00000334464.5	-	5	1959	c.1720G>T	c.(1720-1722)Gac>Tac	p.D574Y	PDZD8_ENST00000482496.1_5'UTR	NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	574	Pro-rich.				cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|regulation of cell morphogenesis (GO:0022604)|viral process (GO:0016032)	membrane (GO:0016020)	metal ion binding (GO:0046872)			kidney(3)|large_intestine(8)|lung(24)|upper_aerodigestive_tract(3)	38		Colorectal(252;0.19)		all cancers(201;0.0121)		TGTGCTGGGTCTGTTATCTCA	0.468																																																	0			10											130.0	131.0	131.0					10																	119044524		2203	4300	6503	119034514	SO:0001583	missense	118987			AL122051	CCDS7600.1	10q26.12	2006-01-24		2006-01-24	ENSG00000165650	ENSG00000165650			26974	protein-coding gene	gene with protein product		614235		PDZK8		12477932	Standard	NM_173791		Approved	bA129M16.2, FLJ34427	uc001lde.1	Q8NEN9	OTTHUMG00000019122	ENST00000334464.5:c.1720G>T	10.37:g.119044524C>A	ENSP00000334642:p.Asp574Tyr		119034514	Q86WE0|Q86WE5|Q9UFF1	Missense_Mutation	SNP	ENST00000334464.5	37	CCDS7600.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.208659	0.79240	.	.	ENSG00000165650	ENST00000334464	D	0.89485	-2.52	5.93	5.93	0.95920	.	0.154165	0.56097	D	0.000023	D	0.88055	0.6334	L	0.27053	0.805	0.36314	D	0.857848	P	0.47191	0.891	P	0.51918	0.684	D	0.91103	0.4916	10	0.72032	D	0.01	-10.0189	15.789	0.78338	0.0:0.8646:0.1354:0.0	.	574	Q8NEN9	PDZD8_HUMAN	Y	574	ENSP00000334642:D574Y	ENSP00000334642:D574Y	D	-	1	0	PDZD8	119034514	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	3.569000	0.53827	2.814000	0.96858	0.591000	0.81541	GAC		0.468	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791	
APC	324	hgsc.bcm.edu	37	5	112173958	112173958	+	Silent	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr5:112173958A>G	ENST00000457016.1	+	16	3047	c.2667A>G	c.(2665-2667)aaA>aaG	p.K889K	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.K889K|APC_ENST00000508376.2_Silent_p.K889K			P25054	APC_HUMAN	adenomatous polyposis coli	889	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGATTGCCAAAGTCATGGAAG	0.463		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	1	Unknown(1)	skin(1)	5											80.0	79.0	79.0					5																	112173958		2202	4300	6502	112201857	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2667A>G	5.37:g.112173958A>G			112201857	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.463	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	hgsc.bcm.edu	37	5	112175193	112175193	+	Missense_Mutation	SNP	C	C	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr5:112175193C>T	ENST00000457016.1	+	16	4282	c.3902C>T	c.(3901-3903)aCc>aTc	p.T1301I	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.T1301I|APC_ENST00000508376.2_Missense_Mutation_p.T1301I			P25054	APC_HUMAN	adenomatous polyposis coli	1301	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.T1301fs*10(3)|p.T1301S(2)|p.?(1)|p.T1293fs*2(1)|p.K1192fs*3(1)|p.L1302fs*13(1)|p.L1302fs*3(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCTGCTAATACCCTGCAAATA	0.403		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	10	Deletion - Frameshift(6)|Substitution - Missense(2)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(6)|stomach(2)|soft_tissue(1)|skin(1)	5											54.0	56.0	55.0					5																	112175193		2202	4300	6502	112203092	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3902C>T	5.37:g.112175193C>T	ENSP00000413133:p.Thr1301Ile		112203092	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	11.81	1.750684	0.31046	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D	0.91180	-2.54;-2.54;-2.54;-2.8	5.73	4.84	0.62591	.	