#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
NFE2L3	9603	hgsc.bcm.edu	37	7	26224622	26224622	+	Missense_Mutation	SNP	C	C	G			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr7:26224622C>G	ENST00000056233.3	+	4	1563	c.1304C>G	c.(1303-1305)tCt>tGt	p.S435C		NM_004289.6	NP_004280.5	Q9Y4A8	NF2L3_HUMAN	nuclear factor, erythroid 2-like 3	435					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 negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						GTCATCAAGTCTAATTCCTCT	0.403																																																	0			7											126.0	134.0	131.0					7																	26224622		2203	4300	6503	26191147	SO:0001583	missense	9603			AB010812	CCDS5396.1	7p15.2	2013-08-23	2013-08-23		ENSG00000050344	ENSG00000050344		"""basic leucine zipper proteins"""	7783	protein-coding gene	gene with protein product		604135	"""nuclear factor (erythroid-derived 2)-like 3"""			10037736	Standard	NM_004289		Approved	Nrf3	uc003sxq.3	Q9Y4A8	OTTHUMG00000023882	ENST00000056233.3:c.1304C>G	7.37:g.26224622C>G	ENSP00000056233:p.Ser435Cys		26191147	Q6NUS0|Q7Z498|Q86UJ4|Q86VR5|Q9UQA4	Missense_Mutation	SNP	ENST00000056233.3	37	CCDS5396.1	.	.	.	.	.	.	.	.	.	.	C	6.439	0.449123	0.12223	.	.	ENSG00000050344	ENST00000056233;ENST00000398175	T	0.40756	1.02	5.23	2.33	0.28932	.	0.228514	0.46758	D	0.000274	T	0.42787	0.1218	M	0.85630	2.765	0.09310	N	1	B	0.17038	0.02	B	0.16722	0.016	T	0.48843	-0.8999	10	0.87932	D	0	-0.6589	4.5559	0.12136	0.1269:0.6134:0.1227:0.137	.	435	Q9Y4A8	NF2L3_HUMAN	C	435;141	ENSP00000056233:S435C	ENSP00000056233:S435C	S	+	2	0	NFE2L3	26191147	0.000000	0.05858	0.003000	0.11579	0.058000	0.15608	0.488000	0.22371	0.262000	0.21774	-0.216000	0.12614	TCT		0.403	NFE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214088.1		
HECW1	23072	hgsc.bcm.edu	37	7	43591930	43591930	+	Missense_Mutation	SNP	G	G	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr7:43591930G>C	ENST00000395891.2	+	28	5110	c.4505G>C	c.(4504-4506)cGg>cCg	p.R1502P	HECW1_ENST00000453890.1_Missense_Mutation_p.R1468P	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1502	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						ACTGAGTACCGGGGAGGTGAG	0.478																																																	0			7											86.0	91.0	89.0					7																	43591930		2028	4174	6202	43558455	SO:0001583	missense	23072			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.4505G>C	7.37:g.43591930G>C	ENSP00000379228:p.Arg1502Pro		43558455	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	37	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	G	32	5.181288	0.94846	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.57752	0.38;0.38	5.81	5.81	0.92471	HECT (4);	0.058126	0.64402	D	0.000001	T	0.79399	0.4439	M	0.90252	3.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.99	T	0.82733	-0.0311	10	0.87932	D	0	.	20.0628	0.97684	0.0:0.0:1.0:0.0	.	1468;1502	B4DH42;Q76N89	.;HECW1_HUMAN	P	1502;1468;1502	ENSP00000379228:R1502P;ENSP00000407774:R1468P	ENSP00000265522:R1502P	R	+	2	0	HECW1	43558455	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.414000	0.97362	2.745000	0.94114	0.655000	0.94253	CGG		0.478	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
AKAP9	10142	hgsc.bcm.edu	37	7	91711952	91711952	+	Silent	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr7:91711952T>C	ENST00000359028.2	+	33	8397	c.8172T>C	c.(8170-8172)gcT>gcC	p.A2724A	AKAP9_ENST00000358100.2_Silent_p.A2724A|AKAP9_ENST00000356239.3_Silent_p.A2712A			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	2724	Glu-rich.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AAGAAAAGGCTGAAAAACTTC	0.338			T	BRAF	papillary thyroid																																			Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	0			7											51.0	53.0	52.0					7																	91711952		2203	4300	6503	91549888	SO:0001819	synonymous_variant	10142			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.8172T>C	7.37:g.91711952T>C			91549888	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37																																																																																					0.338	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
SMO	6608	hgsc.bcm.edu	37	7	128846154	128846154	+	Silent	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr7:128846154C>T	ENST00000249373.3	+	5	1364	c.1084C>T	c.(1084-1086)Ctg>Ttg	p.L362L		NM_005631.4	NP_005622.1	Q99835	SMO_HUMAN	smoothened, frizzled class receptor	362					adenohypophysis development (GO:0021984)|anterior/posterior pattern specification (GO:0009952)|atrial septum morphogenesis (GO:0060413)|axon extension involved in axon guidance (GO:0048846)|canonical Wnt signaling pathway (GO:0060070)|cardioblast differentiation (GO:0010002)|cell fate specification (GO:0001708)|cellular response to cholesterol (GO:0071397)|central nervous system neuron differentiation (GO:0021953)|cerebellar cortex morphogenesis (GO:0021696)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|detection of cell density by contact stimulus involved in contact inhibition (GO:0060248)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|epithelial-mesenchymal cell signaling (GO:0060684)|exocrine pancreas development (GO:0031017)|facial nerve development (GO:0021561)|floor plate formation (GO:0021508)|forebrain morphogenesis (GO:0048853)|gonad development (GO:0008406)|hair follicle morphogenesis (GO:0031069)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal to epithelial transition involved in metanephric renal vesicle formation (GO:0072285)|midgut development (GO:0007494)|multicellular organism growth (GO:0035264)|muscle cell fate commitment (GO:0042693)|myoblast migration (GO:0051451)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of gene expression (GO:0010629)|negative regulation of hair follicle development (GO:0051799)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate commitment (GO:0048663)|neuron projection regeneration (GO:0031102)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|otolith morphogenesis (GO:0032474)|pancreas morphogenesis (GO:0061113)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of heart morphogenesis (GO:2000826)|regulation of stem cell maintenance (GO:2000036)|renal system development (GO:0072001)|semicircular canal morphogenesis (GO:0048752)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021910)|somite development (GO:0061053)|spermatogenesis (GO:0007283)|thalamus development (GO:0021794)|type B pancreatic cell development (GO:0003323)|vasculogenesis (GO:0001570)|ventral midline determination (GO:0007371)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	drug binding (GO:0008144)|G-protein coupled receptor activity (GO:0004930)|patched binding (GO:0005113)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			biliary_tract(1)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(14)|liver(1)|lung(11)|pancreas(2)|prostate(1)|skin(20)|upper_aerodigestive_tract(3)|urinary_tract(1)	64					Fluocinonide(DB01047)|Vismodegib(DB08828)	CTACTTCCACCTGCTCACCTG	0.567			Mis		skin basal cell																																			Dom	yes		7	7q31-q32	6608	smoothened homolog (Drosophila)		E	0			7											209.0	166.0	181.0					7																	128846154		2203	4300	6503	128633390	SO:0001819	synonymous_variant	54498			U84401	CCDS5811.1	7q32.1	2014-01-29	2014-01-29	2003-01-17	ENSG00000128602	ENSG00000128602		"""GPCR / Class F : Frizzled receptors"""	11119	protein-coding gene	gene with protein product	"""frizzled family member 11"""	601500	"""smoothened (Drosophila) homolog"", ""smoothened homolog (Drosophila)"", ""smoothened, seven transmembrane spanning receptor"", ""smoothened, frizzled family receptor"""	SMOH		9628830	Standard	NM_005631		Approved	FZD11	uc003vor.3	Q99835	OTTHUMG00000158421	ENST00000249373.3:c.1084C>T	7.37:g.128846154C>T			128633390	A4D1K5	Silent	SNP	ENST00000249373.3	37	CCDS5811.1																																																																																				0.567	SMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350986.1	NM_005631	
KMT2C	58508	hgsc.bcm.edu	37	7	151879124	151879124	+	Missense_Mutation	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr7:151879124T>C	ENST00000262189.6	-	36	6039	c.5821A>G	c.(5821-5823)Aca>Gca	p.T1941A	KMT2C_ENST00000355193.2_Missense_Mutation_p.T1941A	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1941	Pro-rich.				histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TTTGCTGTTGTCTCATTCATT	0.453																																																	0			7											112.0	117.0	115.0					7																	151879124		2203	4300	6503	151510057	SO:0001583	missense	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.5821A>G	7.37:g.151879124T>C	ENSP00000262189:p.Thr1941Ala		151510057	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	T	2.114	-0.402965	0.04865	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	T;T	0.40476	1.03;1.03	5.09	-0.457	0.12186	.	0.513490	0.15780	N	0.244982	T	0.18173	0.0436	N	0.17082	0.46	0.19300	N	0.999975	B;B	0.17667	0.001;0.023	B;B	0.08055	0.002;0.003	T	0.15925	-1.0420	10	0.15952	T	0.53	.	2.0138	0.03493	0.1121:0.2247:0.1287:0.5346	.	1941;1002	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	A	1941	ENSP00000262189:T1941A;ENSP00000347325:T1941A	ENSP00000262189:T1941A	T	-	1	0	MLL3	151510057	0.429000	0.25530	0.001000	0.08648	0.497000	0.33675	-0.061000	0.11693	-0.327000	0.08551	-0.490000	0.04691	ACA		0.453	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
SNX5	27131	hgsc.bcm.edu	37	20	17929566	17929566	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr20:17929566G>A	ENST00000377768.3	-	11	1198	c.886C>T	c.(886-888)Cga>Tga	p.R296*	SNX5_ENST00000377759.4_Nonsense_Mutation_p.R296*|SNX5_ENST00000483485.1_5'UTR	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5	296	BAR.				intracellular protein transport (GO:0006886)|pinocytosis (GO:0006907)	cytoplasmic vesicle (GO:0031410)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|extrinsic component of endosome membrane (GO:0031313)|macropinocytic cup (GO:0070685)	phosphatidylinositol binding (GO:0035091)	p.R296*(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	11						ATGTAGTATCGGAGGAGCTCT	0.413																																																	1	Substitution - Nonsense(1)	large_intestine(1)	20											94.0	90.0	91.0					20																	17929566		2203	4300	6503	17877566	SO:0001587	stop_gained	27131			AF121855	CCDS13130.1	20p11	2008-05-22			ENSG00000089006	ENSG00000089006		"""Sorting nexins"""	14969	protein-coding gene	gene with protein product		605937				10600472, 17148574	Standard	NM_152227		Approved		uc002wqc.3	Q9Y5X3	OTTHUMG00000031953	ENST00000377768.3:c.886C>T	20.37:g.17929566G>A	ENSP00000366998:p.Arg296*		17877566	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Nonsense_Mutation	SNP	ENST00000377768.3	37	CCDS13130.1	.	.	.	.	.	.	.	.	.	.	G	34	5.318136	0.95682	.	.	ENSG00000089006	ENST00000377768;ENST00000377759;ENST00000431277	.	.	.	4.97	1.37	0.22104	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.1945	0.25845	0.0896:0.0:0.362:0.5484	.	.	.	.	X	296;296;259	.	ENSP00000366988:R296X	R	-	1	2	SNX5	17877566	1.000000	0.71417	0.738000	0.30950	0.879000	0.50718	3.189000	0.50965	0.612000	0.30071	-0.878000	0.02970	CGA		0.413	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4		
EMILIN3	90187	hgsc.bcm.edu	37	20	39991144	39991144	+	Silent	SNP	A	A	G	rs41307177	byFrequency	TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr20:39991144A>G	ENST00000332312.3	-	4	1257	c.1065T>C	c.(1063-1065)ctT>ctC	p.L355L		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	355						cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				CCCGGCCATCAAGGCTCTGGT	0.682													A|||	406	0.0810703	0.0598	0.1225	5008	,	,		15115	0.003		0.1799	False		,,,				2504	0.0593																0			20						A		377,4021		11,355,1833	13.0	16.0	15.0		1065	-1.5	1.0	20	dbSNP_127	15	1411,7175		132,1147,3014	no	coding-synonymous	EMILIN3	NM_052846.1		143,1502,4847	GG,GA,AA		16.4337,8.5721,13.7708		355/767	39991144	1788,11196	2199	4293	6492	39424558	SO:0001819	synonymous_variant	90187			AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"""EMI domain containing"""	16123	protein-coding gene	gene with protein product	"""chromosome 20 open reading frame 130"""	608929	"""elastin microfibril interfacer 5"""	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.1065T>C	20.37:g.39991144A>G			39424558	Q495S5|Q495S6|Q495S7|Q76KT4	Silent	SNP	ENST00000332312.3	37	CCDS13316.1																																																																																				0.682	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741	
EMILIN3	90187	hgsc.bcm.edu	37	20	39991171	39991171	+	Silent	SNP	G	G	A	rs61739307	byFrequency	TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr20:39991171G>A	ENST00000332312.3	-	4	1230	c.1038C>T	c.(1036-1038)gcC>gcT	p.A346A		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	346						cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				TCCGGCTGGCGGCCTGACCCT	0.672													G|||	405	0.0808706	0.059	0.1225	5008	,	,		14633	0.003		0.1799	False		,,,				2504	0.0593																0			20						G		390,4012		16,358,1827	15.0	17.0	16.0		1038	-10.3	0.2	20	dbSNP_129	16	1433,7165		130,1173,2996	no	coding-synonymous	EMILIN3	NM_052846.1		146,1531,4823	AA,AG,GG		16.6667,8.8596,14.0231		346/767	39991171	1823,11177	2201	4299	6500	39424585	SO:0001819	synonymous_variant	90187			AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"""EMI domain containing"""	16123	protein-coding gene	gene with protein product	"""chromosome 20 open reading frame 130"""	608929	"""elastin microfibril interfacer 5"""	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.1038C>T	20.37:g.39991171G>A			39424585	Q495S5|Q495S6|Q495S7|Q76KT4	Silent	SNP	ENST00000332312.3	37	CCDS13316.1																																																																																				0.672	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741	
SALL4	57167	hgsc.bcm.edu	37	20	50406985	50406985	+	Silent	SNP	G	G	A	rs13043248	byFrequency	TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr20:50406985G>A	ENST00000217086.4	-	2	2148	c.2037C>T	c.(2035-2037)acC>acT	p.T679T	SALL4_ENST00000395997.3_Intron|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	679					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						AGATAGCGCCGGTGCTGCCGT	0.587													G|||	221	0.0441294	0.0038	0.0562	5008	,	,		18487	0.0268		0.1153	False		,,,				2504	0.0348																0			20						G		103,4303	80.4+/-118.8	0,103,2100	63.0	53.0	56.0		2037	-10.3	0.0	20	dbSNP_121	56	960,7640	211.0+/-251.7	62,836,3402	no	coding-synonymous	SALL4	NM_020436.3		62,939,5502	AA,AG,GG		11.1628,2.3377,8.1732		679/1054	50406985	1063,11943	2203	4300	6503	49840392	SO:0001819	synonymous_variant	57167			AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.2037C>T	20.37:g.50406985G>A			49840392	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																				0.587	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
CLTCL1	8218	hgsc.bcm.edu	37	22	19208966	19208966	+	Missense_Mutation	SNP	C	C	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr22:19208966C>A	ENST00000263200.10	-	17	2802	c.2730G>T	c.(2728-2730)gaG>gaT	p.E910D	CLTCL1_ENST00000427926.1_Missense_Mutation_p.E910D|CLTCL1_ENST00000353891.5_Missense_Mutation_p.E910D	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	910	Heavy chain arm.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					GGTCTCGCTTCTCACAGTAGC	0.557			T	?	ALCL																																			Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	0			22											31.0	33.0	32.0					22																	19208966		2090	4235	6325	17588966	SO:0001583	missense	8218				CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"""clathrin, heavy polypeptide-like 1"""	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.2730G>T	22.37:g.19208966C>A	ENSP00000445677:p.Glu910Asp		17588966	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	CCDS46662.1	.	.	.	.	.	.	.	.	.	.	C	14.17	2.454318	0.43634	.	.	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.27402	1.67;1.67;1.67	3.63	1.31	0.21738	Tetratricopeptide-like helical (1);Armadillo-type fold (2);	0.000000	0.64402	D	0.000001	T	0.58104	0.2099	H	0.94886	3.595	0.52099	D	0.999946	D;D	0.76494	0.999;0.998	D;D	0.91635	0.999;0.998	T	0.58295	-0.7661	10	0.87932	D	0	-15.0034	4.2723	0.10792	0.0:0.4141:0.0:0.5859	.	910;910	P53675-2;P53675	.;CLH2_HUMAN	D	910	ENSP00000439662:E910D;ENSP00000445677:E910D;ENSP00000441158:E910D	ENSP00000445677:E910D	E	-	3	2	CLTCL1	17588966	1.000000	0.71417	0.998000	0.56505	0.110000	0.19582	1.386000	0.34419	0.733000	0.32492	0.462000	0.41574	GAG		0.557	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
NF2	4771	hgsc.bcm.edu	37	22	30035156	30035156	+	Silent	SNP	A	A	G	rs535626069		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr22:30035156A>G	ENST00000338641.4	+	3	759	c.318A>G	c.(316-318)gaA>gaG	p.E106E	NF2_ENST00000413209.2_Silent_p.E106E|NF2_ENST00000403435.1_Silent_p.E106E|NF2_ENST00000397789.3_Silent_p.E106E|NF2_ENST00000403999.3_Silent_p.E106E|NF2_ENST00000361676.4_Silent_p.E64E|NF2_ENST00000334961.7_Intron|NF2_ENST00000347330.5_Intron|NF2_ENST00000361452.4_Intron|NF2_ENST00000353887.4_Intron|NF2_ENST00000361166.4_Silent_p.E106E	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	106	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.		E -> G (in NF2). {ECO:0000269|PubMed:8081368, ECO:0000269|PubMed:9643284}.		actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(3)|p.H95fs*3(1)|p.V86_Q111>E(1)|p.A105fs*20(1)|p.L97fs*17(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						AGAATGCTGAAGAGGAGCTGG	0.448			"""D, Mis, N, F, S, O"""		"""meningioma, acoustic neuroma, renal """	"""meningioma, acoustic neuroma"""			Neurofibromatosis, type 2				A|||	1	0.000199681	0.0008	0.0	5008	,	,		20266	0.0		0.0	False		,,,				2504	0.0						yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	7	Unknown(3)|Deletion - Frameshift(3)|Complex - deletion inframe(1)	soft_tissue(3)|stomach(1)|large_intestine(1)|lung(1)|kidney(1)	22											137.0	120.0	126.0					22																	30035156		2203	4300	6503	28365156	SO:0001819	synonymous_variant	4771	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"""A-kinase anchor proteins"""	7773	protein-coding gene	gene with protein product	"""moesin-ezrin-radixin like"", ""schwannomin"""	607379	"""neurofibromin 2 (bilateral acoustic neuroma)"""			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.318A>G	22.37:g.30035156A>G			28365156	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Silent	SNP	ENST00000338641.4	37	CCDS13861.1																																																																																				0.448	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268	