0.183957	0.48286	D	0.000185	D	0.85084	0.5616	L	0.32530	0.975	0.45515	D	0.998472	B;B	0.24132	0.098;0.041	B;B	0.17433	0.018;0.018	T	0.80616	-0.1303	9	.	.	.	-20.5918	15.94	0.79747	0.1362:0.8638:0.0:0.0	.	1303;1301	Q4LE70;P25054	.;APC_HUMAN	I	1301	ENSP00000413133:T1301I;ENSP00000257430:T1301I;ENSP00000427089:T1301I;ENSP00000423828:T1301I	.	T	+	2	0	APC	112203092	1.000000	0.71417	0.993000	0.49108	0.874000	0.50279	4.731000	0.62022	1.515000	0.48885	0.655000	0.94253	ACC		0.403	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
HTR4	3360	hgsc.bcm.edu	37	5	147889227	147889227	+	Missense_Mutation	SNP	G	G	A			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr5:147889227G>A	ENST00000377888.3	-	6	1006	c.868C>T	c.(868-870)Cct>Tct	p.P290S	HTR4_ENST00000521530.1_Missense_Mutation_p.P290S|HTR4_ENST00000521735.1_Missense_Mutation_p.P290S|HTR4_ENST00000517929.1_Missense_Mutation_p.P290S|HTR4_ENST00000520514.1_Missense_Mutation_p.P290S|HTR4_ENST00000354217.2_Missense_Mutation_p.P290S|HTR4_ENST00000362016.2_Missense_Mutation_p.P304S|HTR4_ENST00000360693.3_Missense_Mutation_p.P290S|HTR4_ENST00000314512.6_Missense_Mutation_p.P290S	NM_000870.5	NP_000861.1	Q13639	5HT4R_HUMAN	5-hydroxytryptamine (serotonin) receptor 4, G protein-coupled	290					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|regulation of appetite (GO:0032098)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)			endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cinitapride(DB08810)|Cisapride(DB00604)|Ergoloid mesylate(DB01049)|Metoclopramide(DB01233)|Ondansetron(DB00904)	ACCTGCCCAGGGACAGTGTAG	0.493																																					GBM(120;370 1604 14007 17804 41573)												0			5											91.0	90.0	90.0					5																	147889227		2203	4300	6503	147869420	SO:0001583	missense	3360			Y08756	CCDS4291.1, CCDS34270.1, CCDS34271.1, CCDS34272.1, CCDS34273.1, CCDS34273.2, CCDS75353.1	5q31-q33	2012-08-08	2012-02-03		ENSG00000164270	ENSG00000164270		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5299	protein-coding gene	gene with protein product		602164	"""5-hydroxytryptamine (serotonin) receptor 4"""			9371406, 9276448	Standard	NM_199453		Approved	5-HT4	uc021yfj.1	Q13639	OTTHUMG00000129931	ENST00000377888.3:c.868C>T	5.37:g.147889227G>A	ENSP00000367120:p.Pro290Ser		147869420	C4WYH4|Q546Q1|Q684M0|Q712M9|Q96KH9|Q96KI0|Q9H199|Q9NY73|Q9UBM6|Q9UBT4|Q9UE22|Q9UE23|Q9UQR6	Missense_Mutation	SNP	ENST00000377888.3	37	CCDS4291.1	.	.	.	.	.	.	.	.	.	.	G	12.19	1.864225	0.32977	.	.	ENSG00000164270	ENST00000521530;ENST00000354217;ENST00000314512;ENST00000521735;ENST00000517929;ENST00000520514;ENST00000377888;ENST00000360693;ENST00000362016	T;T;T;T;T;T;T;T;T	0.37752	1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18	6.07	6.07	0.98685	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.52533	0.1740	L	0.42487	1.325	0.80722	D	1	D;D;P;P;D;D;D	0.76494	0.993;0.973;0.952;0.941;0.995;0.999;0.996	D;P;P;P;D;D;D	0.70227	0.965;0.846;0.81;0.808;0.92;0.968;0.952	T	0.21724	-1.0237	10	0.23891	T	0.37	.	19.2231	0.93806	0.0:0.0:1.0:0.0	.	290;290;290;304;290;290;290	C4WYH4;Q13639;Q712M9;Q13639-6;Q13639-3;Q13639-2;Q684M0	.;5HT4R_HUMAN;.;.;.;.;.	S	290;290;290;290;290;290;290;290;304	ENSP00000428320:P290S;ENSP00000346156:P290S;ENSP00000314906:P290S;ENSP00000430979:P290S;ENSP00000435904:P290S;ENSP00000427913:P290S;ENSP00000367120:P290S;ENSP00000353915:P290S;ENSP00000355037:P304S	ENSP00000314906:P290S	P	-	1	0	HTR4	147869420	1.000000	0.71417	0.639000	0.29394	0.024000	0.10985	9.869000	0.99810	2.885000	0.99019	0.655000	0.94253	CCT		0.493	HTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252187.2	NM_000870	
SPDL1	54908	hgsc.bcm.edu	37	5	169025559	169025559	+	Missense_Mutation	SNP	T	T	C			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr5:169025559T>C	ENST00000265295.4	+	9	1391	c.1112T>C	c.(1111-1113)cTt>cCt	p.L371P		NM_017785.4	NP_060255.3			spindle apparatus coiled-coil protein 1																		ACAGATTTACTTCAGATGAAG	0.363																																																	0			5											150.0	156.0	154.0					5																	169025559		2203	4300	6503	168958137	SO:0001583	missense	54908			BC012568	CCDS4370.1	5q35.1	2012-09-27	2012-09-27	2012-09-27	ENSG00000040275	ENSG00000040275			26010	protein-coding gene	gene with protein product	"""spindly homolog (Drosophila)"""		"""coiled-coil domain containing 99"""	CCDC99		20427577	Standard	NM_017785		Approved	FLJ20364, hSpindly	uc003mae.4	Q96EA4	OTTHUMG00000130438	ENST00000265295.4:c.1112T>C	5.37:g.169025559T>C	ENSP00000265295:p.Leu371Pro		168958137		Missense_Mutation	SNP	ENST00000265295.4	37	CCDS4370.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.384589	0.82792	.	.	ENSG00000040275	ENST00000265295;ENST00000274631	T	0.57595	0.39	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.72317	0.3445	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.75249	-0.3384	10	0.72032	D	0.01	-11.0546	16.2332	0.82358	0.0:0.0:0.0:1.0	.	293;272;371	B4E393;Q96EA4-2;Q96EA4	.;.;SPDLY_HUMAN	P	371;272	ENSP00000265295:L371P	ENSP00000265295:L371P	L	+	2	0	CCDC99	168958137	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	6.656000	0.74396	2.233000	0.73108	0.523000	0.50628	CTT		0.363	SPDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252829.2	NM_017785	
NEURL1B	54492	hgsc.bcm.edu	37	5	172113859	172113859	+	Silent	SNP	A	A	G			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr5:172113859A>G	ENST00000369800.5	+	5	1740	c.1599A>G	c.(1597-1599)cgA>cgG	p.R533R	NEURL1B_ENST00000520919.1_Silent_p.R293R|NEURL1B_ENST00000522853.1_Silent_p.R351R	NM_001142651.1	NP_001136123.1	A8MQ27	NEU1B_HUMAN	neuralized E3 ubiquitin protein ligase 1B	533					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(2)	2						GGCTCAAGCGACAGGCCCGGG	0.647																																																	0			5											22.0	24.0	23.0					5																	172113859		692	1591	2283	172046464	SO:0001819	synonymous_variant	54492				CCDS47342.1	5q35.1	2013-10-24	2013-10-24		ENSG00000214357	ENSG00000214357			35422	protein-coding gene	gene with protein product		615893	"""neuralized homolog 1B (Drosophila)"""			17003037	Standard	NM_001142651		Approved	DKFZP761M1511, Neur2	uc003mbt.3	A8MQ27	OTTHUMG00000163281	ENST00000369800.5:c.1599A>G	5.37:g.172113859A>G			172046464	C9DQJ5|C9DQJ6|C9DQJ7	Silent	SNP	ENST00000369800.5	37	CCDS47342.1																																																																																				0.647	NEURL1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372453.2		