CYTH4	27128	hgsc.bcm.edu	37	22	37690749	37690749	+	Missense_Mutation	SNP	G	G	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr22:37690749G>A	ENST00000248901.6	+	3	338	c.151G>A	c.(151-153)Gag>Aag	p.E51K	CYTH4_ENST00000405206.3_Missense_Mutation_p.E51K|CYTH4_ENST00000439667.1_3'UTR|CYTH4_ENST00000402997.1_Missense_Mutation_p.E51K	NM_013385.3	NP_037517.1	Q9UIA0	CYH4_HUMAN	cytohesin 4	51					positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|lipid binding (GO:0008289)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(2)|stomach(1)	15						CGACTGCTTCGAGAGTGCGGA	0.587																																																	0			22											131.0	120.0	124.0					22																	37690749		2203	4300	6503	36020695	SO:0001583	missense	27128			AF075458	CCDS13946.1	22q12.3-q13.1	2014-05-02	2008-08-14	2008-08-14	ENSG00000100055	ENSG00000100055		"""Pleckstrin homology (PH) domain containing"""	9505	protein-coding gene	gene with protein product		606514	"""pleckstrin homology, Sec7 and coiled/coil domains 4"", ""pleckstrin homology, Sec7 and coiled-coil domains 4"""	PSCD4		10591208	Standard	NM_013385		Approved	CYT4, cytohesin-4	uc003arf.3	Q9UIA0	OTTHUMG00000150562	ENST00000248901.6:c.151G>A	22.37:g.37690749G>A	ENSP00000248901:p.Glu51Lys		36020695	Q5R3F9|Q9UGT6	Missense_Mutation	SNP	ENST00000248901.6	37	CCDS13946.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.917968	0.33815	.	.	ENSG00000100055	ENST00000457992;ENST00000248901;ENST00000422721;ENST00000402997;ENST00000405206	T;T;T;T	0.47869	0.83;3.23;0.84;0.84	4.78	4.78	0.61160	.	0.459587	0.24258	N	0.040111	T	0.40694	0.1127	L	0.58810	1.83	0.44380	D	0.997286	B;B	0.27679	0.031;0.185	B;B	0.25614	0.014;0.062	T	0.39272	-0.9622	10	0.44086	T	0.13	.	6.917	0.24365	0.0948:0.1787:0.7265:0.0	.	51;64	Q9UIA0;Q9H7Q0	CYH4_HUMAN;.	K	51;51;64;51;51	ENSP00000405442:E51K;ENSP00000248901:E51K;ENSP00000385997:E51K;ENSP00000384280:E51K	ENSP00000248901:E51K	E	+	1	0	CYTH4	36020695	0.001000	0.12720	0.938000	0.37757	0.723000	0.41478	0.985000	0.29578	2.195000	0.70347	0.561000	0.74099	GAG		0.587	CYTH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318917.1		
C14orf37	145407	hgsc.bcm.edu	37	14	58604742	58604742	+	Silent	SNP	A	A	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr14:58604742A>C	ENST00000267485.7	-	2	1529	c.1335T>G	c.(1333-1335)tcT>tcG	p.S445S	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	445						integral component of membrane (GO:0016021)				breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						GGTCTGCCTCAGACTCATATA	0.358																																																	0			14											77.0	79.0	79.0					14																	58604742		2203	4300	6503	57674495	SO:0001819	synonymous_variant	145407				CCDS32089.1	14q23.1	2012-09-03			ENSG00000139971	ENSG00000139971			19846	protein-coding gene	gene with protein product							Standard	NM_001001872		Approved		uc001xdc.3	Q86TY3	OTTHUMG00000171173	ENST00000267485.7:c.1335T>G	14.37:g.58604742A>C			57674495	A8K8Z8|Q6P5Q1|Q86TY1	Silent	SNP	ENST00000267485.7	37	CCDS32089.1																																																																																				0.358	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872	
C14orf39	317761	hgsc.bcm.edu	37	14	60903654	60903654	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr14:60903654G>T	ENST00000321731.3	-	18	1832	c.1673C>A	c.(1672-1674)tCa>tAa	p.S558*		NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39	558					multicellular organismal development (GO:0007275)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		CTGTCCAAATGAAAATGGAAA	0.338																																																	0			14											148.0	168.0	161.0					14																	60903654		2203	4296	6499	59973407	SO:0001587	stop_gained	317761			AK098187	CCDS9746.1	14q23.1	2012-11-05	2012-11-05	2012-11-05	ENSG00000179008	ENSG00000179008			19849	protein-coding gene	gene with protein product							Standard	NM_174978		Approved	SIX6OS1	uc001xez.4	Q8N1H7	OTTHUMG00000140332	ENST00000321731.3:c.1673C>A	14.37:g.60903654G>T	ENSP00000324920:p.Ser558*		59973407	Q08AQ4	Nonsense_Mutation	SNP	ENST00000321731.3	37	CCDS9746.1	.	.	.	.	.	.	.	.	.	.	G	37	6.205991	0.97376	.	.	ENSG00000179008	ENST00000321731	.	.	.	5.17	5.17	0.71159	.	0.287405	0.25159	N	0.032686	.	.	.	.	.	.	0.53688	D	0.999976	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.5617	17.6578	0.88182	0.0:0.0:1.0:0.0	.	.	.	.	X	558	.	ENSP00000324920:S558X	S	-	2	0	C14orf39	59973407	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	6.202000	0.72131	2.408000	0.81797	0.557000	0.71058	TCA		0.338	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978	
PAPLN	89932	hgsc.bcm.edu	37	14	73729497	73729497	+	Silent	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr14:73729497C>T	ENST00000554301.1	+	18	2848	c.2685C>T	c.(2683-2685)gcC>gcT	p.A895A	PAPLN_ENST00000381166.3_Silent_p.A895A|PAPLN_ENST00000555445.1_Silent_p.A879A|PAPLN_ENST00000427855.1_Silent_p.A895A|PAPLN_ENST00000340738.5_Silent_p.A868A|PAPLN_ENST00000554314.1_3'UTR			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	895						basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		GTGGAGATGCCGGATCACCAG	0.667																																																	0			14											14.0	16.0	15.0					14																	73729497		2198	4293	6491	72799250	SO:0001819	synonymous_variant	89932			BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"""Immunoglobulin superfamily / I-set domain containing"""	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.2685C>T	14.37:g.73729497C>T			72799250	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Silent	SNP	ENST00000554301.1	37																																																																																					0.667	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462	
TLE6	79816	hgsc.bcm.edu	37	19	2978266	2978266	+	Missense_Mutation	SNP	C	C	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr19:2978266C>A	ENST00000246112.4	+	2	236	c.35C>A	c.(34-36)cCc>cAc	p.P12H	TLE6_ENST00000482627.1_Missense_Mutation_p.P12H|TLE6_ENST00000452088.1_Intron	NM_001143986.1	NP_001137458.1	Q9H808	TLE6_HUMAN	transducin-like enhancer of split 6	12					regulation of transcription, DNA-templated (GO:0006355)	cell cortex (GO:0005938)|nucleus (GO:0005634)|protein complex (GO:0043234)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|urinary_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCAAGGGCCCCCCGAAAAGC	0.577																																																	0			19											24.0	25.0	25.0					19																	2978266		692	1591	2283	2929266	SO:0001583	missense	79816			AK024071	CCDS12100.1, CCDS45910.1	19p13.3	2014-03-07	2014-03-07		ENSG00000104953	ENSG00000104953		"""WD repeat domain containing"""	30788	protein-coding gene	gene with protein product		612399	"""transducin-like enhancer of split 6 (E(sp1) homolog, Drosophila)"""			11486032	Standard	NM_024760		Approved	FLJ14009, GRG6	uc002lwt.2	Q9H808	OTTHUMG00000156793	ENST00000246112.4:c.35C>A	19.37:g.2978266C>A	ENSP00000246112:p.Pro12His		2929266	J3KMZ1	Missense_Mutation	SNP	ENST00000246112.4	37	CCDS45910.1	.	.	.	.	.	.	.	.	.	.	C	11.35	1.613579	0.28712	.	.	ENSG00000104953	ENST00000447920;ENST00000453329;ENST00000246112	T	0.25250	1.81	1.59	1.59	0.23543	.	.	.	.	.	T	0.16685	0.0401	N	0.08118	0	0.21064	N	0.999794	P	0.43352	0.804	P	0.47015	0.534	T	0.11179	-1.0598	9	0.87932	D	0	.	6.6424	0.22917	0.0:1.0:0.0:0.0	.	12	C9JGZ7	.	H	12	ENSP00000246112:P12H	ENSP00000246112:P12H	P	+	2	0	TLE6	2929266	0.008000	0.16893	0.006000	0.13384	0.002000	0.02628	0.453000	0.21811	1.227000	0.43598	0.462000	0.41574	CCC		0.577	TLE6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345996.3	NM_024760	
RFX1	5989	hgsc.bcm.edu	37	19	14076266	14076266	+	Missense_Mutation	SNP	C	C	A	rs377533889		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr19:14076266C>A	ENST00000254325.4	-	16	2440	c.2206G>T	c.(2206-2208)Gtg>Ttg	p.V736L		NM_002918.4	NP_002909.4	P22670	RFX1_HUMAN	regulatory factor X, 1 (influences HLA class II expression)	736					immune response (GO:0006955)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(19;6.67e-23)			CTCACCTTCACCCGCAGCATC	0.617																																																	0			19											171.0	181.0	178.0					19																	14076266		2203	4300	6503	13937266	SO:0001583	missense	5989				CCDS12301.1	19p13.1	2008-07-17				ENSG00000132005			9982	protein-coding gene	gene with protein product	"""trans-acting regulatory factor 1"", ""enhancer factor C"", ""MHC class II regulatory factor RFX"""	600006				1505960, 8289803	Standard	NM_002918		Approved	EF-C	uc002mxv.3	P22670		ENST00000254325.4:c.2206G>T	19.37:g.14076266C>A	ENSP00000254325:p.Val736Leu		13937266		Missense_Mutation	SNP	ENST00000254325.4	37	CCDS12301.1	.	.	.	.	.	.	.	.	.	.	c	14.07	2.424629	0.43020	.	.	ENSG00000132005	ENST00000254325	T	0.07908	3.15	4.02	4.02	0.46733	.	0.130838	0.52532	D	0.000076	T	0.08758	0.0217	L	0.39245	1.2	0.41086	D	0.985564	B	0.21688	0.059	B	0.20184	0.028	T	0.19614	-1.0300	10	0.27785	T	0.31	-22.0861	15.0907	0.72192	0.0:1.0:0.0:0.0	.	736	P22670	RFX1_HUMAN	L	736	ENSP00000254325:V736L	ENSP00000254325:V736L	V	-	1	0	RFX1	13937266	0.998000	0.40836	1.000000	0.80357	0.919000	0.55068	2.463000	0.45058	2.074000	0.62210	0.462000	0.41574	GTG		0.617	RFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458510.1	NM_002918	
HAPLN4	404037	hgsc.bcm.edu	37	19	19372262	19372262	+	Silent	SNP	G	G	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr19:19372262G>A	ENST00000291481.7	-	2	177	c.114C>T	c.(112-114)caC>caT	p.H38H	AC138430.4_ENST00000586064.2_RNA	NM_023002.2	NP_075378.1	Q86UW8	HPLN4_HUMAN	hyaluronan and proteoglycan link protein 4	38					cell adhesion (GO:0007155)	proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(1)	16			Epithelial(12;0.00575)		Hyaluronan(DB08818)	CACCCAGCACGTGCACGACCT	0.706																																																	0			19											31.0	25.0	27.0					19																	19372262		2197	4292	6489	19233262	SO:0001819	synonymous_variant	404037			AB107883	CCDS12398.1	19p13.1	2013-01-11						"""Immunoglobulin superfamily / V-set domain containing"""	31357	protein-coding gene	gene with protein product	"""brain link protein 2"""					12663660	Standard	NM_023002		Approved	BRAL2, KIAA1926	uc002nmb.3	Q86UW8		ENST00000291481.7:c.114C>T	19.37:g.19372262G>A			19233262	A5PKW5|Q96PW2	Silent	SNP	ENST00000291481.7	37	CCDS12398.1																																																																																				0.706	HAPLN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460117.2	NM_023002	
URI1	8725	hgsc.bcm.edu	37	19	30477315	30477315	+	Silent	SNP	C	C	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr19:30477315C>A	ENST00000542441.2	+	4	655	c.358C>A	c.(358-360)Cgg>Agg	p.R120R	URI1_ENST00000312051.6_Silent_p.R80R|URI1_ENST00000392271.1_Silent_p.R44R|URI1_ENST00000360605.4_Silent_p.R102R			O94763	RMP_HUMAN	URI1, prefoldin-like chaperone	120					cellular response to growth factor stimulus (GO:0071363)|cellular response to steroid hormone stimulus (GO:0071383)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to virus (GO:0009615)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	chromatin binding (GO:0003682)|protein phosphatase inhibitor activity (GO:0004864)|RNA polymerase II transcription corepressor activity (GO:0001106)	p.R120W(1)									AGTTGAGCACCGGAAAGAACG	0.423																																																	1	Substitution - Missense(1)	kidney(1)	19											147.0	140.0	143.0					19																	30477315		2203	4300	6503	35169155	SO:0001819	synonymous_variant	8725			AF091095	CCDS12420.1, CCDS58658.1	19q12	2012-04-17	2011-11-21	2011-11-21	ENSG00000105176	ENSG00000105176		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	13236	protein-coding gene	gene with protein product	"""unconventional prefoldin RPB5 interactor"", ""RPB5-mediating protein"", ""protein phosphatase 1, regulatory subunit 19"""	603494	"""chromosome 19 open reading frame 2"""	C19orf2		9878255, 9819440	Standard	NM_003796		Approved	RMP, NNX3, FLJ10575, URI, PPP1R19	uc002nsr.3	O94763		ENST00000542441.2:c.358C>A	19.37:g.30477315C>A			35169155	A8K805|H7BY42|Q8TC23|Q9UNU3	Silent	SNP	ENST00000542441.2	37	CCDS12420.1																																																																																				0.423	URI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439756.1	NM_134447	
TSHZ3	57616	hgsc.bcm.edu	37	19	31768401	31768401	+	Silent	SNP	C	C	T	rs368908849		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr19:31768401C>T	ENST00000240587.4	-	2	2625	c.2298G>A	c.(2296-2298)ccG>ccA	p.P766P		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	766					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P766P(1)|p.P583P(1)		breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					GCAGGGGCGGCGGGGTGGCCA	0.597													C|||	1	0.000199681	0.0008	0.0	5008	,	,		16006	0.0		0.0	False		,,,				2504	0.0																2	Substitution - coding silent(2)	large_intestine(2)	19						C		0,4406		0,0,2203	65.0	64.0	64.0		2298	-8.0	0.2	19		64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TSHZ3	NM_020856.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		766/1082	31768401	1,13005	2203	4300	6503	36460241	SO:0001819	synonymous_variant	57616			AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	30700	protein-coding gene	gene with protein product	"""teashirt 3"""	614119	"""zinc finger protein 537"", ""teashirt family zinc finger 3"""	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.2298G>A	19.37:g.31768401C>T			36460241	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																				0.597	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
ZNF568	374900	hgsc.bcm.edu	37	19	37441552	37441552	+	Silent	SNP	G	G	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr19:37441552G>A	ENST00000333987.7	+	7	2003	c.1497G>A	c.(1495-1497)gaG>gaA	p.E499E	ZNF568_ENST00000415168.1_Silent_p.E435E|ZNF568_ENST00000455427.2_Intron|ZNF568_ENST00000427117.1_Intron	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	499					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)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ATACGGGTGAGAAACCCTATG	0.383																																																	0			19											67.0	73.0	71.0					19																	37441552		2183	4294	6477	42133392	SO:0001819	synonymous_variant	374900			BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"""Zinc fingers, C2H2-type"", ""-"""	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.1497G>A	19.37:g.37441552G>A			42133392	B4DS92|E7ER33|Q6N060|Q8NA64	Silent	SNP	ENST00000333987.7	37	CCDS42558.1																																																																																				0.383	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539	
RYR1	6261	hgsc.bcm.edu	37	19	38976617	38976617	+	Silent	SNP	G	G	A	rs572516017	byFrequency	TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr19:38976617G>A	ENST00000359596.3	+	34	5322	c.5322G>A	c.(5320-5322)ccG>ccA	p.P1774P	RYR1_ENST00000360985.3_Silent_p.P1774P|RYR1_ENST00000355481.4_Silent_p.P1774P			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1774	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	TGAGGCCCCCGCATCATTTCT	0.692													G|||	2	0.000399361	0.0	0.0	5008	,	,		15752	0.002		0.0	False		,,,				2504	0.0																0			19											37.0	36.0	36.0					19																	38976617		2203	4300	6503	43668457	SO:0001819	synonymous_variant	6261			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.5322G>A	19.37:g.38976617G>A			43668457	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																				0.692	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
ZNF160	90338	hgsc.bcm.edu	37	19	53571463	53571463	+	Missense_Mutation	SNP	C	C	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr19:53571463C>A	ENST00000429604.1	-	7	2739	c.2324G>T	c.(2323-2325)aGt>aTt	p.S775I	ZNF160_ENST00000418871.1_Missense_Mutation_p.S775I|ZNF160_ENST00000601421.1_Missense_Mutation_p.S739I|ZNF160_ENST00000599056.1_Missense_Mutation_p.S775I	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	775					hemopoiesis (GO:0030097)|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)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	35				GBM - Glioblastoma multiforme(134;0.02)		GGTAGTTAGACTTGATCTTAC	0.433																																																	0			19											134.0	123.0	127.0					19																	53571463		2203	4300	6503	58263275	SO:0001583	missense	90338			X78928	CCDS12859.1	19q13.42	2013-01-08				ENSG00000170949		"""Zinc fingers, C2H2-type"", ""-"""	12948	protein-coding gene	gene with protein product		600398				7774943, 7865130	Standard	NM_198893		Approved	HZF5, F11, KR18, HKr18, FLJ00032, KIAA1611	uc002qar.4	Q9HCG1		ENST00000429604.1:c.2324G>T	19.37:g.53571463C>A	ENSP00000406201:p.Ser775Ile		58263275	Q14589|Q504Q8|Q96JC5|Q9BVY9|Q9H7N6	Missense_Mutation	SNP	ENST00000429604.1	37	CCDS12859.1	.	.	.	.	.	.	.	.	.	.	C	4.458	0.084920	0.08583	.	.	ENSG00000170949	ENST00000429604;ENST00000418871	T;T	0.15952	2.38;2.38	2.24	-2.7	0.06004	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18759	0.0450	L	0.35341	1.055	0.09310	N	1	D	0.61697	0.99	P	0.61658	0.892	T	0.13335	-1.0513	9	0.30854	T	0.27	.	3.1973	0.06637	0.3482:0.4148:0.0:0.237	.	775	Q9HCG1	ZN160_HUMAN	I	775	ENSP00000406201:S775I;ENSP00000409597:S775I	ENSP00000409597:S775I	S	-	2	0	ZNF160	58263275	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-4.557000	0.00216	-0.622000	0.05626	0.467000	0.42956	AGT		0.433	ZNF160-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463994.2	NM_033288	
DLC1	10395	hgsc.bcm.edu	37	8	12960306	12960306	+	Missense_Mutation	SNP	C	C	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr8:12960306C>A	ENST00000276297.4	-	8	1968	c.1559G>T	c.(1558-1560)cGg>cTg	p.R520L	DLC1_ENST00000520226.1_Missense_Mutation_p.R9L|DLC1_ENST00000358919.2_Missense_Mutation_p.R83L|DLC1_ENST00000512044.2_Missense_Mutation_p.R117L	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	520					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						CACTCGTTTCCGATGAGGACT	0.368																																																	0			8											186.0	180.0	182.0					8																	12960306		2203	4300	6503	13004677	SO:0001583	missense	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	2897	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 12"""	604258	"""deleted in liver cancer 1"""			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1559G>T	8.37:g.12960306C>A	ENSP00000276297:p.Arg520Leu		13004677	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	37	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.688264	0.88639	.	.	ENSG00000164741	ENST00000276297;ENST00000358919;ENST00000512044;ENST00000520226	T;T;T;T	0.50277	0.75;0.75;0.75;3.11	5.85	5.85	0.93711	.	0.052329	0.85682	D	0.000000	T	0.68265	0.2982	L	0.58810	1.83	0.80722	D	1	D;P;D	0.89917	1.0;0.95;0.98	D;P;D	0.87578	0.998;0.737;0.961	T	0.67309	-0.5703	10	0.72032	D	0.01	.	20.5471	0.99284	0.0:1.0:0.0:0.0	.	520;117;83	Q96QB1;E9PDZ8;Q96QB1-1	RHG07_HUMAN;.;.	L	520;83;117;9	ENSP00000276297:R520L;ENSP00000351797:R83L;ENSP00000422595:R117L;ENSP00000428028:R9L	ENSP00000276297:R520L	R	-	2	0	DLC1	13004677	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.113000	0.50376	2.941000	0.99782	0.655000	0.94253	CGG		0.368	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
OPRK1	4986	hgsc.bcm.edu	37	8	54141940	54141940	+	Missense_Mutation	SNP	G	G	A	rs202165724		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr8:54141940G>A	ENST00000265572.3	-	4	1357	c.1060C>T	c.(1060-1062)Cgg>Tgg	p.R354W	RP11-162D9.3_ENST00000524425.1_RNA|OPRK1_ENST00000520287.1_Missense_Mutation_p.R354W|OPRK1_ENST00000524278.1_Missense_Mutation_p.R265W	NM_000912.3	NP_000903.2	P41145	OPRK_HUMAN	opioid receptor, kappa 1	354					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-inhibiting opioid receptor signaling pathway (GO:0031635)|behavior (GO:0007610)|defense response to virus (GO:0051607)|immune response (GO:0006955)|locomotory behavior (GO:0007626)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of saliva secretion (GO:0046877)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dynorphin receptor activity (GO:0038048)|opioid receptor activity (GO:0004985)			NS(2)|breast(3)|endometrium(3)|kidney(12)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	43		all_epithelial(80;0.066)|Lung NSC(129;0.0804)|all_lung(136;0.136)			Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Fentanyl(DB00813)|Heroin(DB01452)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Menthol(DB00825)|Methylnaltrexone(DB06800)|Mianserin(DB06148)|Mirtazapine(DB00370)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pentazocine(DB00652)|Pethidine(DB00454)|Progesterone(DB00396)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	GTGCTCTGCCGCTCCATCCTC	0.483													G|||	1	0.000199681	0.0	0.0	5008	,	,		21096	0.001		0.0	False		,,,				2504	0.0																0			8											100.0	90.0	93.0					8																	54141940		2203	4300	6503	54304493	SO:0001583	missense	4986				CCDS6152.1, CCDS64895.1	8q11.2	2014-05-21			ENSG00000082556	ENSG00000082556		"""GPCR / Class A : Opioid receptors"""	8154	protein-coding gene	gene with protein product		165196				8188308	Standard	XM_005251252		Approved	KOR, OPRK	uc003xri.1	P41145	OTTHUMG00000164276	ENST00000265572.3:c.1060C>T	8.37:g.54141940G>A	ENSP00000265572:p.Arg354Trp		54304493	E5RHC9|Q499G4	Missense_Mutation	SNP	ENST00000265572.3	37	CCDS6152.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	10.54	1.378101	0.24944	.	.	ENSG00000082556	ENST00000265572;ENST00000524278;ENST00000520287;ENST00000396798	T;T;T	0.61040	0.14;0.14;0.14	5.8	2.88	0.33553	.	0.456643	0.24896	N	0.034723	T	0.55970	0.1954	M	0.73962	2.25	0.39824	D	0.972871	P	0.35242	0.492	B	0.35727	0.209	T	0.60642	-0.7223	10	0.66056	D	0.02	.	9.7171	0.40281	0.0681:0.0:0.551:0.3808	.	354	P41145	OPRK_HUMAN	W	354;265;354;340	ENSP00000265572:R354W;ENSP00000430923:R265W;ENSP00000429706:R354W	ENSP00000265572:R354W	R	-	1	2	OPRK1	54304493	0.994000	0.37717	0.933000	0.37362	0.288000	0.27193	1.542000	0.36137	0.765000	0.33221	0.650000	0.86243	CGG		0.483	OPRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378048.1		
PREX2	80243	hgsc.bcm.edu	37	8	69028025	69028025	+	Missense_Mutation	SNP	C	C	T	rs200550325		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr8:69028025C>T	ENST00000288368.4	+	26	3461	c.3184C>T	c.(3184-3186)Cgt>Tgt	p.R1062C		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1062					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TAAATTAGAACGTAAGACATC	0.348													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19240	0.0		0.0	False		,,,				2504	0.0																0			8						C	CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	122.0	115.0	117.0		3184	5.9	1.0	8		117	0,8600		0,0,4300	no	missense	PREX2	NM_024870.2	180	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	possibly-damaging	1062/1607	69028025	2,13004	2203	4300	6503	69190579	SO:0001583	missense	80243			AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.3184C>T	8.37:g.69028025C>T	ENSP00000288368:p.Arg1062Cys		69190579	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	37	CCDS6201.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	18.27	3.587503	0.66105	4.54E-4	0.0	ENSG00000046889	ENST00000288368;ENST00000396539	T	0.60040	0.22	5.86	5.86	0.93980	.	0.323970	0.35040	N	0.003495	T	0.46444	0.1393	N	0.22421	0.69	0.58432	D	0.99999	P	0.40000	0.698	B	0.33799	0.17	T	0.51529	-0.8694	10	0.62326	D	0.03	.	20.5632	0.99335	0.0:1.0:0.0:0.0	.	1062	Q70Z35	PREX2_HUMAN	C	1062;1065	ENSP00000288368:R1062C	ENSP00000288368:R1062C	R	+	1	0	PREX2	69190579	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	4.680000	0.61656	2.937000	0.99478	0.650000	0.86243	CGT		0.348	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
CSMD3	114788	hgsc.bcm.edu	37	8	113988189	113988189	+	Missense_Mutation	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr8:113988189C>T	ENST00000297405.5	-	7	1463	c.1219G>A	c.(1219-1221)Gac>Aac	p.D407N	CSMD3_ENST00000343508.3_Missense_Mutation_p.D367N|CSMD3_ENST00000352409.3_Missense_Mutation_p.D407N|CSMD3_ENST00000455883.2_Intron	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	407						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D407Y(1)|p.D367Y(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						GTGTTGGGGTCCAGACCTGAA	0.478										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																							2	Substitution - Missense(2)	lung(2)	8											217.0	189.0	199.0					8																	113988189		2203	4300	6503	114057365	SO:0001583	missense	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.1219G>A	8.37:g.113988189C>T	ENSP00000297405:p.Asp407Asn		114057365	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	18.91	3.724099	0.68959	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000352409	T;T;T	0.19532	2.14;2.14;2.16	6.17	6.17	0.99709	.	0.629156	0.14680	N	0.304829	T	0.21761	0.0524	N	0.22421	0.69	0.35922	D	0.831885	B;B	0.32245	0.247;0.361	B;B	0.37304	0.078;0.246	T	0.20405	-1.0276	10	0.22706	T	0.39	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	407;367	Q7Z407;Q7Z407-2	CSMD3_HUMAN;.	N	367;407;407	ENSP00000345799:D367N;ENSP00000297405:D407N;ENSP00000343124:D407N	ENSP00000297405:D407N	D	-	1	0	CSMD3	114057365	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.742000	0.55097	2.941000	0.99782	0.655000	0.94253	GAC		0.478	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
CHD5	26038	hgsc.bcm.edu	37	1	6181181	6181181	+	Silent	SNP	C	C	T	rs35026547		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:6181181C>T	ENST00000262450.3	-	33	4995	c.4896G>A	c.(4894-4896)ccG>ccA	p.P1632P	CHD5_ENST00000378021.1_Silent_p.P489P	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		GCAGCTGCTCCGGGGAGGGCG	0.657																																																	0			1											21.0	25.0	24.0					1																	6181181		2203	4300	6503	6103768	SO:0001819	synonymous_variant	450091			AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"""Zinc fingers, PHD-type"""	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.4896G>A	1.37:g.6181181C>T			6103768	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000262450.3	37	CCDS57.1																																																																																				0.657	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557	
CAMTA1	23261	hgsc.bcm.edu	37	1	7792593	7792593	+	Silent	SNP	A	A	G			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:7792593A>G	ENST00000303635.7	+	12	3207	c.3000A>G	c.(2998-3000)aaA>aaG	p.K1000K	CAMTA1_ENST00000439411.2_Silent_p.K1000K	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	1000					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		AGCAGCACAAACAGGCGAGCG	0.632			T	WWTR1	epitheliod hemangioendothelioma																																			Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	0			1											55.0	61.0	59.0					1																	7792593		2203	4299	6502	7715180	SO:0001819	synonymous_variant	23261			AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.3000A>G	1.37:g.7792593A>G			7715180	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Silent	SNP	ENST00000303635.7	37	CCDS30576.1																																																																																				0.632	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215	
DFFA	1676	hgsc.bcm.edu	37	1	10527267	10527267	+	Missense_Mutation	SNP	G	G	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:10527267G>T	ENST00000377038.3	-	3	488	c.421C>A	c.(421-423)Cta>Ata	p.L141I	DFFA_ENST00000377036.2_Missense_Mutation_p.L141I	NM_004401.2	NP_004392.1	O00273	DFFA_HUMAN	DNA fragmentation factor, 45kDa, alpha polypeptide	141					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|negative regulation of apoptotic DNA fragmentation (GO:1902511)|negative regulation of execution phase of apoptosis (GO:1900118)|positive regulation of apoptotic process (GO:0043065)|thymocyte apoptotic process (GO:0070242)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				large_intestine(3)|lung(2)	5	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;7.25e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000296)|Kidney(185;0.00074)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487)		TCCTCTGATAGGAGGATGATG	0.532																																																	0			1											156.0	148.0	151.0					1																	10527267		2203	4300	6503	10449854	SO:0001583	missense	1676			AF087573	CCDS118.1, CCDS119.1	1p36.3-p36.2	2008-07-18	2002-08-29		ENSG00000160049	ENSG00000160049			2772	protein-coding gene	gene with protein product	"""DNA fragmentation factor, 45 kD, alpha subunit"""	601882	"""DNA fragmentation factor, 45 kD, alpha polypeptide"""			9605855, 9108473	Standard	NM_004401		Approved	DFF-45, DFF45, ICAD, DFF1	uc001arj.3	O00273	OTTHUMG00000001909	ENST00000377038.3:c.421C>A	1.37:g.10527267G>T	ENSP00000366237:p.Leu141Ile		10449854	Q5T6G5|Q5T6G6|Q96I97|Q9Y6C6	Missense_Mutation	SNP	ENST00000377038.3	37	CCDS118.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.520700	0.44866	.	.	ENSG00000160049	ENST00000377038;ENST00000377036	.	.	.	5.68	3.7	0.42460	DNA fragmentation factor 45kDa, C-terminal (2);	0.044831	0.85682	D	0.000000	T	0.51210	0.1661	L	0.60455	1.87	0.33457	D	0.584437	P;P	0.52692	0.814;0.955	B;P	0.52424	0.38;0.698	T	0.65191	-0.6228	9	0.62326	D	0.03	-3.7304	7.3501	0.26686	0.084:0.0:0.6002:0.3158	.	141;141	O00273-2;O00273	.;DFFA_HUMAN	I	141	.	ENSP00000366235:L141I	L	-	1	2	DFFA	10449854	1.000000	0.71417	0.986000	0.45419	0.118000	0.20060	4.178000	0.58284	1.407000	0.46875	0.650000	0.86243	CTA		0.532	DFFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005418.1	NM_004401	
MPL	4352	hgsc.bcm.edu	37	1	43805160	43805160	+	Missense_Mutation	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:43805160T>C	ENST00000372470.3	+	4	652	c.610T>C	c.(610-612)Tct>Cct	p.S204P	MPL_ENST00000413998.2_Missense_Mutation_p.S204P	NM_005373.2	NP_005364.1	P40238	TPOR_HUMAN	MPL proto-oncogene, thrombopoietin receptor	204	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|platelet activation (GO:0030168)|regulation of chemokine production (GO:0032642)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|transmembrane signaling receptor activity (GO:0004888)	p.S204P(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(551)|large_intestine(3)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	567	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			Eltrombopag(DB06210)|Romiplostim(DB05332)	TCACTCAGCCTCTGCTCTGGA	0.567			Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia																														NSCLC(52;534 1204 10016 41452 44427)		yes	Dom	yes	Familial essential thrombocythemia	1	p34	4352	"""myeloproliferative leukemia virus oncogene, thrombopoietin receptor"""	yes	L	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	1											87.0	84.0	85.0					1																	43805160		2203	4300	6503	43577747	SO:0001583	missense	4352			M90102	CCDS483.1	1p34	2014-09-17	2014-06-26		ENSG00000117400	ENSG00000117400		"""CD molecules"", ""Fibronectin type III domain containing"""	7217	protein-coding gene	gene with protein product		159530	"""myeloproliferative leukemia virus oncogene"""			1608974	Standard	NM_005373		Approved	CD110, TPOR	uc001ciw.3	P40238	OTTHUMG00000007429	ENST00000372470.3:c.610T>C	1.37:g.43805160T>C	ENSP00000361548:p.Ser204Pro		43577747	Q5JUZ0	Missense_Mutation	SNP	ENST00000372470.3	37	CCDS483.1	.	.	.	.	.	.	.	.	.	.	T	1.415	-0.574377	0.03882	.	.	ENSG00000117400	ENST00000372468;ENST00000372470;ENST00000413998	T;T	0.80824	-1.42;-1.16	4.5	-5.13	0.02884	Fibronectin, type III (3);	0.842808	0.10744	N	0.639085	T	0.48370	0.1496	N	0.02916	-0.46	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.33979	-0.9847	10	0.28530	T	0.3	1.2049	2.0421	0.03553	0.1264:0.32:0.1245:0.4292	.	197;204;204	Q308M1;P40238;Q5JUY5	.;TPOR_HUMAN;.	P	204	ENSP00000361548:S204P;ENSP00000414004:S204P	ENSP00000361546:S204P	S	+	1	0	MPL	43577747	0.000000	0.05858	0.000000	0.03702	0.159000	0.22180	-1.137000	0.03219	-1.090000	0.03069	-0.345000	0.07892	TCT		0.567	MPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019522.1	NM_005373	
BSND	7809	hgsc.bcm.edu	37	1	55472904	55472904	+	Silent	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:55472904C>T	ENST00000371265.4	+	3	761	c.507C>T	c.(505-507)gaC>gaT	p.D169D		NM_057176.2	NP_476517.1	Q8WZ55	BSND_HUMAN	barttin CLCNK-type chloride channel accessory beta subunit	169					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	chloride channel activity (GO:0005254)|chloride channel regulator activity (GO:0017081)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17						AGGGCTCAGACGAGAGTGAAG	0.607																																					Ovarian(191;1657 2078 22894 42033 48899)												0			1											85.0	76.0	79.0					1																	55472904		2203	4300	6503	55245492	SO:0001819	synonymous_variant	7809			AY034632	CCDS602.1	1p32.3	2014-06-17	2014-06-17		ENSG00000162399	ENSG00000162399			16512	protein-coding gene	gene with protein product		606412	"""deafness, autosomal recessive 73"", ""Bartter syndrome, infantile, with sensorineural deafness (Barttin)"""	DFNB73		11687798, 11734858, 19646679	Standard	NM_057176		Approved	BART	uc001cye.3	Q8WZ55	OTTHUMG00000008112	ENST00000371265.4:c.507C>T	1.37:g.55472904C>T			55245492	Q6NT28	Silent	SNP	ENST00000371265.4	37	CCDS602.1																																																																																				0.607	BSND-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022213.4	NM_057176	
MIER1	57708	hgsc.bcm.edu	37	1	67411869	67411869	+	Missense_Mutation	SNP	C	C	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:67411869C>A	ENST00000355356.3	+	3	220	c.71C>A	c.(70-72)cCa>cAa	p.P24Q	MIER1_ENST00000371018.3_Missense_Mutation_p.P41Q|MIER1_ENST00000371014.1_Missense_Mutation_p.P77Q|MIER1_ENST00000371016.1_Missense_Mutation_p.P41Q|MIER1_ENST00000401041.1_Missense_Mutation_p.P77Q|MIER1_ENST00000479067.1_3'UTR|MIER1_ENST00000371012.2_Missense_Mutation_p.P41Q|MIER1_ENST00000357692.2_Missense_Mutation_p.P41Q|MIER1_ENST00000401042.3_Missense_Mutation_p.P24Q|MIER1_ENST00000355977.6_Intron	NM_001077701.2|NM_001077704.2	NP_001071169.1|NP_001071172.1	Q8N108	MIER1_HUMAN	mesoderm induction early response 1, transcriptional regulator	24					positive regulation of chromatin silencing (GO:0031937)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(3)	15						GAATTTGATCCATCAGCTGAC	0.343																																																	0			1											118.0	107.0	111.0					1																	67411869		1853	4092	5945	67184457	SO:0001583	missense	57708				CCDS41347.1, CCDS41348.1, CCDS53325.1, CCDS53326.1, CCDS53327.1, CCDS53328.1, CCDS53329.1, CCDS53330.1, CCDS60163.1	1p31.2	2013-07-23	2013-07-23		ENSG00000198160	ENSG00000198160			29657	protein-coding gene	gene with protein product			"""mesoderm induction early response 1 homolog (Xenopus laevis)"""			12242014, 12482978	Standard	NM_020948		Approved	hMI-ER1, MI-ER1, KIAA1610	uc001dde.2	Q8N108	OTTHUMG00000009194	ENST00000355356.3:c.71C>A	1.37:g.67411869C>A	ENSP00000347514:p.Pro24Gln		67184457	C9JFD4|Q08AE0|Q32NC4|Q5T104|Q5TAD1|Q5TAD2|Q5TAD4|Q5TAD5|Q6AHY8|Q86TB4|Q8N156|Q8N161|Q8NC37|Q8NES4|Q8NES5|Q8NES6|Q8WWG2|Q9HCG2	Missense_Mutation	SNP	ENST00000355356.3	37	CCDS41348.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.891634	0.91889	.	.	ENSG00000198160	ENST00000371017;ENST00000371018;ENST00000357692;ENST00000401041;ENST00000371016;ENST00000371014;ENST00000371012;ENST00000401042;ENST00000355356	T;T;T;T;T;T;T;T	0.22743	1.94;1.94;1.94;1.94;1.94;1.94;1.94;1.94	5.24	5.24	0.73138	.	0.110094	0.64402	D	0.000006	T	0.41604	0.1166	M	0.72353	2.195	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.979;0.998;0.999;0.998;0.999;0.996;0.991	T	0.35871	-0.9771	10	0.87932	D	0	-27.2707	19.2207	0.93795	0.0:1.0:0.0:0.0	.	41;41;24;24;41;77;77	Q5TAD2;Q32NC4;Q8N108-3;Q8N108-6;Q8N108-10;Q5TAD5;Q5TAD4	.;.;.;.;.;.;.	Q	45;41;41;77;41;77;41;24;24	ENSP00000360057:P41Q;ENSP00000350321:P41Q;ENSP00000383820:P77Q;ENSP00000360055:P41Q;ENSP00000360053:P77Q;ENSP00000360051:P41Q;ENSP00000383821:P24Q;ENSP00000347514:P24Q	ENSP00000347514:P24Q	P	+	2	0	MIER1	67184457	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.466000	0.80914	2.621000	0.88768	0.655000	0.94253	CCA		0.343	MIER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025491.2	NM_020948	
USP33	23032	hgsc.bcm.edu	37	1	78180333	78180333	+	Silent	SNP	A	A	G			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:78180333A>G	ENST00000370793.1	-	20	2620	c.2274T>C	c.(2272-2274)ccT>ccC	p.P758P	USP33_ENST00000370792.3_Silent_p.P750P|USP33_ENST00000357428.1_Silent_p.P758P|USP33_ENST00000370794.3_Silent_p.P727P	NM_015017.4	NP_055832.3	Q8TEY7	UBP33_HUMAN	ubiquitin specific peptidase 33	758	DUSP 1. {ECO:0000255|PROSITE- ProRule:PRU00613}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|centrosome duplication (GO:0051298)|endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell body (GO:0044297)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|VCB complex (GO:0030891)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	44						TATTTGAAATAGGGCCAGGTT	0.348																																					Melanoma(152;72 1870 11110 26780 42647)												0			1											93.0	94.0	93.0					1																	78180333		2203	4300	6503	77952921	SO:0001819	synonymous_variant	23032			AF383173	CCDS678.1, CCDS679.1, CCDS680.1	1p31	2008-02-05	2005-08-08		ENSG00000077254	ENSG00000077254		"""Ubiquitin-specific peptidases"""	20059	protein-coding gene	gene with protein product		615146	"""ubiquitin specific protease 33"""			12838346	Standard	NM_015017		Approved	KIAA1097, VDU1	uc001dht.4	Q8TEY7	OTTHUMG00000009651	ENST00000370793.1:c.2274T>C	1.37:g.78180333A>G			77952921	Q8TEY6|Q96AV6|Q9H9F0|Q9UPQ5	Silent	SNP	ENST00000370793.1	37	CCDS678.1	.	.	.	.	.	.	.	.	.	.	A	9.584	1.124357	0.20959	.	.	ENSG00000077254	ENST00000481579	.	.	.	5.21	0.0388	0.14202	.	.	.	.	.	T	0.28764	0.0713	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.17167	-1.0378	4	.	.	.	.	4.4599	0.11661	0.463:0.0:0.3293:0.2077	.	.	.	.	P	363	.	.	L	-	2	0	USP33	77952921	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.711000	0.25764	0.375000	0.24679	-0.250000	0.11733	CTA		0.348	USP33-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026923.2	NM_015017	
KCNA2	3737	hgsc.bcm.edu	37	1	111146775	111146775	+	Silent	SNP	G	G	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:111146775G>A	ENST00000485317.1	-	3	1303	c.630C>T	c.(628-630)atC>atT	p.I210I	KCNA2_ENST00000316361.4_Silent_p.I210I|KCNA2_ENST00000369770.3_Silent_p.I210I|KCNA2_ENST00000525120.1_Intron|KCNA2_ENST00000440270.1_Silent_p.I210I			P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 2	210					optic nerve structural organization (GO:0021633)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)	Dalfampridine(DB06637)	GCTGGTACCCGATGGTGCTGT	0.483																																					Pancreas(18;568 735 10587 23710 36357)												0			1											155.0	152.0	153.0					1																	111146775		2203	4300	6503	110948298	SO:0001819	synonymous_variant	3737			L02752	CCDS827.1, CCDS55625.1	1p13	2012-07-05			ENSG00000177301	ENSG00000177301		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6220	protein-coding gene	gene with protein product		176262				16382104	Standard	NM_004974		Approved	Kv1.2, HK4	uc009wfw.3	P16389	OTTHUMG00000011567	ENST00000485317.1:c.630C>T	1.37:g.111146775G>A			110948298	Q86XG6	Silent	SNP	ENST00000485317.1	37	CCDS827.1																																																																																				0.483	KCNA2-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128001.2	NM_004974	