GSTM4	2948	hgsc.bcm.edu	37	1	110201532	110201532	+	Splice_Site	SNP	G	G	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:110201532G>T	ENST00000369836.4	+	6	765		c.e6+1		GSTM4_ENST00000336075.5_Splice_Site|GSTM4_ENST00000369833.1_Splice_Site|GSTM4_ENST00000495742.1_Splice_Site|GSTM4_ENST00000326729.5_Splice_Site	NM_000850.4	NP_000841.1	Q03013	GSTM4_HUMAN	glutathione S-transferase mu 4						glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	enzyme binding (GO:0019899)|glutathione binding (GO:0043295)|glutathione transferase activity (GO:0004364)|protein homodimerization activity (GO:0042803)			endometrium(3)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	12		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		all cancers(265;0.0123)|Colorectal(144;0.0129)|Epithelial(280;0.0147)|Lung(183;0.0422)|COAD - Colon adenocarcinoma(174;0.0471)|LUSC - Lung squamous cell carcinoma(189;0.227)	Glutathione(DB00143)	TGGAGACAAGGTAATGGGGGC	0.478																																																	0			1											252.0	236.0	241.0					1																	110201532		2203	4300	6503	110003055	SO:0001630	splice_region_variant	2948			M96234	CCDS806.1, CCDS807.1	1p13.3	2012-06-22	2008-11-26		ENSG00000168765	ENSG00000168765	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4636	protein-coding gene	gene with protein product		138333	"""glutathione S-transferase M4"""			8276420	Standard	NM_000850		Approved		uc001dyf.3	Q03013	OTTHUMG00000011642	ENST00000369836.4:c.456+1G>T	1.37:g.110201532G>T			110003055	A8K765|Q05465|Q32NC1|Q4JNT8|Q6FH87	Splice_Site	SNP	ENST00000369836.4	37	CCDS807.1	.	.	.	.	.	.	.	.	.	.	G	15.20	2.764174	0.49574	.	.	ENSG00000168765	ENST00000369836;ENST00000336075;ENST00000326729;ENST00000369833	.	.	.	4.0	4.0	0.46444	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5221	0.61574	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GSTM4	110003055	1.000000	0.71417	1.000000	0.80357	0.668000	0.39293	6.215000	0.72206	2.256000	0.74724	0.298000	0.19748	.		0.478	GSTM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032187.1	NM_000850	Intron
AMPD1	270	hgsc.bcm.edu	37	1	115229401	115229413	+	Frame_Shift_Del	DEL	GAAAATCAGGCAC	GAAAATCAGGCAC	-	rs61741025	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	GAAAATCAGGCAC	GAAAATCAGGCAC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr1:115229401_115229413delGAAAATCAGGCAC	ENST00000520113.2	-	4	448_460	c.433_445delGTGCCTGATTTTC	c.(433-447)gtgcctgattttcagfs	p.VPDFQ145fs	AMPD1_ENST00000369538.3_Frame_Shift_Del_p.VPDFQ141fs|AMPD1_ENST00000353928.6_Frame_Shift_Del_p.VPDFQ112fs			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	145					IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	TGCACTCTCTGAAAATCAGGCACGGTCTGGTAG	0.465																																																	0			1																																								115030936	SO:0001589	frameshift_variant	270			M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"""AMPD isoform M"", ""skeletal muscle AMPD"""	102770	"""adenosine monophosphate deaminase 1 (isoform M)"""			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.433_445delGTGCCTGATTTTC	1.37:g.115229401_115229413delGAAAATCAGGCAC	ENSP00000430075:p.Val145fs		115030924	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Frame_Shift_Del	DEL	ENST00000520113.2	37	CCDS876.2																																																																																				0.465	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4		
KIAA1211	57482	hgsc.bcm.edu	37	4	57180576	57180577	+	In_Frame_Ins	INS	-	-	GGAGCGGAGGGAGCGGAG	rs71921617|rs138358443|rs11276076	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr4:57180576_57180577insGGAGCGGAGGGAGCGGAG	ENST00000504228.1	+	6	1013_1014	c.908_909insGGAGCGGAGGGAGCGGAG	c.(907-912)gcggag>gcGGAGCGGAGGGAGCGGAGggag	p.304_305insRRERRE	KIAA1211_ENST00000264229.6_In_Frame_Ins_p.304_305insRRERRE|KIAA1211_ENST00000541073.1_In_Frame_Ins_p.297_298insRRERRE			Q6ZU35	K1211_HUMAN	KIAA1211	304	Glu-rich.									endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					TGGGAGGACGCGGAGCGGAGGG	0.733														1350	0.269569	0.2716	0.2781	5008	,	,		14300	0.0694		0.4076	False		,,,				2504	0.3252																0			4								903,2311		258,387,962						-10.2	0.0		dbSNP_130	6	2065,4451		612,841,1805	no	coding	KIAA1211	NM_020722.1		870,1228,2767	A1A1,A1R,RR		31.6912,28.0958,30.5036				2968,6762				56875334	SO:0001652	inframe_insertion	57482			AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	Exception_encountered	4.37:g.57180576_57180577insGGAGCGGAGGGAGCGGAG	ENSP00000423366:p.Glu304_Arg305insArgArgGluArgArgGlu		56875333	Q9NTE2|Q9NTP8|Q9ULK9	In_Frame_Ins	INS	ENST00000504228.1	37	CCDS43230.1																																																																																				0.733	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
Unknown	0	hgsc.bcm.edu	37	9	18075	18075	+	IGR	DEL	G	G	-			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr9:18075delG								None (None upstream) : MIR1302-2 (9581 downstream)																							TGGATCCTGTGGCGGGGGCGT	0.662																																																	0			9																																								8075	SO:0001628	intergenic_variant	375690																															9.37:g.18075delG			8075		Frame_Shift_Del	DEL		37																																																																																				0	0.662								
PDZD8	118987	hgsc.bcm.edu	37	10	119044524	119044535	+	In_Frame_Del	DEL	CTGTTATCTCAG	CTGTTATCTCAG	-			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	CTGTTATCTCAG	CTGTTATCTCAG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr10:119044524_119044535delCTGTTATCTCAG	ENST00000334464.5	-	5	1948_1959	c.1709_1720delCTGAGATAACAG	c.(1708-1722)tctgagataacagac>tac	p.570_574SEITD>Y	PDZD8_ENST00000482496.1_5'UTR	NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	570	Pro-rich.				cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|regulation of cell morphogenesis (GO:0022604)|viral process (GO:0016032)	membrane (GO:0016020)	metal ion binding (GO:0046872)			kidney(3)|large_intestine(8)|lung(24)|upper_aerodigestive_tract(3)	38		Colorectal(252;0.19)		all cancers(201;0.0121)		TGTGCTGGGTCTGTTATCTCAGAAGTTTTTAG	0.462																																																	0			10																																								119034525	SO:0001651	inframe_deletion	118987			AL122051	CCDS7600.1	10q26.12	2006-01-24		2006-01-24	ENSG00000165650	ENSG00000165650			26974	protein-coding gene	gene with protein product		614235		PDZK8		12477932	Standard	NM_173791		Approved	bA129M16.2, FLJ34427	uc001lde.1	Q8NEN9	OTTHUMG00000019122	ENST00000334464.5:c.1709_1720delCTGAGATAACAG	10.37:g.119044524_119044535delCTGTTATCTCAG	ENSP00000334642:p.Ser570_Asp574delinsTyr		119034514	Q86WE0|Q86WE5|Q9UFF1	In_Frame_Del	DEL	ENST00000334464.5	37	CCDS7600.1																																																																																				0.462	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791	
NDUFS8	4728	hgsc.bcm.edu	37	11	67795378	67795379	+	5'Flank	INS	-	-	C	rs11436139|rs397801590|rs58238184		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr11:67795378_67795379insC	ENST00000313468.5	+	0	0				RP5-901A4.1_ENST00000532296.1_RNA|NDUFS8_ENST00000528492.1_5'Flank|ALDH3B1_ENST00000539229.1_Splice_Site|ALDH3B1_ENST00000007633.8_Splice_Site|ALDH3B1_ENST00000434449.1_3'UTR|ALDH3B1_ENST00000342456.6_Splice_Site|ALDH3B1_ENST00000316367.6_Intron	NM_002496.3	NP_002487.1	O00217	NDUS8_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 8, 23kDa (NADH-coenzyme Q reductase)						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|mitochondrial respiratory chain complex I assembly (GO:0032981)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(1)|kidney(1)|lung(5)|skin(1)	8						GGCCATGGAGGCCAAGGCTGCA	0.703													CCC|CC|CCC|deletion	5007	0.9998	0.9992	1.0	5008	,	,		16547	1.0		1.0	False		,,,				2504	1.0				Colon(116;1205 2770 20054)												0			11							,,	4124,30		2052,20,5					,,	-1.9	0.2		dbSNP_120	21	8086,22		4038,10,6	no	frameshift,frameshift,frameshift	ALDH3B1	NM_001161473.1,NM_001030010.1,NM_000694.2	,,	6090,30,11	A1A1,A1R,RR		0.2713,0.7222,0.4241	,,	,,		12210,52				67551955	SO:0001631	upstream_gene_variant	221			U65579	CCDS8176.1	11q13.2	2011-07-04	2002-08-29		ENSG00000110717	ENSG00000110717	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7715	protein-coding gene	gene with protein product	"""complex I 23kDa subunit"", ""NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial"""	602141	"""NADH dehydrogenase (ubiquinone) Fe-S protein 8 (23kD) (NADH-coenzyme Q reductase)"""			9666055, 9116042	Standard	NM_002496		Approved	TYKY, CI-23k	uc001onc.3	O00217	OTTHUMG00000167331		11.37:g.67795380_67795380dupC	Exception_encountered		67551954	B2RB86|Q0VDA8	Frame_Shift_Ins	INS	ENST00000313468.5	37	CCDS8176.1																																																																																				0.703	NDUFS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394193.1	NM_002496	
KRT4	3851	hgsc.bcm.edu	37	12	53207602	53207603	+	Frame_Shift_Ins	INS	-	-	G	rs7135148|rs71092788		TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr12:53207602_53207603insG	ENST00000551956.1	-	1	732_733	c.240_241insC	c.(238-243)tttggcfs	p.G81fs	KRT4_ENST00000458244.2_Frame_Shift_Ins_p.G61fs|KRT4_ENST00000293774.4_Frame_Shift_Ins_p.G155fs			P19013	K2C4_HUMAN	keratin 4	81	Gly-rich.|Head.				cytoskeleton organization (GO:0007010)|epithelial cell differentiation (GO:0030855)|negative regulation of epithelial cell proliferation (GO:0050680)	cell surface (GO:0009986)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|prostate(2)|skin(2)	29						CCACCAGTGCCAAAGCCTCCAG	0.599																																					Pancreas(190;284 2995 41444 45903)												0			12																																								51493870	SO:0001589	frameshift_variant	3851				CCDS41787.1, CCDS41787.2	12q13.13	2013-01-16			ENSG00000170477	ENSG00000170477		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6441	protein-coding gene	gene with protein product	"""cytokeratin 4"", ""keratin, type II cytoskeletal 4"""	123940		CYK4		16831889	Standard	NM_002272		Approved	CK4, K4	uc031qhk.1	P19013		ENST00000551956.1:c.240_241insC	12.37:g.53207602_53207603insG	ENSP00000448220:p.Gly81fs		51493869	F8VS64|Q6GTR8|Q96LA7|Q9BTL1	Frame_Shift_Ins	INS	ENST00000551956.1	37	CCDS41787.2																																																																																				0.599	KRT4-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405931.1	NM_002272	
DDHD1	80821	hgsc.bcm.edu	37	14	53619480	53619481	+	In_Frame_Ins	INS	-	-	GCCGCC	rs140904345|rs55671452|rs200797826	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr14:53619480_53619481insGCCGCC	ENST00000323669.5	-	1	335_336	c.336_337insGGCGGC	c.