FLG	2312	hgsc.bcm.edu	37	1	152285797	152285797	+	Missense_Mutation	SNP	G	G	A	rs146559843		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:152285797G>A	ENST00000368799.1	-	3	1600	c.1565C>T	c.(1564-1566)tCa>tTa	p.S522L	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	522	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCCTCTGCTTGACCCCGGGTG	0.587									Ichthyosis																																								0			1											358.0	357.0	357.0					1																	152285797		2203	4300	6503	150552421	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.1565C>T	1.37:g.152285797G>A	ENSP00000357789:p.Ser522Leu		150552421	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	12.06	1.823358	0.32237	.	.	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.03745	3.82	3.19	-0.57	0.11753	.	.	.	.	.	T	0.05227	0.0139	M	0.77616	2.38	0.09310	N	1	D	0.62365	0.991	D	0.65573	0.936	T	0.24584	-1.0156	9	0.40728	T	0.16	.	5.0672	0.14587	0.0:0.2058:0.3751:0.4191	.	522	P20930	FILA_HUMAN	L	522;54	ENSP00000357789:S522L	ENSP00000357789:S522L	S	-	2	0	FLG	150552421	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.196000	0.17176	0.130000	0.18549	0.603000	0.83216	TCA		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
FLG2	388698	hgsc.bcm.edu	37	1	152324057	152324057	+	Missense_Mutation	SNP	G	G	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:152324057G>T	ENST00000388718.5	-	3	6277	c.6205C>A	c.(6205-6207)Cac>Aac	p.H2069N	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	2069					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTAGTTCCGTGTCTCTCATGA	0.537																																																	0			1											544.0	480.0	502.0					1																	152324057		2203	4300	6503	150590681	SO:0001583	missense	388698			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"""EF-hand domain containing"""	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.6205C>A	1.37:g.152324057G>T	ENSP00000373370:p.His2069Asn		150590681	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	G	7.239	0.600831	0.13939	.	.	ENSG00000143520	ENST00000388718	T	0.03689	3.84	4.32	2.24	0.28232	.	.	.	.	.	T	0.01061	0.0035	L	0.50333	1.59	0.09310	N	1	B	0.34061	0.436	B	0.27796	0.083	T	0.44802	-0.9304	9	0.13470	T	0.59	.	6.8391	0.23953	0.0:0.1962:0.601:0.2028	.	2069	Q5D862	FILA2_HUMAN	N	2069	ENSP00000373370:H2069N	ENSP00000373370:H2069N	H	-	1	0	FLG2	150590681	0.019000	0.18553	0.184000	0.23157	0.006000	0.05464	0.895000	0.28363	1.167000	0.42706	-0.190000	0.12839	CAC		0.537	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
FLG2	388698	hgsc.bcm.edu	37	1	152328900	152328900	+	Silent	SNP	G	G	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:152328900G>T	ENST00000388718.5	-	3	1434	c.1362C>A	c.(1360-1362)ggC>ggA	p.G454G	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	454	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.G454G(1)		NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACTCATGCTGGCCACAAGTTT	0.493																																																	1	Substitution - coding silent(1)	lung(1)	1											185.0	178.0	180.0					1																	152328900		2203	4300	6503	150595524	SO:0001819	synonymous_variant	388698			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"""EF-hand domain containing"""	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.1362C>A	1.37:g.152328900G>T			150595524	Q9H4U1	Silent	SNP	ENST00000388718.5	37	CCDS30861.1																																																																																				0.493	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
SHC1	6464	hgsc.bcm.edu	37	1	154942742	154942742	+	Silent	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:154942742T>C	ENST00000368445.5	-	1	475	c.261A>G	c.(259-261)gcA>gcG	p.A87A	SHC1_ENST00000606391.1_Intron|SHC1_ENST00000368453.4_Intron|SHC1_ENST00000368450.1_Intron|SHC1_ENST00000448116.2_Silent_p.A87A|SHC1_ENST00000368449.4_Intron	NM_183001.4	NP_892113.4	P29353	SHC1_HUMAN	SHC (Src homology 2 domain containing) transforming protein 1	87					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|Ras protein signal transduction (GO:0007265)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of growth (GO:0040008)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|Shc-EGFR complex (GO:0070435)	ephrin receptor binding (GO:0046875)|epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phospholipid binding (GO:0005543)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	20	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CATCATCAGCTGCCCTTCCTG	0.672																																					NSCLC(4;32 234 1864 2492 3259 13747 17376)												0			1											26.0	31.0	30.0					1																	154942742		2203	4297	6500	153209366	SO:0001819	synonymous_variant	6464			U73377	CCDS1076.1, CCDS30881.1, CCDS44233.1, CCDS44234.1	1q21	2013-02-14	2002-01-14		ENSG00000160691	ENSG00000160691		"""SH2 domain containing"""	10840	protein-coding gene	gene with protein product		600560	"""SHC (Src homology 2 domain-containing) transforming protein 1"""	SHC		1623525	Standard	NM_003029		Approved	p66	uc001ffw.3	P29353	OTTHUMG00000037295	ENST00000368445.5:c.261A>G	1.37:g.154942742T>C			153209366	B5BU19|D3DV78|O15290|Q5T180|Q5T183|Q5T184|Q5T185|Q5T186|Q8N4K5|Q96CL1	Silent	SNP	ENST00000368445.5	37	CCDS30881.1																																																																																				0.672	SHC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090781.2	NM_183001	
IFI16	3428	hgsc.bcm.edu	37	1	159023463	159023463	+	Silent	SNP	G	G	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:159023463G>A	ENST00000295809.7	+	11	2481	c.2226G>A	c.(2224-2226)ccG>ccA	p.P742P	IFI16_ENST00000340979.6_Silent_p.P630P|IFI16_ENST00000448393.2_Silent_p.P630P|IFI16_ENST00000359709.3_Silent_p.P686P|IFI16_ENST00000368132.3_Silent_p.P686P|IFI16_ENST00000430894.2_Silent_p.P690P|IFI16_ENST00000368131.4_Silent_p.P686P			Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	742	HIN-200 2. {ECO:0000255|PROSITE- ProRule:PRU00106}.|Interaction with TP53 core domain.				activation of cysteine-type endopeptidase activity (GO:0097202)|activation of innate immune response (GO:0002218)|autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular response to glucose starvation (GO:0042149)|cellular response to ionizing radiation (GO:0071479)|defense response to virus (GO:0051607)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|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)|monocyte differentiation (GO:0030224)|myeloid cell differentiation (GO:0030099)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|negative regulation of DNA binding (GO:0043392)|negative regulation of innate immune response (GO:0045824)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|positive regulation of cytokine production (GO:0001819)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of autophagy (GO:0010506)|regulation of gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0429)					AATTGGCACCGAAAAGTGGGA	0.423																																																	0			1											136.0	132.0	133.0					1																	159023463		2203	4300	6503	157290087	SO:0001819	synonymous_variant	3428			M63838	CCDS1180.3, CCDS58039.1	1q22	2008-02-05			ENSG00000163565	ENSG00000163565			5395	protein-coding gene	gene with protein product		147586				1526658, 7959953	Standard	NM_005531		Approved	IFNGIP1, PYHIN2	uc010pis.2	Q16666	OTTHUMG00000037108	ENST00000295809.7:c.2226G>A	1.37:g.159023463G>A			157290087	B4DJT8|H3BLV7|Q59GX0|Q5T3W7|Q5T3W8|Q5T3X0|Q5T3X1|Q5T3X2|Q8N9E5|Q8NEQ7|Q96AJ5|Q9UH78	Silent	SNP	ENST00000295809.7	37		.	.	.	.	.	.	.	.	.	.	G	0.689	-0.795272	0.02862	.	.	ENSG00000163565	ENST00000448393	.	.	.	0.628	-1.26	0.09376	.	.	.	.	.	T	0.06554	0.0168	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.37103	-0.9720	3	.	.	.	.	.	.	.	.	.	.	.	Q	451	.	.	R	+	2	0	IFI16	157290087	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.043000	0.12043	-1.359000	0.02174	-1.362000	0.01212	CGA		0.423	IFI16-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000421720.1	NM_005531	
CAMSAP2	23271	hgsc.bcm.edu	37	1	200818159	200818159	+	Missense_Mutation	SNP	G	G	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:200818159G>T	ENST00000236925.4	+	12	2344	c.2295G>T	c.(2293-2295)agG>agT	p.R765S	CAMSAP2_ENST00000358823.2_Missense_Mutation_p.R754S|CAMSAP2_ENST00000413307.2_Missense_Mutation_p.R738S			Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein family, member 2	765					microtubule cytoskeleton organization (GO:0000226)|regulation of organelle organization (GO:0033043)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)	microtubule minus-end binding (GO:0051011)										TGCATCTTAGGATGAAACTAG	0.468																																																	0			1											74.0	80.0	78.0					1																	200818159		2203	4300	6503	199084782	SO:0001583	missense	23271			AB029001	CCDS1404.1, CCDS72998.1, CCDS72999.1	1q32	2011-08-18	2011-08-18	2011-08-18	ENSG00000118200	ENSG00000118200			29188	protein-coding gene	gene with protein product		613775	"""calmodulin regulated spectrin-associated protein 1-like 1"""	CAMSAP1L1		15897902, 19508979	Standard	XM_005245040		Approved	KIAA1078	uc001gvk.3	Q08AD1	OTTHUMG00000035740	ENST00000236925.4:c.2295G>T	1.37:g.200818159G>T	ENSP00000236925:p.Arg765Ser		199084782	B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4	Missense_Mutation	SNP	ENST00000236925.4	37		.	.	.	.	.	.	.	.	.	.	G	13.66	2.303709	0.40795	.	.	ENSG00000118200	ENST00000358823;ENST00000413307;ENST00000236925	T;T;T	0.69175	-0.38;-0.38;-0.38	5.41	2.5	0.30297	.	0.000000	0.85682	D	0.000000	T	0.59197	0.2176	L	0.48877	1.53	0.58432	D	0.999997	P;P;P	0.48764	0.915;0.745;0.9	P;B;P	0.45610	0.474;0.293;0.487	T	0.52230	-0.8603	10	0.32370	T	0.25	-17.2843	8.7163	0.34414	0.1378:0.1246:0.7376:0.0	.	738;765;754	Q08AD1-2;Q08AD1;Q08AD1-3	.;CAMP2_HUMAN;.	S	754;738;765	ENSP00000351684:R754S;ENSP00000416800:R738S;ENSP00000236925:R765S	ENSP00000236925:R765S	R	+	3	2	CAMSAP1L1	199084782	1.000000	0.71417	0.994000	0.49952	0.952000	0.60782	2.224000	0.42945	0.249000	0.21456	0.484000	0.47621	AGG		0.468	CAMSAP2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086956.2	NM_203459	
PTPN14	5784	hgsc.bcm.edu	37	1	214549631	214549631	+	Missense_Mutation	SNP	C	C	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:214549631C>A	ENST00000366956.5	-	15	3032	c.2838G>T	c.(2836-2838)gaG>gaT	p.E946D	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	946	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)	p.E946E(1)		NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		CTCGATTCTCCTCATAGGGGA	0.463																																					Colon(92;557 1424 24372 34121 40073)												1	Substitution - coding silent(1)	kidney(1)	1											186.0	179.0	181.0					1																	214549631		2203	4300	6503	212616254	SO:0001583	missense	5784			X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.2838G>T	1.37:g.214549631C>A	ENSP00000355923:p.Glu946Asp		212616254	Q5VSI0	Missense_Mutation	SNP	ENST00000366956.5	37	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	C	4.693	0.128794	0.08981	.	.	ENSG00000152104	ENST00000366956	T	0.78707	-1.2	5.29	5.29	0.74685	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	T	0.66733	0.2819	N	0.02334	-0.595	0.80722	D	1	D	0.61080	0.989	D	0.71414	0.973	T	0.65998	-0.6032	10	0.02654	T	1	.	12.3131	0.54940	0.0:0.9227:0.0:0.0773	.	946	Q15678	PTN14_HUMAN	D	946	ENSP00000355923:E946D	ENSP00000355923:E946D	E	-	3	2	PTPN14	212616254	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.040000	0.41203	2.468000	0.83385	0.655000	0.94253	GAG		0.463	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401	
RAB4A	5867	hgsc.bcm.edu	37	1	229433367	229433367	+	Silent	SNP	A	A	G			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:229433367A>G	ENST00000366690.4	+	5	637	c.429A>G	c.(427-429)agA>agG	p.R143R	RAB4A_ENST00000473894.1_3'UTR	NM_004578.2	NP_004569.2	P20338	RAB4A_HUMAN	RAB4A, member RAS oncogene family	143					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|regulation of endocytosis (GO:0030100)|small GTPase mediated signal transduction (GO:0007264)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein transporter activity (GO:0008565)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|skin(1)	11	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.178)				AAGCCTCCAGATTTGCTCAAG	0.378																																					Esophageal Squamous(11;250 603 9619 16563)												0			1											93.0	91.0	92.0					1																	229433367		2203	4300	6503	227499990	SO:0001819	synonymous_variant	5867			BC004309	CCDS31050.1, CCDS73046.1	1q42-q43	2014-04-03		2002-02-28	ENSG00000168118	ENSG00000168118		"""RAB, member RAS oncogene"""	9781	protein-coding gene	gene with protein product		179511		RAB4			Standard	NM_004578		Approved	HRES-1/RAB4	uc001hth.4	P20338	OTTHUMG00000037627	ENST00000366690.4:c.429A>G	1.37:g.229433367A>G			227499990	Q5T7P7|Q9BQ44	Silent	SNP	ENST00000366690.4	37	CCDS31050.1																																																																																				0.378	RAB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091727.3	NM_004578	
C1orf101	257044	hgsc.bcm.edu	37	1	244780890	244780890	+	Silent	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:244780890C>T	ENST00000366534.4	+	20	2604	c.2550C>T	c.(2548-2550)taC>taT	p.Y850Y	C1orf101_ENST00000366531.3_Silent_p.Y699Y|C1orf101_ENST00000366533.4_Intron	NM_001130957.1	NP_001124429.1	Q5SY80	CA101_HUMAN	chromosome 1 open reading frame 101	850						CatSper complex (GO:0036128)				NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	36	all_cancers(71;2.99e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)		all cancers(7;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.001)|GBM - Glioblastoma multiforme(7;0.0154)			ATCAACCATACGAGATTATCA	0.338																																																	0			1											232.0	184.0	199.0					1																	244780890		692	1589	2281	242847513	SO:0001819	synonymous_variant	257044			BC032859	CCDS1625.1, CCDS44340.1, CCDS55693.1	1q44	2012-12-20			ENSG00000179397	ENSG00000179397			28491	protein-coding gene	gene with protein product						12477932	Standard	NM_173807		Approved	MGC33370	uc001iam.3	Q5SY80	OTTHUMG00000040103	ENST00000366534.4:c.2550C>T	1.37:g.244780890C>T			242847513	B4DZR4|B7Z7X5|E9PEA3|Q8IYZ6	Silent	SNP	ENST00000366534.4	37	CCDS44340.1																																																																																				0.338	C1orf101-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096701.1	NM_173807	
OR51T1	401665	hgsc.bcm.edu	37	11	4903553	4903553	+	Missense_Mutation	SNP	A	A	G			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:4903553A>G	ENST00000322049.1	+	1	424	c.424A>G	c.(424-426)Atg>Gtg	p.M142V	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron|OR51T1_ENST00000380378.1_Missense_Mutation_p.M169V			Q8NGJ9	O51T1_HUMAN	olfactory receptor, family 51, subfamily T, member 1	142						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		CACAGACAGGATGGTCCTGGT	0.502																																																	0			11											157.0	137.0	144.0					11																	4903553		2201	4298	6499	4860129	SO:0001583	missense	401665			BK004283	CCDS31363.1	11p15.4	2012-08-09			ENSG00000176900	ENSG00000176900		"""GPCR / Class A : Olfactory receptors"""	15205	protein-coding gene	gene with protein product							Standard	NM_001004759		Approved		uc010qyp.2	Q8NGJ9	OTTHUMG00000066507	ENST00000322049.1:c.424A>G	11.37:g.4903553A>G	ENSP00000322679:p.Met142Val		4860129	Q6IFH9	Missense_Mutation	SNP	ENST00000322049.1	37		.	.	.	.	.	.	.	.	.	.	A	0	-2.755926	0.00085	.	.	ENSG00000176900	ENST00000380378;ENST00000322049	T;T	0.34667	1.35;1.35	4.68	0.947	0.19555	GPCR, rhodopsin-like superfamily (1);	0.745901	0.11988	N	0.510130	T	0.13072	0.0317	N	0.03304	-0.355	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.31530	-0.9940	10	0.05721	T	0.95	.	8.3607	0.32357	0.7502:0.0:0.2498:0.0	.	142	Q8NGJ9	O51T1_HUMAN	V	169;142	ENSP00000369738:M169V;ENSP00000322679:M142V	ENSP00000322679:M142V	M	+	1	0	OR51T1	4860129	0.001000	0.12720	0.140000	0.22221	0.009000	0.06853	1.282000	0.33226	0.303000	0.22785	0.397000	0.26171	ATG		0.502	OR51T1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000142180.1	NM_001004759	
STK33	65975	hgsc.bcm.edu	37	11	8435184	8435184	+	Missense_Mutation	SNP	C	C	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:8435184C>A	ENST00000447869.1	-	11	2120	c.1202G>T	c.(1201-1203)tGg>tTg	p.W401L	STK33_ENST00000534493.1_Missense_Mutation_p.W360L|STK33_ENST00000396672.1_Missense_Mutation_p.W401L|STK33_ENST00000315204.1_Missense_Mutation_p.W401L|STK33_ENST00000473980.1_5'UTR|STK33_ENST00000358872.3_Missense_Mutation_p.W214L|STK33_ENST00000396673.1_Intron			Q9BYT3	STK33_HUMAN	serine/threonine kinase 33	401					protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|skin(3)	23				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)		GTTATTTTTCCATTCCTTCAT	0.358																																																	0			11											218.0	193.0	201.0					11																	8435184		2201	4296	6497	8391760	SO:0001583	missense	65975			AJ303380	CCDS7789.1, CCDS73253.1, CCDS73254.1	11p15.3	2010-03-10			ENSG00000130413	ENSG00000130413			14568	protein-coding gene	gene with protein product		607670				11738831	Standard	NM_030906		Approved		uc001mgj.1	Q9BYT3	OTTHUMG00000140275	ENST00000447869.1:c.1202G>T	11.37:g.8435184C>A	ENSP00000416750:p.Trp401Leu		8391760	Q658S6|Q8NEF5	Missense_Mutation	SNP	ENST00000447869.1	37	CCDS7789.1	.	.	.	.	.	.	.	.	.	.	C	16.81	3.225391	0.58668	.	.	ENSG00000130413	ENST00000447869;ENST00000315204;ENST00000396672;ENST00000358872;ENST00000534493	T;T;T;T;T	0.19669	2.13;2.13;2.13;2.13;2.13	5.9	5.9	0.94986	Protein kinase-like domain (1);	0.630533	0.16861	N	0.196522	T	0.20536	0.0494	L	0.47190	1.495	0.80722	D	1	P	0.34864	0.473	B	0.24848	0.056	T	0.02404	-1.1164	10	0.72032	D	0.01	.	15.7822	0.78269	0.0:1.0:0.0:0.0	.	401	Q9BYT3	STK33_HUMAN	L	401;401;401;214;360	ENSP00000416750:W401L;ENSP00000320754:W401L;ENSP00000379905:W401L;ENSP00000351743:W214L;ENSP00000436418:W360L	ENSP00000320754:W401L	W	-	2	0	STK33	8391760	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.600000	0.54052	2.786000	0.95864	0.563000	0.77884	TGG		0.358	STK33-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276819.2	NM_030906	
IGSF22	283284	hgsc.bcm.edu	37	11	18735520	18735520	+	Silent	SNP	G	G	A	rs369745010		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:18735520G>A	ENST00000513874.1	-	14	2113	c.1974C>T	c.(1972-1974)cgC>cgT	p.R658R	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	658	Ig-like 4.									NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						GGTCTTCCCCGCGCTCCATGG	0.592													g|||	1	0.000199681	0.0	0.0	5008	,	,		24225	0.001		0.0	False		,,,				2504	0.0																0			11								0,4390		0,0,2195	113.0	118.0	116.0		1974	-0.6	0.0	11		116	1,8565	1.2+/-3.3	0,1,4282	no	coding-synonymous	IGSF22	NM_173588.3		0,1,6477	AA,AG,GG		0.0117,0.0,0.0077		658/1327	18735520	1,12955	2195	4283	6478	18692096	SO:0001819	synonymous_variant	283284			AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.1974C>T	11.37:g.18735520G>A			18692096	A6NNA0|D6RGV7	Silent	SNP	ENST00000513874.1	37	CCDS41625.2																																																																																				0.592	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
OR5D16	390144	hgsc.bcm.edu	37	11	55606580	55606580	+	Missense_Mutation	SNP	C	C	T	rs562661348		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:55606580C>T	ENST00000378396.1	+	1	353	c.353C>T	c.(352-354)gCg>gTg	p.A118V		NM_001005496.1	NP_001005496.1	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D, member 16	118						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A118V(1)		cervix(1)|endometrium(2)|large_intestine(4)|lung(26)|ovary(5)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_epithelial(135;0.208)				ATTCTATTTGCGGTGATGGCC	0.423													-|||	1	0.000199681	0.0	0.0014	5008	,	,		18662	0.0		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	ovary(1)	11											122.0	118.0	119.0					11																	55606580		2201	4296	6497	55363156	SO:0001583	missense	390144			AB065783	CCDS31512.1	11q11	2012-08-09			ENSG00000205029	ENSG00000205029		"""GPCR / Class A : Olfactory receptors"""	15283	protein-coding gene	gene with protein product							Standard	NM_001005496		Approved		uc010rio.2	Q8NGK9	OTTHUMG00000154233	ENST00000378396.1:c.353C>T	11.37:g.55606580C>T	ENSP00000367649:p.Ala118Val		55363156	Q6IF65|Q96RB4	Missense_Mutation	SNP	ENST00000378396.1	37	CCDS31512.1	.	.	.	.	.	.	.	.	.	.	.	14.25	2.478779	0.44044	.	.	ENSG00000205029	ENST00000378396	T	0.02015	4.5	4.47	3.56	0.40772	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.07954	0.0199	M	0.76433	2.335	0.09310	N	1	D	0.55605	0.972	P	0.53593	0.73	T	0.08994	-1.0695	9	0.72032	D	0.01	-5.0358	11.1707	0.48569	0.0:0.9083:0.0:0.0917	.	118	Q8NGK9	OR5DG_HUMAN	V	118	ENSP00000367649:A118V	ENSP00000367649:A118V	A	+	2	0	OR5D16	55363156	0.001000	0.12720	0.009000	0.14445	0.743000	0.42351	1.590000	0.36654	1.048000	0.40298	0.530000	0.56133	GCG		0.423	OR5D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334506.1	NM_001005496	
AHNAK	79026	hgsc.bcm.edu	37	11	62300430	62300430	+	Missense_Mutation	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:62300430T>C	ENST00000378024.4	-	5	1733	c.1459A>G	c.(1459-1461)Aaa>Gaa	p.K487E	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	487					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GTCTTCACTTTAGTACCTTTC	0.468																																																	0			11											121.0	130.0	127.0					11																	62300430		2202	4299	6501	62057006	SO:0001583	missense	79026			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.1459A>G	11.37:g.62300430T>C	ENSP00000367263:p.Lys487Glu		62057006	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	T	13.66	2.302606	0.40795	.	.	ENSG00000124942	ENST00000378024	T	0.01665	4.7	5.52	5.52	0.82312	.	0.405543	0.19048	N	0.124117	T	0.11024	0.0269	M	0.88105	2.93	0.24841	N	0.992462	D	0.60575	0.988	D	0.79108	0.992	T	0.37934	-0.9684	10	0.08837	T	0.75	-7.8668	14.6263	0.68624	0.0:0.0:0.0:1.0	.	487	Q09666	AHNK_HUMAN	E	487	ENSP00000367263:K487E	ENSP00000367263:K487E	K	-	1	0	AHNAK	62057006	0.596000	0.26866	0.984000	0.44739	0.683000	0.39861	1.807000	0.38902	2.096000	0.63516	0.454000	0.30748	AAA		0.468	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
CATSPER1	117144	hgsc.bcm.edu	37	11	65793355	65793355	+	Missense_Mutation	SNP	C	C	T	rs543744984		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:65793355C>T	ENST00000312106.5	-	1	633	c.496G>A	c.(496-498)Gtg>Atg	p.V166M		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	166	His-rich.				calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)	p.V166M(2)		breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						TGGTGGGGCACGCCAGAGGAA	0.582																																																	2	Substitution - Missense(2)	ovary(1)|endometrium(1)	11											57.0	53.0	54.0					11																	65793355		2201	4296	6497	65549931	SO:0001583	missense	117144			AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"""Voltage-gated ion channels / Cation channels, sperm associated"""	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.496G>A	11.37:g.65793355C>T	ENSP00000309052:p.Val166Met		65549931	Q96P76	Missense_Mutation	SNP	ENST00000312106.5	37	CCDS8127.1	.	.	.	.	.	.	.	.	.	.	C	4.959	0.178073	0.09443	.	.	ENSG00000175294	ENST00000312106	D	0.96940	-4.18	3.43	1.5	0.22942	.	.	.	.	.	D	0.84556	0.5498	N	0.03115	-0.41	0.09310	N	1	D	0.56287	0.975	B	0.32090	0.14	T	0.79339	-0.1844	9	0.22706	T	0.39	2.3962	8.0048	0.30319	0.0:0.7774:0.0:0.2226	.	166	Q8NEC5	CTSR1_HUMAN	M	166	ENSP00000309052:V166M	ENSP00000309052:V166M	V	-	1	0	CATSPER1	65549931	0.996000	0.38824	0.000000	0.03702	0.049000	0.14656	0.009000	0.13219	0.228000	0.21019	-0.657000	0.03884	GTG		0.582	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054	
TSKU	25987	hgsc.bcm.edu	37	11	76507126	76507126	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:76507126C>T	ENST00000527881.1	+	2	1492	c.466C>T	c.(466-468)Cag>Tag	p.Q156*	TSKU_ENST00000333090.4_Nonsense_Mutation_p.Q156*			Q8WUA8	TSK_HUMAN	tsukushi, small leucine rich proteoglycan	156					anterior commissure morphogenesis (GO:0021960)|ciliary body morphogenesis (GO:0061073)|corpus callosum morphogenesis (GO:0021540)|lateral ventricle development (GO:0021670)|negative regulation of Wnt signaling pathway (GO:0030178)|regulation of gene expression (GO:0010468)	extracellular space (GO:0005615)				NS(1)|large_intestine(4)|lung(6)|urinary_tract(1)	12	Ovarian(111;0.112)					GACGCACAGTCAGGGCCGGGC	0.657																																																	0			11											79.0	77.0	78.0					11																	76507126		2200	4292	6492	76184774	SO:0001587	stop_gained	25987			AK075476	CCDS8246.1	11q13.5	2012-12-05	2012-12-05	2006-11-21	ENSG00000182704	ENSG00000182704			28850	protein-coding gene	gene with protein product		608015	"""leucine rich repeat containing 54"", ""tsukushin"", ""tsukushi small leucine rich proteoglycan homolog (Xenopus laevis)"""	LRRC54		11085516, 19710929, 22880013	Standard	NM_001258210		Approved	E2IG4, TSK	uc031qcw.1	Q8WUA8		ENST00000527881.1:c.466C>T	11.37:g.76507126C>T	ENSP00000434847:p.Gln156*		76184774	B3KQT7|Q6UXK1|Q9UG10|Q9UJX9	Nonsense_Mutation	SNP	ENST00000527881.1	37	CCDS8246.1	.	.	.	.	.	.	.	.	.	.	C	13.52	2.261694	0.39995	.	.	ENSG00000182704	ENST00000333090;ENST00000439807;ENST00000527881	.	.	.	5.0	4.08	0.47627	.	0.364149	0.31554	N	0.007460	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	-15.6443	13.3926	0.60832	0.1589:0.8411:0.0:0.0	.	.	.	.	X	156;124;156	.	ENSP00000332668:Q156X	Q	+	1	0	TSKU	76184774	1.000000	0.71417	0.847000	0.33407	0.008000	0.06430	4.043000	0.57354	1.081000	0.41110	-0.188000	0.12872	CAG		0.657	TSKU-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382871.1	NM_015516	
INTS4	92105	hgsc.bcm.edu	37	11	77639588	77639588	+	Missense_Mutation	SNP	G	G	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:77639588G>A	ENST00000534064.1	-	11	1205	c.1171C>T	c.(1171-1173)Cgt>Tgt	p.R391C	INTS4_ENST00000529807.1_Missense_Mutation_p.R391C|INTS4_ENST00000525931.1_5'UTR	NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	391					snRNA processing (GO:0016180)	integrator complex (GO:0032039)			INTS4/GAB2(2)	NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			GCAGCAATACGAACCTCTAGA	0.493																																																	0			11											7.0	6.0	6.0					11																	77639588		2159	4178	6337	77317236	SO:0001583	missense	92105			BC015664	CCDS31644.1	11q14.1	2006-04-26			ENSG00000149262	ENSG00000149262			25048	protein-coding gene	gene with protein product		611348				16239144	Standard	NM_033547		Approved	INT4, MGC16733, MST093	uc001oys.3	Q96HW7	OTTHUMG00000166629	ENST00000534064.1:c.1171C>T	11.37:g.77639588G>A	ENSP00000434466:p.Arg391Cys		77317236	Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Missense_Mutation	SNP	ENST00000534064.1	37	CCDS31644.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.741648	0.69304	.	.	ENSG00000149262	ENST00000534064;ENST00000354849;ENST00000529807	T;T	0.74315	-0.83;0.26	3.84	3.84	0.44239	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.84999	0.5597	M	0.80616	2.505	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.86773	0.1974	10	0.87932	D	0	-10.8824	11.5458	0.50693	0.0:0.0:0.821:0.179	.	391	Q96HW7	INT4_HUMAN	C	391;242;391	ENSP00000434466:R391C;ENSP00000433644:R391C	ENSP00000346913:R242C	R	-	1	0	INTS4	77317236	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	5.779000	0.68948	2.132000	0.65825	0.471000	0.43371	CGT		0.493	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390927.1	NM_033547	
SYTL2	54843	hgsc.bcm.edu	37	11	85436931	85436931	+	Intron	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:85436931C>T	ENST00000528231.1	-	7	1737				SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000359152.5_Missense_Mutation_p.G714E|SYTL2_ENST00000525423.1_Missense_Mutation_p.G190E|SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000354566.3_Missense_Mutation_p.G190E|SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000524452.1_Intron	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)	p.G190V(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CACTTGTTTTCCATGAACTTT	0.403																																																	1	Substitution - Missense(1)	large_intestine(1)	11											118.0	111.0	114.0					11																	85436931		2203	4299	6502	85114579	SO:0001627	intron_variant	54843			AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+2007G>A	11.37:g.85436931C>T			85114579	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	.	.	.	.	.	.	.	.	.	.	C	8.776	0.926992	0.18056	.	.	ENSG00000137501	ENST00000359152;ENST00000354566;ENST00000525423	T;T;T	0.25579	1.79;1.81;1.81	6.17	-3.84	0.04256	.	1.580750	0.03505	N	0.218707	T	0.11623	0.0283	N	0.12746	0.255	0.09310	N	0.999997	B;B;B	0.11235	0.004;0.004;0.004	B;B;B	0.08055	0.003;0.003;0.003	T	0.18493	-1.0335	9	.	.	.	1.7323	2.926	0.05784	0.12:0.3509:0.0956:0.4335	.	190;190;190	Q9HCH5-11;Q9HCH5-7;Q9HCH5-8	.;.;.	E	714;190;190	ENSP00000352065:G714E;ENSP00000346576:G190E;ENSP00000432694:G190E	.	G	-	2	0	SYTL2	85114579	0.000000	0.05858	0.001000	0.08648	0.686000	0.39977	-2.817000	0.00751	-0.200000	0.10300	0.655000	0.94253	GGA		0.403	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
MMP27	64066	hgsc.bcm.edu	37	11	102573488	102573488	+	Silent	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:102573488T>C	ENST00000260229.4	-	4	706	c.615A>G	c.(613-615)ggA>ggG	p.G205G		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	205					collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	ACTCACCTGCTCCATCCTTGG	0.418																																																	0			11											93.0	101.0	98.0					11																	102573488		2203	4299	6502	102078698	SO:0001819	synonymous_variant	64066			AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"""matrix metalloprotease 27"""		"""matrix metalloproteinase 27"""			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.615A>G	11.37:g.102573488T>C			102078698	Q6UWK6	Silent	SNP	ENST00000260229.4	37	CCDS8319.1																																																																																				0.418	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103173911	103173911	+	Missense_Mutation	SNP	C	C	A	rs199766341		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:103173911C>A	ENST00000375735.2	+	76	11329	c.11185C>A	c.(11185-11187)Ccg>Acg	p.P3729T	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.P3736T	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3729	AAA 6. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		AATTATTTCTCCGGGTGCTGA	0.403																																																	0			11											86.0	82.0	83.0					11																	103173911		1812	4082	5894	102679121	SO:0001583	missense	79659			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.11185C>A	11.37:g.103173911C>A	ENSP00000364887:p.Pro3729Thr		102679121	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.632884	0.67015	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.14893	2.47;2.47	5.35	5.35	0.76521	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.35098	0.0920	M	0.70108	2.13	0.54753	D	0.999985	P;P	0.42123	0.771;0.729	P;B	0.49953	0.627;0.32	T	0.03384	-1.1042	10	0.49607	T	0.09	.	19.0562	0.93066	0.0:1.0:0.0:0.0	.	3729;3736	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	T	3729;3736	ENSP00000364887:P3729T;ENSP00000381167:P3736T	ENSP00000364887:P3729T	P	+	1	0	DYNC2H1	102679121	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	5.269000	0.65542	2.520000	0.84964	0.655000	0.94253	CCG		0.403	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
CASP1	834	hgsc.bcm.edu	37	11	104899870	104899870	+	Silent	SNP	A	A	G			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:104899870A>G	ENST00000533400.1	-	7	1022	c.987T>C	c.(985-987)gcT>gcC	p.A329A	CASP1_ENST00000528974.1_Silent_p.A290A|CASP1_ENST00000436863.3_Silent_p.A329A|CASP1_ENST00000527979.1_Silent_p.A292A|CASP1_ENST00000415981.2_Intron|CASP1_ENST00000594519.1_Intron|CASP1_ENST00000526568.1_Silent_p.A236A|CASP1_ENST00000393136.4_Silent_p.A308A|CASP1_ENST00000534497.1_Intron|CASP1_ENST00000593315.1_Silent_p.A308A|CASP1_ENST00000598974.1_Silent_p.A329A|CASP1_ENST00000353247.5_Intron|CASP1_ENST00000525825.1_Silent_p.A308A|CASP1_ENST00000531166.1_Intron|CASP1_ENST00000446369.1_Intron	NM_001257118.1	NP_001244047.1	P29466	CASP1_HUMAN	caspase 1, apoptosis-related cysteine peptidase	329					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic substance (GO:0071310)|execution phase of apoptosis (GO:0097194)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|membrane hyperpolarization (GO:0060081)|mitochondrial depolarization (GO:0051882)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|programmed necrotic cell death (GO:0097300)|proteolysis (GO:0006508)|pyroptosis (GO:0070269)|regulation of inflammatory response (GO:0050727)|response to ATP (GO:0033198)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|IPAF inflammasome complex (GO:0072557)|NLRP1 inflammasome complex (GO:0072558)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|endopeptidase activity (GO:0004175)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482)	Minocycline(DB01017)	AAGAGCAGAAAGCGATAAAAT	0.398																																					NSCLC(41;1246 1743 4934)												0			11											122.0	113.0	116.0					11																	104899870		2202	4299	6501	104405080	SO:0001819	synonymous_variant	834			U13697	CCDS8329.1, CCDS8330.1, CCDS8331.1, CCDS8332.1, CCDS53704.1	11q23	2012-02-29	2012-02-29		ENSG00000137752	ENSG00000137752		"""Caspases"""	1499	protein-coding gene	gene with protein product	"""caspase-1"", ""interleukin 1, beta, convertase"""	147678	"""caspase 1, apoptosis-related cysteine protease (interleukin 1, beta, convertase)"", ""caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, convertase)"""	IL1BC		1373520, 9250871	Standard	NM_033292		Approved	ICE	uc001pim.5	P29466	OTTHUMG00000048072	ENST00000533400.1:c.987T>C	11.37:g.104899870A>G			104405080	B5MDZ1|Q53EY6|Q6DMQ1|Q6GSS3|Q6PI75|Q9UCN3	Silent	SNP	ENST00000533400.1	37	CCDS8330.1																																																																																				0.398	CASP1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388116.1	NM_033292	
ATM	472	hgsc.bcm.edu	37	11	108216547	108216547	+	Silent	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:108216547T>C	ENST00000452508.2	+	59	8685	c.8496T>C	c.(8494-8496)cgT>cgC	p.R2832R	C11orf65_ENST00000526725.1_Intron|C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Silent_p.R2832R			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2832	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		R -> C (in AT and B-cell non-Hodgkin lymphoma). {ECO:0000269|PubMed:10817650, ECO:0000269|PubMed:9288106, ECO:0000269|PubMed:9443866}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	CAGTTTTCCGTTACTTCTGCA	0.348			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																													yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	0			11											150.0	156.0	154.0					11																	108216547		2200	4298	6498	107721757	SO:0001819	synonymous_variant	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.8496T>C	11.37:g.108216547T>C			107721757	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	37	CCDS31669.1																																																																																				0.348	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
NQO2	4835	hgsc.bcm.edu	37	6	3010339	3010339	+	Silent	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr6:3010339C>T	ENST00000338130.2	+	6	800	c.88C>T	c.(88-90)Ctg>Ttg	p.L30L	NQO2_ENST00000380430.1_Silent_p.L30L|NQO2_ENST00000380441.1_Silent_p.L30L|NQO2_ENST00000380454.4_Silent_p.L30L|NQO2_ENST00000606474.1_3'UTR|NQO2_ENST00000380455.4_Silent_p.L30L			P16083	NQO2_HUMAN	NAD(P)H dehydrogenase, quinone 2	30					memory (GO:0007613)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	dihydronicotinamide riboside quinone reductase activity (GO:0001512)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADPH dehydrogenase (quinone) activity (GO:0008753)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Dabigatran etexilate(DB06695)|Flavin adenine dinucleotide(DB03147)|Melatonin(DB01065)|Menadione(DB00170)|Primaquine(DB01087)	TGTAGATGAACTGAGCAGGCA	0.463																																																	0			6											113.0	98.0	103.0					6																	3010339		2203	4300	6503	2955338	SO:0001819	synonymous_variant	4835			U07736	CCDS4481.1, CCDS75388.1	6p25.2	2012-09-20	2001-11-30	2001-12-07	ENSG00000124588	ENSG00000124588	1.6.5.2		7856	protein-coding gene	gene with protein product		160998	"""NAD(P)H menadione oxidoreductase 2, dioxin-inducible"""	NMOR2		1691923	Standard	XM_005249152		Approved	QR2, DHQV, DIA6	uc003mus.2	P16083	OTTHUMG00000014130	ENST00000338130.2:c.88C>T	6.37:g.3010339C>T			2955338	B2R492|Q5TD04	Silent	SNP	ENST00000338130.2	37	CCDS4481.1																																																																																				0.463	NQO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039651.1		
AIF1	199	hgsc.bcm.edu	37	6	31584094	31584094	+	Intron	SNP	C	C	G	rs13195276		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr6:31584094C>G	ENST00000376059.3	+	5	342				AIF1_ENST00000376049.4_Intron	NM_001623.3	NP_001614.3	P55008	AIF1_HUMAN	allograft inflammatory factor 1						actin filament bundle assembly (GO:0051017)|actin filament polymerization (GO:0030041)|cellular response to interferon-gamma (GO:0071346)|inflammatory response (GO:0006954)|microglial cell activation (GO:0001774)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell proliferation (GO:0048662)|phagocytosis, engulfment (GO:0006911)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of smooth muscle cell chemotaxis (GO:0071673)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell migration (GO:2000406)|positive regulation of T cell proliferation (GO:0042102)|Rac protein signal transduction (GO:0016601)|ruffle assembly (GO:0097178)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|phagocytic cup (GO:0001891)|ruffle membrane (GO:0032587)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)			lung(2)|ovary(1)	3						TCCCCACCTTCTCCCCATCCC	0.537																																					Ovarian(23;358 734 36938 38933 52312)												0			6											72.0	56.0	62.0					6																	31584094		1511	2709	4220	31692073	SO:0001627	intron_variant	199			U19713	CCDS4706.1, CCDS34398.1	6p21.3	2013-01-10			ENSG00000204472	ENSG00000204472		"""EF-hand domain containing"""	352	protein-coding gene	gene with protein product	"""interferon gamma responsive transcript"", ""ionized calcium-binding adapter molecule 1"""	601833				8912632	Standard	NM_032955		Approved	IRT-1, AIF-1, Em:AF129756.17, IBA1	uc003nuy.3	P55008	OTTHUMG00000031246	ENST00000376059.3:c.197-27C>G	6.37:g.31584094C>G			31692073	A8K406|O43904|Q9UIV4|Q9UKS9	Missense_Mutation	SNP	ENST00000376059.3	37	CCDS4706.1																																																																																				0.537	AIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076512.3		