(334-339)ggcagc>ggcGGCGGCagc	p.111_112insGG	RP11-547D23.1_ENST00000554235.1_RNA|AL356020.1_ENST00000584587.1_RNA|DDHD1_ENST00000395606.1_In_Frame_Ins_p.111_112insGG|DDHD1_ENST00000357758.3_In_Frame_Ins_p.111_112insGG	NM_001160148.1	NP_001153620.1	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1	111					cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)	25	Breast(41;0.037)					GACAAGGAGCTGCCGCCGCCGC	0.703														3933	0.785343	0.4962	0.8718	5008	,	,		9770	0.9673		0.833	False		,,,				2504	0.8783																0			14																																								52689231	SO:0001652	inframe_insertion	80821			AB051492	CCDS9714.1, CCDS53895.1, CCDS53896.1	14q21	2012-11-23			ENSG00000100523	ENSG00000100523			19714	protein-coding gene	gene with protein product	"""phosphatidic acid-preferring phospholipase A1"""	614603	"""spastic paraplegia 28 (autosomal recessive)"""	SPG28		11214970, 20359546	Standard	NM_030637		Approved	KIAA1705, PA-PLA1	uc001xai.3	Q8NEL9	OTTHUMG00000140305	ENST00000323669.5:c.331_336dupGGCGGC	14.37:g.53619481_53619486dupGCCGCC	ENSP00000327104:p.Gly110_Gly111dup		52689230	G5E9D1|Q8WVH3|Q96LL2|Q9C0F8	In_Frame_Ins	INS	ENST00000323669.5	37	CCDS53895.1																																																																																				0.703	DDHD1-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276901.1		
Unknown	0	hgsc.bcm.edu	37	Unknown	0	0	+	IGR	DEL	AACCCCGAGGCCCTCAAGGGCTTCCACCCT	AACCCCGAGGCCCTCAAGGGCTTCCACCCT	-			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	AACCCCGAGGCCCTCAAGGGCTTCCACCCT	AACCCCGAGGCCCTCAAGGGCTTCCACCCT					Unknown	Invalid:failed_liftOver	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chrUnknown:0delAACCCCGAGGCCCTCAAGGGCTTCCACCCT								None (None upstream) : None (None downstream)																								0.0																																																	0			17																																								263631	SO:0001628	intergenic_variant	400566																															Unknown.37:g.0delAACCCCGAGGCCCTCAAGGGCTTCCACCCT			263602		Frame_Shift_Del	DEL		37																																																																																				0	0								
KRTAP4-1	85285	hgsc.bcm.edu	37	17	39340796	39340852	+	In_Frame_Del	DEL	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	-	rs483929|rs543483191|rs79048996|rs1985673|rs2320229|rs483893|rs572749|rs543006020|rs71155126|rs554407371|rs2320230	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr17:39340796_39340852delCGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	ENST00000398472.1	-	1	742_798	c.255_311delCCCACTCTGCTGTCAGACCACCTGCCACCCCAGCTGTGGTATGTCCAGCTGCTGCCG	c.(253-312)cgcccactctgctgtcagaccacctgccaccccagctgtggtatgtccagctgctgccgt>cgt	p.85_104RPLCCQTTCHPSCGMSSCCR>R				Q9BYQ7	KRA41_HUMAN	keratin associated protein 4-1	85	18 X 5 AA repeats of C-C-[GRQC]-[SPT]- [VSTL].		Missing (in allele KAP4.10). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)		p.H90_C108delHPSCGMSSCCRPLCCQTTC(2)|p.H94_C112delHPSCGMSSCCRPLCCQTTC(2)		kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			ACAGAGTGGACGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGGCGGCAGCAGC	0.646																																																	4	Deletion - In frame(4)	upper_aerodigestive_tract(2)|prostate(2)	17																																								36594378	SO:0001651	inframe_deletion	85285			AC006070		17q21.2	2013-06-25			ENSG00000198443	ENSG00000198443		"""Keratin associated proteins"""	18907	protein-coding gene	gene with protein product			"""keratin associated protein 4-10"""	KRTAP4-10		11279113	Standard	NM_033060		Approved	KAP4.1, KAP4.10	uc002hwe.4	Q9BYQ7	OTTHUMG00000132081	ENST00000398472.1:c.255_311delCCCACTCTGCTGTCAGACCACCTGCCACCCCAGCTGTGGTATGTCCAGCTGCTGCCG	17.37:g.39340796_39340852delCGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	ENSP00000381489:p.Arg85_Cys103del		36594322	A8MWS7|Q3SYF2	Frame_Shift_Del	DEL	ENST00000398472.1	37																																																																																					0.646	KRTAP4-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255108.1	NM_033060	