FOXP4	116113	hgsc.bcm.edu	37	6	41533605	41533605	+	Missense_Mutation	SNP	G	G	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr6:41533605G>T	ENST00000307972.4	+	1	119	c.107G>T	c.(106-108)gGg>gTg	p.G36V	FOXP4_ENST00000373060.1_Missense_Mutation_p.G36V|FOXP4_ENST00000373057.3_Missense_Mutation_p.G36V|FOXP4_ENST00000409208.1_Missense_Mutation_p.G36V|FOXP4_ENST00000373063.3_Missense_Mutation_p.G36V			Q8IVH2	FOXP4_HUMAN	forkhead box P4	36					embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					GGGGCCACAGGGACAACTGCA	0.622																																																	0			6											78.0	79.0	78.0					6																	41533605		2203	4300	6503	41641583	SO:0001583	missense	116113			AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"""Forkhead boxes"""	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.107G>T	6.37:g.41533605G>T	ENSP00000309823:p.Gly36Val		41641583	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Missense_Mutation	SNP	ENST00000307972.4	37	CCDS34447.1	.	.	.	.	.	.	.	.	.	.	G	11.93	1.786378	0.31593	.	.	ENSG00000137166	ENST00000373060;ENST00000373063;ENST00000409208;ENST00000373057;ENST00000307972	D;D;D;D;D	0.90133	-2.62;-2.61;-2.62;-2.62;-2.62	5.21	4.34	0.51931	.	0.360853	0.28847	N	0.013945	T	0.74876	0.3774	N	0.22421	0.69	0.41096	D	0.98563	B;B;B	0.34372	0.451;0.451;0.451	B;B;B	0.28709	0.093;0.093;0.093	T	0.76016	-0.3113	10	0.42905	T	0.14	.	13.9996	0.64424	0.0:0.1512:0.8488:0.0	.	36;36;36	Q8IW55;Q7Z7F8;Q8IVH2	.;.;FOXP4_HUMAN	V	36	ENSP00000362151:G36V;ENSP00000362154:G36V;ENSP00000386958:G36V;ENSP00000362148:G36V;ENSP00000309823:G36V	ENSP00000309823:G36V	G	+	2	0	FOXP4	41641583	0.560000	0.26570	0.170000	0.22879	0.321000	0.28281	0.000000	0.12993	1.194000	0.43101	0.655000	0.94253	GGG		0.622	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457	
TCTE1	202500	hgsc.bcm.edu	37	6	44254085	44254085	+	Missense_Mutation	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr6:44254085C>T	ENST00000371505.4	-	3	584	c.462G>A	c.(460-462)atG>atA	p.M154I	TMEM151B_ENST00000438774.2_Intron|RP11-444E17.6_ENST00000505802.1_Intron|TCTE1_ENST00000371504.1_Start_Codon_SNP_p.M1I|TCTE1_ENST00000371503.3_Start_Codon_SNP_p.M1I	NM_182539.3	NP_872345.2	Q5JU00	TCTE1_HUMAN	t-complex-associated-testis-expressed 1	154										breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GCTCGAAGAACATGCGTTTCC	0.612																																																	0			6											66.0	57.0	60.0					6																	44254085		2203	4300	6503	44362063	SO:0001583	missense	202500			BC035022	CCDS4910.1	6q21.1	2014-07-18			ENSG00000146221	ENSG00000146221			11693	protein-coding gene	gene with protein product		186975				2568335, 8646886	Standard	NM_182539		Approved	D6S46, MGC33600, FAP155	uc003oxi.2	Q5JU00	OTTHUMG00000014763	ENST00000371505.4:c.462G>A	6.37:g.44254085C>T	ENSP00000360560:p.Met154Ile		44362063	B4DX59|Q8IYS6	Missense_Mutation	SNP	ENST00000371505.4	37	CCDS4910.1	.	.	.	.	.	.	.	.	.	.	C	17.91	3.504763	0.64410	.	.	ENSG00000146221	ENST00000371505;ENST00000371503;ENST00000371504	T;T;T	0.53423	0.62;0.65;0.65	4.95	4.02	0.46733	.	0.276808	0.45126	D	0.000384	T	0.34600	0.0903	M	0.73962	2.25	0.80722	D	1	B	0.32573	0.376	B	0.28305	0.088	T	0.43540	-0.9385	10	0.45353	T	0.12	-17.2649	14.6954	0.69118	0.0:0.8542:0.1458:0.0	.	154	Q5JU00	TCTE1_HUMAN	I	154;1;1	ENSP00000360560:M154I;ENSP00000360558:M1I;ENSP00000360559:M1I	ENSP00000360558:M1I	M	-	3	0	TCTE1	44362063	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	5.729000	0.68538	2.284000	0.76573	0.563000	0.77884	ATG		0.612	TCTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040736.1	NM_182539	
PHF3	23469	hgsc.bcm.edu	37	6	64416110	64416110	+	Missense_Mutation	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr6:64416110C>T	ENST00000262043.3	+	12	3899	c.3559C>T	c.(3559-3561)Cca>Tca	p.P1187S	PHF3_ENST00000393387.1_Missense_Mutation_p.P1187S			Q92576	PHF3_HUMAN	PHD finger protein 3	1187					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			CTCTCCTGCTCCACGGTAATT	0.363																																					GBM(135;136 1820 29512 34071 46235)												0			6											58.0	55.0	56.0					6																	64416110		2203	4300	6503	64474069	SO:0001583	missense	23469			AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"""Zinc fingers, PHD-type"""	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.3559C>T	6.37:g.64416110C>T	ENSP00000262043:p.Pro1187Ser		64474069	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Missense_Mutation	SNP	ENST00000262043.3	37	CCDS4966.1	.	.	.	.	.	.	.	.	.	.	C	6.972	0.549254	0.13374	.	.	ENSG00000118482	ENST00000506783;ENST00000515594;ENST00000262043;ENST00000393387	T;T;T;T	0.45276	2.17;0.9;2.27;2.27	5.65	5.65	0.86999	.	0.000000	0.35870	N	0.002921	T	0.20659	0.0497	L	0.41236	1.265	0.43141	D	0.994891	P	0.49090	0.919	B	0.42882	0.401	T	0.02581	-1.1138	10	0.24483	T	0.36	-3.9059	9.7272	0.40339	0.0:0.6689:0.2589:0.0722	.	1187	Q92576	PHF3_HUMAN	S	1001;456;1187;1187	ENSP00000424694:P1001S;ENSP00000425338:P456S;ENSP00000262043:P1187S;ENSP00000377048:P1187S	ENSP00000262043:P1187S	P	+	1	0	PHF3	64474069	1.000000	0.71417	1.000000	0.80357	0.290000	0.27261	1.809000	0.38922	2.648000	0.89879	0.655000	0.94253	CCA		0.363	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2		
GRIK2	2898	hgsc.bcm.edu	37	6	102483299	102483299	+	Silent	SNP	A	A	G			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr6:102483299A>G	ENST00000421544.1	+	14	2659	c.2169A>G	c.(2167-2169)gaA>gaG	p.E723E	GRIK2_ENST00000369138.1_Silent_p.E723E|GRIK2_ENST00000369137.3_Silent_p.E647E|GRIK2_ENST00000413795.1_Silent_p.E723E|GRIK2_ENST00000318991.6_Silent_p.E723E|GRIK2_ENST00000369134.4_Silent_p.E674E	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	723					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GTAATGAAGAAGGAATCCAGC	0.423																																																	0			6											147.0	146.0	147.0					6																	102483299		2203	4299	6502	102589992	SO:0001819	synonymous_variant	2901				CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.2169A>G	6.37:g.102483299A>G			102589992	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Silent	SNP	ENST00000421544.1	37	CCDS5048.1																																																																																				0.423	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1		
RSPH4A	345895	hgsc.bcm.edu	37	6	116951622	116951622	+	Missense_Mutation	SNP	C	C	G			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr6:116951622C>G	ENST00000229554.5	+	5	1960	c.1823C>G	c.(1822-1824)aCa>aGa	p.T608R	RSPH4A_ENST00000368580.4_Missense_Mutation_p.T361R|RSPH4A_ENST00000368581.4_Missense_Mutation_p.Q563E	NM_001010892.2	NP_001010892.1	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A (Chlamydomonas)	608					axoneme assembly (GO:0035082)|cilium movement (GO:0003341)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|radial spoke (GO:0001534)				breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						CCCCCCTGGACAACACGGTTA	0.393									Kartagener syndrome																																								0			6											185.0	162.0	170.0					6																	116951622		2203	4300	6503	117058315	SO:0001583	missense	345895	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome		CCDS34521.1, CCDS55051.1	6q22.1	2012-05-03	2009-02-17	2009-02-17	ENSG00000111834	ENSG00000111834			21558	protein-coding gene	gene with protein product		612647	"""radial spokehead-like 3"""	RSHL3		19200523	Standard	NM_001010892		Approved	dJ412I7.1, FLJ37974, RSPH6B, CILD11	uc003pxe.2	Q5TD94	OTTHUMG00000015444	ENST00000229554.5:c.1823C>G	6.37:g.116951622C>G	ENSP00000229554:p.Thr608Arg		117058315	B4DSI1|Q3KP24|Q5TD95	Missense_Mutation	SNP	ENST00000229554.5	37	CCDS34521.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.90|10.90	1.482414|1.482414	0.26598|0.26598	.|.	.|.	ENSG00000111834|ENSG00000111834	ENST00000368581|ENST00000229554;ENST00000447842;ENST00000368580	T|T;T	0.62364|0.19669	0.03|2.13;2.13	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	.|0.098018	.|0.64402	.|D	.|0.000002	T|T	0.32556|0.32556	0.0833|0.0833	.|.	.|.	.|.	0.20926|0.20926	N|N	0.999828|0.999828	P|D	0.36837|0.60575	0.571|0.988	B|D	0.30855|0.63283	0.121|0.913	T|T	0.09335|0.09335	-1.0679|-1.0679	8|9	0.42905|0.72032	T|D	0.14|0.01	-12.7041|-12.7041	16.8765|16.8765	0.86053|0.86053	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	563|608	Q5TD94-3|Q5TD94	.|RSH4A_HUMAN	E|R	563|608;403;361	ENSP00000357570:Q563E|ENSP00000229554:T608R;ENSP00000357569:T361R	ENSP00000357570:Q563E|ENSP00000229554:T608R	Q|T	+|+	1|2	0|0	RSPH4A|RSPH4A	117058315|117058315	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.195000|0.195000	0.23768|0.23768	3.668000|3.668000	0.54554|0.54554	2.592000|2.592000	0.87571|0.87571	0.591000|0.591000	0.81541|0.81541	CAA|ACA		0.393	RSPH4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041960.1	NM_001010892	
PTPRK	5796	hgsc.bcm.edu	37	6	128326363	128326363	+	Missense_Mutation	SNP	G	G	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr6:128326363G>T	ENST00000368215.3	-	15	2356	c.2357C>A	c.(2356-2358)gCc>gAc	p.A786D	PTPRK_ENST00000368207.3_Missense_Mutation_p.A797D|PTPRK_ENST00000532331.1_Missense_Mutation_p.A787D|PTPRK_ENST00000368226.4_Missense_Mutation_p.A787D|PTPRK_ENST00000368213.5_Missense_Mutation_p.A787D|PTPRK_ENST00000368227.3_Missense_Mutation_p.A787D|PTPRK_ENST00000368210.3_Missense_Mutation_p.A787D|PTPRK_ENST00000524481.1_5'UTR			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	786					cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.A787V(1)	PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		ATTCCCCATGGCATCTTTGCG	0.453																																																	1	Substitution - Missense(1)	central_nervous_system(1)	6											87.0	73.0	78.0					6																	128326363		2203	4299	6502	128368056	SO:0001583	missense	5796			L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.2357C>A	6.37:g.128326363G>T	ENSP00000357198:p.Ala786Asp		128368056	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Missense_Mutation	SNP	ENST00000368215.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.42|17.42	3.384015|3.384015	0.61845|0.61845	.|.	.|.	ENSG00000152894|ENSG00000152894	ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207;ENST00000415055;ENST00000427676|ENST00000415046	T;T;T;T;T;T;T;T|.	0.12039|.	3.11;3.11;3.12;3.11;3.11;3.11;3.05;2.72|.	5.87|5.87	5.01|5.01	0.66863|0.66863	.|.	0.108147|.	0.64402|.	D|.	0.000006|.	T|T	0.45236|0.45236	0.1332|0.1332	L|L	0.38175|0.38175	1.15|1.15	0.46458|0.46458	D|D	0.999057|0.999057	B;B;B;P;B;P|.	0.39940|.	0.421;0.417;0.382;0.696;0.421;0.557|.	B;B;B;P;B;B|.	0.47206|.	0.203;0.15;0.287;0.541;0.116;0.232|.	T|T	0.43393|0.43393	-0.9394|-0.9394	10|5	0.52906|.	T|.	0.07|.	.|.	15.1687|15.1687	0.72850|0.72850	0.0679:0.0:0.9321:0.0|0.0679:0.0:0.9321:0.0	.|.	797;787;787;668;786;787|.	B4DHC3;B7ZMG0;Q15262-3;F5GWP2;Q15262;Q15262-2|.	.;.;.;.;PTPRK_HUMAN;.|.	D|T	787;787;787;787;787;786;797;30;668|68	ENSP00000357209:A787D;ENSP00000357210:A787D;ENSP00000432973:A787D;ENSP00000357196:A787D;ENSP00000357193:A787D;ENSP00000357198:A786D;ENSP00000357190:A797D;ENSP00000408180:A30D|.	ENSP00000357190:A797D|.	A|P	-|-	2|1	0|0	PTPRK|PTPRK	128368056|128368056	1.000000|1.000000	0.71417|0.71417	0.926000|0.926000	0.36857|0.36857	0.996000|0.996000	0.88848|0.88848	4.762000|4.762000	0.62250|0.62250	1.487000|1.487000	0.48415|0.48415	0.650000|0.650000	0.86243|0.86243	GCC|CCA		0.453	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1		
FNDC1	84624	hgsc.bcm.edu	37	6	159654160	159654160	+	Missense_Mutation	SNP	C	C	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr6:159654160C>A	ENST00000297267.9	+	11	2816	c.2616C>A	c.(2614-2616)agC>agA	p.S872R	FNDC1_ENST00000340366.6_Missense_Mutation_p.S809R	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	872					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		CTAAGCTTAGCTCAGGTATCC	0.637																																																	0			6											27.0	33.0	31.0					6																	159654160		1979	4155	6134	159574150	SO:0001583	missense	84624			AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.2616C>A	6.37:g.159654160C>A	ENSP00000297267:p.Ser872Arg		159574150	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.45|12.45	1.940671|1.940671	0.34283|0.34283	.|.	.|.	ENSG00000164694|ENSG00000164694	ENST00000329629|ENST00000297267;ENST00000340366	.|T;T	.|0.07444	.|3.19;4.01	4.71|4.71	2.49|2.49	0.30216|0.30216	.|.	.|0.797369	.|0.11657	.|N	.|0.542181	T|T	0.01092|0.01092	0.0036|0.0036	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.04013	.|0.001;0.0	T|T	0.48592|0.48592	-0.9022|-0.9022	5|10	.|0.19590	.|T	.|0.45	-4.6351|-4.6351	4.7504|4.7504	0.13057|0.13057	0.0:0.6333:0.0:0.3667|0.0:0.6333:0.0:0.3667	.|.	.|809;872	.|Q4ZHG4-2;Q4ZHG4	.|.;FNDC1_HUMAN	I|R	768|872;809	.|ENSP00000297267:S872R;ENSP00000342460:S809R	.|ENSP00000297267:S872R	L|S	+|+	1|3	0|2	FNDC1|FNDC1	159574150|159574150	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.063000|0.063000	0.16089|0.16089	0.589000|0.589000	0.23939|0.23939	1.122000|1.122000	0.41944|0.41944	-0.136000|-0.136000	0.14681|0.14681	CTC|AGC		0.637	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
TP53	7157	hgsc.bcm.edu	37	17	7577538	7577538	+	Missense_Mutation	SNP	C	C	T	rs11540652		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr17:7577538C>T	ENST00000269305.4	-	7	932	c.743G>A	c.(742-744)cGg>cAg	p.R248Q	TP53_ENST00000445888.2_Missense_Mutation_p.R248Q|TP53_ENST00000455263.2_Missense_Mutation_p.R248Q|TP53_ENST00000413465.2_Missense_Mutation_p.R248Q|TP53_ENST00000359597.4_Missense_Mutation_p.R248Q|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.R248Q	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	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R248Q(580)|p.R248L(75)|p.R248P(19)|p.R155Q(18)|p.0?(8)|p.?(5)|p.R155L(3)|p.R155P(2)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248fs*>39(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(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)	GATGGGCCTCCGGTTCATGCC	0.572	R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(HCC70_BREAST)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYSE150_OESOPHAGUS)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(NCIN87_STOMACH)|R248Q(NIHOVCAR3_OVARY)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(PC14_LUNG)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	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"""	725	Substitution - Missense(698)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(2)|Complex - compound substitution(1)	large_intestine(138)|breast(83)|haematopoietic_and_lymphoid_tissue(74)|lung(71)|upper_aerodigestive_tract(63)|central_nervous_system(46)|oesophagus(37)|urinary_tract(37)|ovary(36)|stomach(35)|endometrium(23)|skin(18)|prostate(11)|bone(10)|biliary_tract(9)|liver(9)|pancreas(7)|vulva(3)|kidney(3)|cervix(3)|peritoneum(2)|thyroid(2)|soft_tissue(1)|pituitary(1)|adrenal_gland(1)|small_intestine(1)|thymus(1)	17	GRCh37	CM920675	TP53	M	rs11540652	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	152.0	112.0	126.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	743,743,743,743,347,347,347	3.7	1.0	17	dbSNP_120	126	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	43,43,43,43,43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	248/394,248/394,248/347,248/342,116/262,116/210,116/215	7577538	1,13005	2203	4300	6503	7518263	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.743G>A	17.37:g.7577538C>T	ENSP00000269305:p.Arg248Gln		7518263	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	27.3	4.822907	0.90873	0.0	1.16E-4	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99864	-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28	4.62	3.65	0.41850	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	0.99840	0.9927	M	0.88640	2.97	0.58432	A	0.999994	D;D;D;D;D;D	0.89917	1.0;0.994;1.0;1.0;1.0;1.0	D;P;D;D;D;D	0.91635	0.996;0.882;0.999;0.995;0.996;0.995	D	0.96819	0.9602	9	0.72032	D	0.01	-9.5643	10.6687	0.45745	0.0:0.9059:0.0:0.0941	rs11540652;rs11540652	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	Q	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248Q;ENSP00000352610:R248Q;ENSP00000269305:R248Q;ENSP00000398846:R248Q;ENSP00000391127:R248Q;ENSP00000391478:R248Q;ENSP00000425104:R116Q;ENSP00000423862:R155Q	ENSP00000269305:R248Q	R	-	2	0	TP53	7518263	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	5.884000	0.69729	1.305000	0.44909	0.462000	0.41574	CGG		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
TP53	7157	hgsc.bcm.edu	37	17	7578282	7578282	+	Silent	SNP	G	G	T	rs55764374		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr17:7578282G>T	ENST00000269305.4	-	6	756	c.567C>A	c.(565-567)gcC>gcA	p.A189A	TP53_ENST00000445888.2_Silent_p.A189A|TP53_ENST00000455263.2_Silent_p.A189A|TP53_ENST00000413465.2_Silent_p.A189A|TP53_ENST00000359597.4_Silent_p.A189A|TP53_ENST00000574684.1_Intron|TP53_ENST00000420246.2_Silent_p.A189A	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	189	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		A -> D (in a sporadic cancer; somatic mutation).|A -> G (in sporadic cancers; somatic mutation).|A -> P (in sporadic cancers; somatic mutation).|A -> S (in a sporadic cancer; somatic mutation).|A -> T (in sporadic cancers; somatic mutation).|A -> V (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).		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.0?(8)|p.A189_V197delAPPQHLIRV(4)|p.G187fs*16(2)|p.A189A(2)|p.D186_P191delDGLAPP(1)|p.?(1)|p.P190fs*19(1)|p.G187fs*64(1)|p.A189_Q192>E(1)|p.L188_P191del(1)|p.A189_P190>X(1)|p.A189fs*53(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)	GCTGAGGAGGGGCCAGACCTA	0.552		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"""	24	Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(3)|Complex - deletion inframe(2)|Substitution - coding silent(2)|Insertion - Frameshift(1)|Complex - frameshift(1)|Unknown(1)	skin(5)|bone(4)|liver(3)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|lung(2)|ovary(2)|breast(2)|upper_aerodigestive_tract(1)|stomach(1)	17											88.0	79.0	82.0					17																	7578282		2203	4300	6503	7519007	SO:0001819	synonymous_variant	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.567C>A	17.37:g.7578282G>T			7519007	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	Silent	SNP	ENST00000269305.4	37	CCDS11118.1																																																																																				0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
EVPL	2125	hgsc.bcm.edu	37	17	74005245	74005245	+	Silent	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr17:74005245C>T	ENST00000301607.3	-	22	4294	c.4041G>A	c.(4039-4041)gcG>gcA	p.A1347A	EVPL_ENST00000586740.1_Silent_p.A1369A	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1347	Central fibrous rod domain.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						CCGCGTCCTCCGCGGCCCGCC	0.682																																																	0			17											48.0	53.0	51.0					17																	74005245		2201	4297	6498	71516840	SO:0001819	synonymous_variant	2125			U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.4041G>A	17.37:g.74005245C>T			71516840	A0AUV5	Silent	SNP	ENST00000301607.3	37	CCDS11737.1																																																																																				0.682	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
RUNX1	861	hgsc.bcm.edu	37	21	36231785	36231785	+	Missense_Mutation	SNP	G	G	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr21:36231785G>T	ENST00000344691.4	-	3	2095	c.518C>A	c.(517-519)cCc>cAc	p.P173H	RUNX1_ENST00000325074.5_Missense_Mutation_p.P188H|RUNX1_ENST00000399240.1_Missense_Mutation_p.P173H|RUNX1_ENST00000300305.3_Missense_Mutation_p.P200H|RUNX1_ENST00000437180.1_Missense_Mutation_p.P200H|RUNX1_ENST00000358356.5_Missense_Mutation_p.P173H|RUNX1_ENST00000486278.2_Missense_Mutation_p.P176H	NM_001001890.2	NP_001001890.1	Q01196	RUNX1_HUMAN	runt-related transcription factor 1	173	Interaction with DNA.|Runt. {ECO:0000255|PROSITE- ProRule:PRU00399}.				behavioral response to pain (GO:0048266)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system development (GO:0007417)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|hair follicle morphogenesis (GO:0031069)|hematopoietic stem cell proliferation (GO:0071425)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|myeloid cell differentiation (GO:0030099)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of granulocyte differentiation (GO:0030853)|peripheral nervous system neuron development (GO:0048935)|positive regulation of angiogenesis (GO:0045766)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of progesterone secretion (GO:2000872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hair follicle cell proliferation (GO:0071336)|regulation of signal transduction (GO:0009966)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(5)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(428)|large_intestine(3)|lung(6)|oesophagus(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	452						AGGTTCTCGGGGCCCATCCAC	0.557			T	"""RPL22, MDS1, EVI1, CBFA2T3, CBFA2T1, ETV6, LAF4"""	"""AML, preB- ALL, T-ALL"""																																			Dom	yes		21	21q22.3	861	runt-related transcription factor 1  (AML1)		L	0			21											286.0	250.0	262.0					21																	36231785		2203	4300	6503	35153655	SO:0001583	missense	861			X79549	CCDS13639.1, CCDS42922.1, CCDS46646.1	21q22.3	2014-09-17	2008-07-29		ENSG00000159216	ENSG00000159216			10471	protein-coding gene	gene with protein product	"""aml1 oncogene"""	151385	"""acute myeloid leukemia 1"""	AML1, CBFA2		1427868, 7835892	Standard	NM_001001890		Approved	PEBP2A2, AMLCR1	uc010gmv.3	Q01196	OTTHUMG00000086299	ENST00000344691.4:c.518C>A	21.37:g.36231785G>T	ENSP00000340690:p.Pro173His		35153655	A8MV94|B2RMS4|D3DSG1|O60472|O60473|O76047|O76089|Q13081|Q13755|Q13756|Q13757|Q13758|Q13759|Q15341|Q15343|Q16122|Q16284|Q16285|Q16286|Q16346|Q16347|Q92479	Missense_Mutation	SNP	ENST00000344691.4	37	CCDS42922.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.477319	0.84640	.	.	ENSG00000159216	ENST00000344691;ENST00000300305;ENST00000437180;ENST00000325074;ENST00000399240;ENST00000399245;ENST00000358356;ENST00000399237;ENST00000486278	D;D;D;D;D;D;D;D	0.99766	-6.69;-6.69;-6.69;-6.69;-6.69;-6.69;-6.69;-6.69	5.12	5.12	0.69794	Acute myeloid leukemia 1 (AML 1)/Runt (2);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99813	0.9918	M	0.91196	3.185	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.998;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.994;0.999;0.995;0.986;0.99;0.936;0.999	D	0.96865	0.9635	10	0.87932	D	0	-28.2152	16.0721	0.80941	0.0:0.0:1.0:0.0	.	200;173;173;176;200;188;173	Q2TAM6;Q01196-5;Q01196-3;C9JK12;Q01196-8;Q01196-10;Q01196	.;.;.;.;.;.;RUNX1_HUMAN	H	173;200;200;188;173;176;173;188;176	ENSP00000340690:P173H;ENSP00000300305:P200H;ENSP00000409227:P200H;ENSP00000319459:P188H;ENSP00000382184:P173H;ENSP00000351123:P173H;ENSP00000382182:P188H;ENSP00000438019:P176H	ENSP00000300305:P200H	P	-	2	0	RUNX1	35153655	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.430000	0.97488	2.377000	0.81083	0.655000	0.94253	CCC		0.557	RUNX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000194230.1		
TTC3	7267	hgsc.bcm.edu	37	21	38525373	38525373	+	Missense_Mutation	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr21:38525373C>T	ENST00000399017.2	+	27	5283	c.2536C>T	c.(2536-2538)Ctt>Ttt	p.L846F	TTC3_ENST00000354749.2_Missense_Mutation_p.L846F|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000355666.1_Missense_Mutation_p.L846F|TTC3_ENST00000540756.1_Missense_Mutation_p.L536F	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	846					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				CAAAGAATTGCTTTCTTGGAA	0.368																																					Ovarian(38;194 1649 35661)												0			21											67.0	72.0	70.0					21																	38525373		2203	4300	6503	37447243	SO:0001583	missense	7267			D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.2536C>T	21.37:g.38525373C>T	ENSP00000381981:p.Leu846Phe		37447243	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	C	18.61	3.662102	0.67700	.	.	ENSG00000182670	ENST00000418766;ENST00000438055;ENST00000355666;ENST00000540756;ENST00000399017;ENST00000354749	T;T;T;T;T;T	0.50548	2.55;2.55;2.86;0.74;2.86;2.86	5.31	4.41	0.53225	.	0.112528	0.39909	N	0.001227	T	0.55940	0.1952	M	0.62723	1.935	0.39186	D	0.962869	P;D	0.59767	0.839;0.986	B;P	0.53954	0.351;0.738	T	0.63107	-0.6711	10	0.87932	D	0	-13.7571	10.7736	0.46338	0.1481:0.7093:0.1426:0.0	.	536;846	B4DSZ9;P53804	.;TTC3_HUMAN	F	846;828;846;536;846;846	ENSP00000403943:L846F;ENSP00000391891:L828F;ENSP00000347889:L846F;ENSP00000442875:L536F;ENSP00000381981:L846F;ENSP00000346791:L846F	ENSP00000346791:L846F	L	+	1	0	TTC3	37447243	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.118000	0.31246	1.341000	0.45600	0.650000	0.86243	CTT		0.368	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
NLRC3	197358	hgsc.bcm.edu	37	16	3614280	3614280	+	RNA	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr16:3614280C>T	ENST00000301749.7	-	0	1063				NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TCATCCAAGCCGTCCAGGATC	0.637																																																	0			16											37.0	42.0	41.0					16																	3614280		1987	4180	6167	3554281			197358			BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3614280C>T			3554281	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		.	.	.	.	.	.	.	.	.	.	C	18.27	3.587266	0.66105	.	.	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023;ENST00000324659	T;T;T;T	0.81415	-1.49;-1.49;-1.49;-1.49	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	D	0.89763	0.6809	.	.	.	0.41104	D	0.985696	D	0.89917	1.0	D	0.85130	0.997	D	0.91494	0.5214	9	0.87932	D	0	.	15.6704	0.77270	0.0:1.0:0.0:0.0	.	267	C9JLH9	.	S	220;220;220;267;202	ENSP00000301749:G220S;ENSP00000352039:G220S;ENSP00000414415:G267S;ENSP00000323897:G202S	ENSP00000301749:G220S	G	-	1	0	NLRC3	3554281	1.000000	0.71417	0.772000	0.31596	0.795000	0.44927	7.818000	0.86416	2.273000	0.75805	0.655000	0.94253	GGC		0.637	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844	
CREBBP	1387	hgsc.bcm.edu	37	16	3786078	3786078	+	Missense_Mutation	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr16:3786078T>C	ENST00000262367.5	-	28	5496	c.4687A>G	c.(4687-4689)Agg>Ggg	p.R1563G	CREBBP_ENST00000382070.3_Missense_Mutation_p.R1525G	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1563	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|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)		TCCTTTTTCCTCTCCTCTTCT	0.517			"""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											308.0	220.0	250.0					16																	3786078		2197	4300	6497	3726079	SO:0001583	missense	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.4687A>G	16.37:g.3786078T>C	ENSP00000262367:p.Arg1563Gly		3726079	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	t	15.42	2.827625	0.50845	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.93547	-3.24;-3.24	5.2	4.09	0.47781	.	0.000000	0.85682	D	0.000000	D	0.96725	0.8931	M	0.88640	2.97	0.58432	D	0.999999	D;D	0.62365	0.991;0.991	D;D	0.78314	0.991;0.991	D	0.96435	0.9322	10	0.62326	D	0.03	-24.6377	11.8222	0.52245	0.0:0.0:0.1466:0.8534	.	1593;1563	Q4LE28;Q92793	.;CBP_HUMAN	G	1563;1593;1525;152	ENSP00000262367:R1563G;ENSP00000371502:R1525G	ENSP00000262367:R1563G	R	-	1	2	CREBBP	3726079	0.722000	0.28017	0.998000	0.56505	0.989000	0.77384	0.982000	0.29539	0.898000	0.36418	0.454000	0.30748	AGG		0.517	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
PRKCB	5579	hgsc.bcm.edu	37	16	24104235	24104235	+	Missense_Mutation	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr16:24104235C>T	ENST00000321728.7	+	6	828	c.653C>T	c.(652-654)tCc>tTc	p.S218F	PRKCB_ENST00000303531.7_Missense_Mutation_p.S218F|PRKCB_ENST00000482000.1_3'UTR	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	218	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				apoptotic process (GO:0006915)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|histone H3-T6 phosphorylation (GO:0035408)|intracellular signal transduction (GO:0035556)|lipoprotein transport (GO:0042953)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|histone kinase activity (H3-T6 specific) (GO:0035403)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			central_nervous_system(3)|large_intestine(1)|lung(2)|ovary(3)	9					Tamoxifen(DB00675)|Vitamin E(DB00163)	ATCAAATGCTCCCTCAACCCT	0.478																																																	0			16											158.0	130.0	140.0					16																	24104235		2197	4300	6497	24011736	SO:0001583	missense	5579			M13975	CCDS10618.1, CCDS10619.1	16p12	2009-07-10	2008-08-18	2008-08-18	ENSG00000166501	ENSG00000166501	2.7.11.1		9395	protein-coding gene	gene with protein product		176970	"""protein kinase C, beta 1"""	PRKCB2, PKCB, PRKCB1		3658678	Standard	NM_002738		Approved		uc002dme.3	P05771	OTTHUMG00000131615	ENST00000321728.7:c.653C>T	16.37:g.24104235C>T	ENSP00000318315:p.Ser218Phe		24011736	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Missense_Mutation	SNP	ENST00000321728.7	37	CCDS10618.1	.	.	.	.	.	.	.	.	.	.	C	17.24	3.340552	0.60963	.	.	ENSG00000166501	ENST00000321728;ENST00000303531	T;T	0.50001	0.76;0.76	5.38	5.38	0.77491	C2 membrane targeting protein (1);C2 region (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.061993	0.64402	D	0.000003	T	0.52306	0.1726	M	0.72576	2.205	0.46279	D	0.99896	B;B	0.13145	0.005;0.007	B;B	0.18263	0.019;0.021	T	0.52917	-0.8511	10	0.72032	D	0.01	.	18.4836	0.90820	0.0:1.0:0.0:0.0	.	218;218	P05771-2;P05771	.;KPCB_HUMAN	F	218	ENSP00000318315:S218F;ENSP00000305355:S218F	ENSP00000305355:S218F	S	+	2	0	PRKCB	24011736	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	4.725000	0.61979	2.681000	0.91329	0.650000	0.86243	TCC		0.478	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535	
SEZ6L2	26470	hgsc.bcm.edu	37	16	29884659	29884659	+	Missense_Mutation	SNP	A	A	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr16:29884659A>C	ENST00000308713.5	-	14	2917	c.2390T>G	c.(2389-2391)tTc>tGc	p.F797C	SEZ6L2_ENST00000537485.1_Missense_Mutation_p.F753C|SEZ6L2_ENST00000346932.5_Missense_Mutation_p.F683C|SEZ6L2_ENST00000350527.3_Missense_Mutation_p.F727C	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	797	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						ATAGCAGAAGAAGCGCAGAGA	0.627																																																	0			16											111.0	110.0	110.0					16																	29884659		2197	4300	6497	29792160	SO:0001583	missense	26470			AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"""type I transmembrane receptor (seizure related protein)"""					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.2390T>G	16.37:g.29884659A>C	ENSP00000312550:p.Phe797Cys		29792160	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Missense_Mutation	SNP	ENST00000308713.5	37	CCDS10659.1	.	.	.	.	.	.	.	.	.	.	A	18.67	3.674506	0.67928	.	.	ENSG00000174938	ENST00000350527;ENST00000308713;ENST00000346932;ENST00000537485	T;T;T;T	0.69685	-0.42;-0.42;-0.42;-0.42	4.39	4.39	0.52855	Complement control module (2);Sushi/SCR/CCP (3);	0.254772	0.28161	N	0.016372	D	0.85234	0.5650	H	0.94808	3.585	0.80722	D	1	D;D;D;D;D;D	0.76494	0.999;0.996;0.999;0.995;0.996;0.995	D;P;D;P;P;P	0.70016	0.967;0.905;0.934;0.847;0.905;0.847	D	0.89043	0.3450	10	0.87932	D	0	.	12.7207	0.57140	1.0:0.0:0.0:0.0	.	753;797;683;727;797;727	F5H293;B7Z5L4;Q9BW82;Q6UXD5-2;Q6UXD5;Q6UXD5-3	.;.;.;.;SE6L2_HUMAN;.	C	727;797;683;753	ENSP00000310206:F727C;ENSP00000312550:F797C;ENSP00000319215:F683C;ENSP00000439412:F753C	ENSP00000312550:F797C	F	-	2	0	SEZ6L2	29792160	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.761000	0.91691	1.831000	0.53308	0.533000	0.62120	TTC		0.627	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410	
SLC9A5	6553	hgsc.bcm.edu	37	16	67300007	67300007	+	Silent	SNP	C	C	T	rs372783358		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr16:67300007C>T	ENST00000299798.11	+	15	2162	c.2097C>T	c.(2095-2097)acC>acT	p.T699T	CTC-277H1.7_ENST00000573063.1_RNA	NM_004594.2	NP_004585.1	Q14940	SL9A5_HUMAN	solute carrier family 9, subfamily A (NHE5, cation proton antiporter 5), member 5	699					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)		TGATATTAACCGTGGAGTCTG	0.577													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20991	0.0		0.0	False		,,,				2504	0.0																0			16											72.0	72.0	72.0					16																	67300007		2073	4217	6290	65857508	SO:0001819	synonymous_variant	6553				CCDS42178.1	16q22.1	2013-05-22	2012-03-22		ENSG00000135740	ENSG00000135740		"""Solute carriers"""	11078	protein-coding gene	gene with protein product		600477	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 5"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 5"""			7759094, 9933642	Standard	NM_004594		Approved	NHE5	uc002esm.3	Q14940	OTTHUMG00000172935	ENST00000299798.11:c.2097C>T	16.37:g.67300007C>T			65857508	A5PKY7|Q9Y626	Silent	SNP	ENST00000299798.11	37	CCDS42178.1																																																																																				0.577	SLC9A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421386.1		
ZNF469	84627	hgsc.bcm.edu	37	16	88501958	88501958	+	Missense_Mutation	SNP	C	C	T	rs540443650		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr16:88501958C>T	ENST00000437464.1	+	2	7996	c.7996C>T	c.(7996-7998)Cgc>Tgc	p.R2666C	ZNF469_ENST00000565624.1_Missense_Mutation_p.R2694C	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2666					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						GCAGCCGCCTCGCTTGGCCAC	0.667																																																	0			16											18.0	21.0	20.0					16																	88501958		691	1589	2280	87029459	SO:0001583	missense	84627			AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.7996C>T	16.37:g.88501958C>T	ENSP00000402343:p.Arg2666Cys		87029459		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.045966	0.36085	.	.	ENSG00000225614	ENST00000437464	T	0.06068	3.35	3.53	0.0733	0.14390	.	.	.	.	.	T	0.03477	0.0100	N	0.14661	0.345	0.09310	N	1	B	0.16802	0.019	B	0.06405	0.002	T	0.42361	-0.9456	9	0.72032	D	0.01	.	2.7139	0.05182	0.1877:0.523:0.1821:0.1072	.	2666	Q96JG9	ZN469_HUMAN	C	2666	ENSP00000402343:R2666C	ENSP00000402343:R2666C	R	+	1	0	ZNF469	87029459	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.181000	0.16880	-0.326000	0.08564	0.313000	0.20887	CGC		0.667	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
GAS8	2622	hgsc.bcm.edu	37	16	90095573	90095573	+	Intron	SNP	C	C	T	rs77382359		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr16:90095573C>T	ENST00000268699.4	+	2	212				GAS8_ENST00000540721.1_Intron|C16orf3_ENST00000408886.2_Missense_Mutation_p.V60I|GAS8_ENST00000536122.1_Intron	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8						cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		gggcaggctacggggcagctt	0.672																																																	0			16											22.0	20.0	21.0					16																	90095573		2194	4299	6493	88623074	SO:0001627	intron_variant	750			AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.90+1443C>T	16.37:g.90095573C>T			88623074	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Missense_Mutation	SNP	ENST00000268699.4	37	CCDS10992.1	.	.	.	.	.	.	.	.	.	.	c	0.708	-0.788068	0.02884	.	.	ENSG00000221819	ENST00000408886	T	0.47177	0.85	.	.	.	.	.	.	.	.	T	0.22244	0.0536	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.22208	-1.0223	4	.	.	.	.	.	.	.	.	68	O95177	CP003_HUMAN	I	60	ENSP00000386218:V60I	.	V	-	1	0	C16orf3	88623074	0.031000	0.19500	0.015000	0.15790	0.017000	0.09413	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	GTA		0.672	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
OSBPL1A	114876	hgsc.bcm.edu	37	18	21897130	21897130	+	Missense_Mutation	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr18:21897130T>C	ENST00000319481.3	-	11	1059	c.853A>G	c.(853-855)Act>Gct	p.T285A		NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	285	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)	p.T285P(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					ACTGCTTGAGTCAGGTGTTTG	0.368																																																	1	Substitution - Missense(1)	ovary(1)	18											109.0	106.0	107.0					18																	21897130		2203	4300	6503	20151128	SO:0001583	missense	114876			AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447		"""Oxysterol binding proteins"", ""Ankyrin repeat domain containing"""	16398	protein-coding gene	gene with protein product		606730	"""oxysterol binding protein-like 1B"""	OSBPL1B		11279184, 10588946	Standard	NM_080597		Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.853A>G	18.37:g.21897130T>C	ENSP00000320291:p.Thr285Ala		20151128	B7Z7D3|Q9BZF5|Q9NW87	Missense_Mutation	SNP	ENST00000319481.3	37	CCDS11884.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.211954	0.79240	.	.	ENSG00000141447	ENST00000319481	T	0.40225	1.04	5.73	5.73	0.89815	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.048710	0.85682	D	0.000000	T	0.55737	0.1939	L	0.50333	1.59	0.80722	D	1	D;D	0.69078	0.997;0.994	D;D	0.75020	0.985;0.97	T	0.49041	-0.8980	10	0.11794	T	0.64	-23.2478	16.0013	0.80294	0.0:0.0:0.0:1.0	.	285;285	B0YJ56;Q9BXW6	.;OSBL1_HUMAN	A	285	ENSP00000320291:T285A	ENSP00000320291:T285A	T	-	1	0	OSBPL1A	20151128	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	6.896000	0.75665	2.180000	0.69256	0.528000	0.53228	ACT		0.368	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597	