CFAP61	26074	hgsc.bcm.edu	37	20	20226845	20226846	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr20:20226845_20226846insT	ENST00000245957.5	+	19	2221_2222	c.2145_2146insT	c.(2146-2148)tttfs	p.F716fs	C20orf26_ENST00000377309.2_Frame_Shift_Ins_p.F72fs|C20orf26_ENST00000377293.1_Frame_Shift_Ins_p.F72fs|C20orf26_ENST00000389656.3_Frame_Shift_Ins_p.F72fs	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		716										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		AACAAAGGAAATTTTTAGCCAG	0.347																																																	0			20																																								20174846	SO:0001589	frameshift_variant	26074																														ENST00000245957.5:c.2150dupT	20.37:g.20226850_20226850dupT	ENSP00000245957:p.Phe716fs		20174845	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Frame_Shift_Ins	INS	ENST00000245957.5	37	CCDS33447.1																																																																																				0.347	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3		
TOX2	84969	hgsc.bcm.edu	37	20	42694558	42694559	+	In_Frame_Ins	INS	-	-	CCG	rs199841880|rs34604629	byFrequency	TCGA-AF-6672-01A-11D-1826-10	TCGA-AF-6672-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	86170567-354c-4c1d-bbb8-537eae1b407d	7cecf885-5d7e-4416-a869-761d11fa1a70	g.chr20:42694558_42694559insCCG	ENST00000358131.5	+	6	1321_1322	c.1113_1114insCCG	c.(1114-1116)ccg>CCGccg	p.372_372P>PP	TOX2_ENST00000372999.1_In_Frame_Ins_p.348_348P>PP|TOX2_ENST00000423191.2_In_Frame_Ins_p.348_348P>PP|TOX2_ENST00000435864.2_3'UTR|TOX2_ENST00000341197.4_In_Frame_Ins_p.390_390P>PP	NM_001098798.1	NP_001092268.1	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	372	Pro-rich.			P -> PP (in Ref. 1; BAF82595). {ECO:0000305}.	female gonad development (GO:0008585)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to gonadotropin (GO:0034698)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S347_P348insR(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|skin(2)	26		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			TCAGTGCGTCCCCGCCGCCGCC	0.713														176	0.0351438	0.0045	0.0648	5008	,	,		13049	0.0		0.1044	False		,,,				2504	0.0204																1	Insertion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	20							,,,	79,4179		2,75,2052					,,,	1.5	0.1		dbSNP_126	33	928,7320		58,812,3254	no	coding,coding,coding,coding	TOX2	NM_032883.2,NM_001098798.1,NM_001098797.1,NM_001098796.1	,,,	60,887,5306	A1A1,A1R,RR		11.2512,1.8553,8.0521	,,,	,,,		1007,11499				42127973	SO:0001652	inframe_insertion	84969			BC007636	CCDS13324.1, CCDS42875.1, CCDS46603.1	20q13.12	2007-03-20	2007-03-20	2007-03-20					16095	protein-coding gene	gene with protein product	"""granulosa cell HMG box 1"""	611163	"""chromosome 20 open reading frame 100"""	C20orf100		14764631	Standard	NM_001098796		Approved	dJ1108D11.2, GCX-1	uc010ggo.3	Q96NM4		ENST00000358131.5:c.1120_1122dupCCG	20.37:g.42694565_42694567dupCCG	ENSP00000350849:p.Pro376dup		42127972	A8K1J1|E1P5X0|G3XAC7|Q5TE33|Q5TE34|Q5TE35|Q96IC9|Q9BQN5	In_Frame_Ins	INS	ENST00000358131.5	37	CCDS42875.1																																																																																				0.713	TOX2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079329.2		