CNTN4	152330	hgsc.bcm.edu	37	3	2942482	2942482	+	Missense_Mutation	SNP	A	A	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr3:2942482A>C	ENST00000397461.1	+	10	1438	c.1054A>C	c.(1054-1056)Aat>Cat	p.N352H	CNTN4_ENST00000427331.1_Missense_Mutation_p.N352H|CNTN4_ENST00000418658.1_Missense_Mutation_p.N352H|CNTN4_ENST00000475817.1_3'UTR|CNTN4_ENST00000448906.2_Missense_Mutation_p.N24H|CNTN4_ENST00000358480.3_Missense_Mutation_p.N133H|CNTN4_ENST00000397459.2_Missense_Mutation_p.N24H	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	352	Ig-like C2-type 4.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|brain development (GO:0007420)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|neuron projection development (GO:0031175)|regulation of synaptic plasticity (GO:0048167)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		GTGGCTAAAAAATGGCGAACC	0.398																																																	0			3											138.0	110.0	119.0					3																	2942482		2203	4300	6503	2917482	SO:0001583	missense	152330			AW665944	CCDS2558.1, CCDS43041.1	3p26.3	2013-02-11			ENSG00000144619	ENSG00000144619		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2174	protein-coding gene	gene with protein product		607280				8586965, 12202991	Standard	NM_175607		Approved	BIG-2	uc003bpc.3	Q8IWV2	OTTHUMG00000119031	ENST00000397461.1:c.1054A>C	3.37:g.2942482A>C	ENSP00000380602:p.Asn352His		2917482	B2RAX3|Q8IX14|Q8TC35	Missense_Mutation	SNP	ENST00000397461.1	37	CCDS43041.1	.	.	.	.	.	.	.	.	.	.	A	19.73	3.881618	0.72294	.	.	ENSG00000144619	ENST00000418658;ENST00000397461;ENST00000427331;ENST00000358480;ENST00000397459;ENST00000448906;ENST00000473845	T;T;T;T;T;T;T	0.76186	0.78;0.78;0.78;0.78;-1.0;-1.0;-1.0	5.41	5.41	0.78517	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.061265	0.64402	D	0.000005	D	0.85965	0.5820	M	0.86343	2.81	0.53005	D	0.999965	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.80764	0.982;0.994;0.962	D	0.87584	0.2486	10	0.87932	D	0	.	8.7563	0.34648	0.8822:0.0:0.1178:0.0	.	352;352;352	Q8IWV2-3;B3KTK4;Q8IWV2	.;.;CNTN4_HUMAN	H	352;352;352;133;24;24;30	ENSP00000396010:N352H;ENSP00000380602:N352H;ENSP00000413642:N352H;ENSP00000351267:N133H;ENSP00000380600:N24H;ENSP00000392077:N24H;ENSP00000422120:N30H	ENSP00000351267:N133H	N	+	1	0	CNTN4	2917482	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.410000	0.66381	2.171000	0.68590	0.533000	0.62120	AAT		0.398	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2		
ITPR1	3708	hgsc.bcm.edu	37	3	4821291	4821291	+	Missense_Mutation	SNP	G	G	A	rs373973399		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr3:4821291G>A	ENST00000443694.2	+	46	6304	c.6304G>A	c.(6304-6306)Gca>Aca	p.A2102T	ITPR1_ENST00000423119.2_Missense_Mutation_p.A2069T|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000302640.8_Missense_Mutation_p.A2102T|ITPR1_ENST00000354582.6_Missense_Mutation_p.A2102T|ITPR1_ENST00000357086.4_Missense_Mutation_p.A2069T|ITPR1_ENST00000456211.2_Missense_Mutation_p.A2054T			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2117					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|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)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)	p.A2054T(1)		NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	CAGTGAAAACGCAGAGAGGAT	0.502																																																	1	Substitution - Missense(1)	large_intestine(1)	3											119.0	120.0	120.0					3																	4821291		1989	4154	6143	4796291	SO:0001583	missense	3708			D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"""Ion channels / Inositol triphosphate receptors"""	6180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 94"""	147265	"""spinocerebellar ataxia 15"", ""spinocerebellar ataxia 16"", ""spinocerebellar ataxia 29"""	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.6304G>A	3.37:g.4821291G>A	ENSP00000401671:p.Ala2102Thr		4796291	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	G	33	5.222462	0.95139	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.92965	-3.12;-3.13;-3.14;-3.14;-3.12;-3.12	5.28	4.39	0.52855	.	0.051084	0.85682	D	0.000000	D	0.95962	0.8685	M	0.90977	3.165	0.80722	D	1	D;D	0.64830	0.994;0.994	P;P	0.58520	0.74;0.84	D	0.95493	0.8571	10	0.33940	T	0.23	.	15.8769	0.79170	0.0:0.1358:0.8642:0.0	.	2117;2069	Q14643;G5E9P1	ITPR1_HUMAN;.	T	2117;2102;2102;2069;563;2069;2054;2102	ENSP00000306253:A2102T;ENSP00000346595:A2102T;ENSP00000405934:A2069T;ENSP00000349597:A2069T;ENSP00000397885:A2054T;ENSP00000401671:A2102T	ENSP00000306253:A2102T	A	+	1	0	ITPR1	4796291	1.000000	0.71417	0.217000	0.23759	0.985000	0.73830	9.772000	0.98984	1.191000	0.43056	0.585000	0.79938	GCA		0.502	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	
VHL	7428	hgsc.bcm.edu	37	3	10188302	10188302	+	Missense_Mutation	SNP	G	G	A	rs587780077		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr3:10188302G>A	ENST00000256474.2	+	2	1285	c.445G>A	c.(445-447)Gcc>Acc	p.A149T	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Intron	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	149	Involved in binding to CCT complex.		A -> T (in VHLD; type II). {ECO:0000269|PubMed:9452106}.		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.A149fs*26(4)|p.A149fs*24(3)|p.F148fs*9(1)|p.F148fs*11(1)|p.I147fs*10(1)|p.A149fs*11(1)|p.A149P(1)|p.P146fs*23(1)|p.G144fs*19(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)		GCCTATTTTTGCCAATATCAC	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"""	14	Deletion - Frameshift(7)|Insertion - Frameshift(5)|Substitution - Missense(1)|Complex - frameshift(1)	kidney(14)	3	GRCh37	CM951288|CM982010|HD971374	VHL	D|M							199.0	186.0	191.0					3																	10188302		2203	4300	6503	10163302	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.445G>A	3.37:g.10188302G>A	ENSP00000256474:p.Ala149Thr		10163302	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.771662	0.90108	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99789	-6.75	4.89	4.89	0.63831	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.111909	0.64402	D	0.000011	D	0.99542	0.9836	L	0.53249	1.67	0.80722	D	1	D	0.69078	0.997	D	0.63597	0.916	D	0.98054	1.0389	10	0.44086	T	0.13	-0.1953	15.9164	0.79521	0.0:0.0:1.0:0.0	.	149	P40337	VHL_HUMAN	T	149;67	ENSP00000256474:A149T	ENSP00000256474:A149T	A	+	1	0	VHL	10163302	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.278000	0.78587	2.428000	0.82296	0.563000	0.77884	GCC		0.413	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551	
LTF	4057	hgsc.bcm.edu	37	3	46479450	46479450	+	Silent	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr3:46479450C>T	ENST00000231751.4	-	16	2374	c.2079G>A	c.(2077-2079)ctG>ctA	p.L693L	LTF_ENST00000426532.2_Silent_p.L649L|LTF_ENST00000417439.1_Silent_p.L691L|LTF_ENST00000493056.1_5'Flank	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	693	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		AGCACTTTTTCAGATTAGTAA	0.458																																																	0			3											215.0	204.0	208.0					3																	46479450		2203	4299	6502	46454454	SO:0001819	synonymous_variant	4057				CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.2079G>A	3.37:g.46479450C>T			46454454	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Silent	SNP	ENST00000231751.4	37	CCDS33747.1																																																																																				0.458	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
SETD2	29072	hgsc.bcm.edu	37	3	47129647	47129647	+	Missense_Mutation	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr3:47129647T>C	ENST00000409792.3	-	10	5275	c.5233A>G	c.(5233-5235)Att>Gtt	p.I1745V	snoU13_ENST00000516129.1_RNA	NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1745					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		AAAGTTTCAATTCTAACCATT	0.418			"""N, F, S, Mis"""		clear cell renal carcinoma																																			Rec	yes		3	3p21.31	29072	SET domain containing 2		E	0			3											127.0	133.0	131.0					3																	47129647		2203	4300	6503	47104651	SO:0001583	missense	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.5233A>G	3.37:g.47129647T>C	ENSP00000386759:p.Ile1745Val		47104651	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	T	18.09	3.545589	0.65198	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	D	0.88046	-2.33	4.46	4.46	0.54185	.	0.000000	0.52532	D	0.000066	T	0.68915	0.3053	N	0.01505	-0.83	0.42176	D	0.99166	B;B	0.30236	0.274;0.274	B;B	0.25614	0.062;0.062	T	0.72571	-0.4253	10	0.48119	T	0.1	.	14.2024	0.65712	0.0:0.0:0.0:1.0	.	1745;1745	F2Z317;Q9BYW2	.;SETD2_HUMAN	V	1745	ENSP00000386759:I1745V	ENSP00000386759:I1745V	I	-	1	0	SETD2	47104651	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.618000	0.67722	1.995000	0.58328	0.528000	0.53228	ATT		0.418	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
WDR6	11180	hgsc.bcm.edu	37	3	49051072	49051072	+	Missense_Mutation	SNP	G	G	A	rs546787787		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr3:49051072G>A	ENST00000608424.1	+	2	2144	c.2105G>A	c.(2104-2106)cGt>cAt	p.R702H	WDR6_ENST00000415265.2_Missense_Mutation_p.R150H|WDR6_ENST00000395474.3_Missense_Mutation_p.R732H|WDR6_ENST00000448293.1_Missense_Mutation_p.R651H			Q9NNW5	WDR6_HUMAN	WD repeat domain 6	702					cell cycle arrest (GO:0007050)|negative regulation of autophagy (GO:0010507)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26				Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155)		CTGCATGGCCGTGAGATCACT	0.587											OREG0015565	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					0			3											82.0	71.0	75.0					3																	49051072		2203	4300	6503	49026076	SO:0001583	missense	11180			AF099100	CCDS2782.2	3p21.31	2013-01-09			ENSG00000178252	ENSG00000178252		"""WD repeat domain containing"""	12758	protein-coding gene	gene with protein product		606031					Standard	NM_018031		Approved		uc003cvj.2	Q9NNW5	OTTHUMG00000133546	ENST00000608424.1:c.2105G>A	3.37:g.49051072G>A	ENSP00000477389:p.Arg702His	959	49026076	B4DHK2|Q3MIT1|Q9UF63	Missense_Mutation	SNP	ENST00000608424.1	37		.	.	.	.	.	.	.	.	.	.	G	17.86	3.491680	0.64074	.	.	ENSG00000178252	ENST00000395474;ENST00000415265;ENST00000448293	T;T;T	0.70631	2.79;-0.5;-0.5	5.49	5.49	0.81192	WD40 repeat-like-containing domain (1);	0.049393	0.85682	D	0.000000	D	0.84777	0.5547	M	0.75264	2.295	0.42134	D	0.991488	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.987;0.948;0.997	D	0.86322	0.1693	10	0.87932	D	0	-23.0479	19.3757	0.94508	0.0:0.0:1.0:0.0	.	150;702;651	E9PBK6;Q9NNW5;E9PDU5	.;WDR6_HUMAN;.	H	732;150;651	ENSP00000378857:R732H;ENSP00000412195:R150H;ENSP00000413432:R651H	ENSP00000378857:R732H	R	+	2	0	WDR6	49026076	1.000000	0.71417	0.971000	0.41717	0.984000	0.73092	6.089000	0.71384	2.583000	0.87209	0.561000	0.74099	CGT		0.587	WDR6-024	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471652.1		
SPICE1	152185	hgsc.bcm.edu	37	3	113187725	113187725	+	Missense_Mutation	SNP	G	G	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr3:113187725G>A	ENST00000295872.4	-	9	1032	c.773C>T	c.(772-774)gCt>gTt	p.A258V		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	258					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						TCTCTTGACAGCATTGGTAGC	0.413																																																	0			3											88.0	79.0	82.0					3																	113187725		2203	4300	6503	114670415	SO:0001583	missense	0			AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"""spindle and centriole protein"""	613447	"""coiled-coil domain containing 52"""	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.773C>T	3.37:g.113187725G>A	ENSP00000295872:p.Ala258Val		114670415	D3DN72|Q8WUX6	Missense_Mutation	SNP	ENST00000295872.4	37	CCDS2973.1	.	.	.	.	.	.	.	.	.	.	G	10.73	1.433986	0.25813	.	.	ENSG00000163611	ENST00000295872	T	0.32515	1.45	5.05	3.24	0.37175	.	0.289600	0.37906	N	0.001898	T	0.17323	0.0416	L	0.33245	0.995	0.41048	D	0.985286	P;P	0.41393	0.748;0.506	B;B	0.36134	0.218;0.218	T	0.04268	-1.0964	10	0.23891	T	0.37	-8.2206	5.4437	0.16523	0.3329:0.0:0.6671:0.0	.	154;258	B3KX77;Q8N0Z3	.;SPICE_HUMAN	V	258	ENSP00000295872:A258V	ENSP00000295872:A258V	A	-	2	0	SPICE1	114670415	0.995000	0.38212	0.996000	0.52242	0.045000	0.14185	2.968000	0.49224	1.263000	0.44181	-0.218000	0.12543	GCT		0.413	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718	
LRP6	4040	hgsc.bcm.edu	37	12	12340026	12340026	+	Silent	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:12340026T>C	ENST00000261349.4	-	4	751	c.675A>G	c.(673-675)ccA>ccG	p.P225P	LRP6_ENST00000543091.1_Silent_p.P225P	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	225	Beta-propeller 1.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				CAAAAGGATGTGGAAGGGAAC	0.398																																																	0			12											110.0	93.0	99.0					12																	12340026		2203	4300	6503	12231293	SO:0001819	synonymous_variant	4040			AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"""Low density lipoprotein receptors"""	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.675A>G	12.37:g.12340026T>C			12231293	Q17RZ2	Silent	SNP	ENST00000261349.4	37	CCDS8647.1																																																																																				0.398	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1		
C2CD5	9847	hgsc.bcm.edu	37	12	22666294	22666294	+	Silent	SNP	A	A	G			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:22666294A>G	ENST00000333957.4	-	9	1227	c.972T>C	c.(970-972)gcT>gcC	p.A324A	C2CD5_ENST00000536386.1_Silent_p.A315A|C2CD5_ENST00000396028.2_Silent_p.A315A|C2CD5_ENST00000544930.1_Silent_p.A117A|C2CD5_ENST00000542676.1_Silent_p.A324A|C2CD5_ENST00000446597.1_Silent_p.A324A|C2CD5_ENST00000545552.1_Silent_p.A315A	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	324					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										CTTCTTTTCCAGCACTACCAC	0.363																																																	0			12											130.0	121.0	124.0					12																	22666294		2203	4300	6503	22557561	SO:0001819	synonymous_variant	9847			AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"""138 kDa C2 domain-containing phosphoprotein"""		"""KIAA0528"""	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.972T>C	12.37:g.22666294A>G			22557561	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Silent	SNP	ENST00000333957.4	37	CCDS31758.1																																																																																				0.363	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802	
KRAS	3845	hgsc.bcm.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_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	
STK38L	23012	hgsc.bcm.edu	37	12	27462048	27462048	+	Splice_Site	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:27462048T>C	ENST00000389032.3	+	5	480	c.311T>C	c.(310-312)gTg>gCg	p.V104A	STK38L_ENST00000539577.1_Splice_Site_p.V11A	NM_015000.3	NP_055815.1			serine/threonine kinase 38 like											breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12	Colorectal(261;0.0847)					ATCTTTTAGGTGCGGTTGGTC	0.348																																																	0			12											78.0	78.0	78.0					12																	27462048		2203	4300	6503	27353315	SO:0001630	splice_region_variant	23012			AB023182	CCDS31761.1	12p11.23	2014-04-23			ENSG00000211455	ENSG00000211455			17848	protein-coding gene	gene with protein product	"""nuclear Dbf2-related 2"""	615836				16488889	Standard	NM_015000		Approved	KIAA0965, NDR2	uc001rhr.3	Q9Y2H1	OTTHUMG00000169284	ENST00000389032.3:c.310-1T>C	12.37:g.27462048T>C			27353315		Missense_Mutation	SNP	ENST00000389032.3	37	CCDS31761.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.361762	0.82353	.	.	ENSG00000211455	ENST00000541191;ENST00000389032;ENST00000545470;ENST00000539577;ENST00000543246;ENST00000544969	T;T;T;T;T;T	0.60672	1.51;1.51;0.17;0.17;1.51;1.51	4.63	4.63	0.57726	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.77343	0.4116	M	0.87328	2.875	0.80722	D	1	P;D	0.55385	0.868;0.971	P;D	0.64506	0.734;0.926	T	0.82390	-0.0481	10	0.87932	D	0	.	14.3604	0.66768	0.0:0.0:0.0:1.0	.	11;104	B4E3J8;Q9Y2H1	.;ST38L_HUMAN	A	104;104;63;11;104;104	ENSP00000437856:V104A;ENSP00000373684:V104A;ENSP00000439457:V63A;ENSP00000446386:V11A;ENSP00000442253:V104A;ENSP00000440279:V104A	ENSP00000373684:V104A	V	+	2	0	STK38L	27353315	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	7.980000	0.88113	1.860000	0.53959	0.383000	0.25322	GTG		0.348	STK38L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403297.1	NM_015000	Missense_Mutation
FAM186A	121006	hgsc.bcm.edu	37	12	50754549	50754549	+	Silent	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:50754549C>T	ENST00000327337.5	-	3	572	c.573G>A	c.(571-573)aaG>aaA	p.K191K	FAM186A_ENST00000543111.1_Silent_p.K191K	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	191																	ATATTTTTTTCTTTTGTTTCT	0.333																																					NSCLC(138;1796 1887 12511 19463 37884)												0			12											66.0	50.0	55.0					12																	50754549		692	1591	2283	49040816	SO:0001819	synonymous_variant	121006				CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.573G>A	12.37:g.50754549C>T			49040816		Silent	SNP	ENST00000327337.5	37	CCDS44878.1																																																																																				0.333	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
HOXC11	3227	hgsc.bcm.edu	37	12	54367195	54367195	+	Missense_Mutation	SNP	G	G	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:54367195G>A	ENST00000546378.1	+	1	286	c.170G>A	c.(169-171)cGt>cAt	p.R57H	HOTAIR_ENST00000455246.1_RNA|HOXC11_ENST00000243082.4_Missense_Mutation_p.R57H|HOTAIR_ENST00000424518.1_RNA			O43248	HXC11_HUMAN	homeobox C11	57					anterior/posterior pattern specification (GO:0009952)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal joint morphogenesis (GO:0060272)|endoderm development (GO:0007492)|metanephros development (GO:0001656)|organ induction (GO:0001759)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)	cytoplasm (GO:0005737)|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)			large_intestine(1)|ovary(1)	2						GCCCCCTCTCGTCAGATCTCC	0.637			T	NUP98	AML																																			Dom	yes		12	12q13.3	3227	homeo box C11		L	0			12											110.0	118.0	115.0					12																	54367195		2203	4300	6503	52653462	SO:0001583	missense	3227				CCDS8867.1	12q13.13	2011-06-20	2005-12-22		ENSG00000123388	ENSG00000123388		"""Homeoboxes / ANTP class : HOXL subclass"""	5123	protein-coding gene	gene with protein product		605559	"""homeo box C11"""	HOX3H		1973146, 1358459	Standard	NM_014212		Approved		uc001sem.3	O43248	OTTHUMG00000160011	ENST00000546378.1:c.170G>A	12.37:g.54367195G>A	ENSP00000446680:p.Arg57His		52653462	A8K7D1|Q96DH2	Missense_Mutation	SNP	ENST00000546378.1	37	CCDS8867.1	.	.	.	.	.	.	.	.	.	.	G	18.30	3.594102	0.66219	.	.	ENSG00000123388	ENST00000546378;ENST00000243082	T;T	0.47177	0.85;0.85	4.32	4.32	0.51571	Domain of unknown function DUF3528, homeobox protein, eukaryotic (1);	0.000000	0.85682	D	0.000000	T	0.55016	0.1894	M	0.63428	1.95	0.54753	D	0.999989	P	0.50710	0.938	P	0.49528	0.614	T	0.60831	-0.7185	10	0.54805	T	0.06	.	16.1042	0.81209	0.0:0.0:1.0:0.0	.	57	O43248	HXC11_HUMAN	H	57	ENSP00000446680:R57H;ENSP00000243082:R57H	ENSP00000243082:R57H	R	+	2	0	HOXC11	52653462	1.000000	0.71417	0.992000	0.48379	0.992000	0.81027	6.221000	0.72243	2.390000	0.81377	0.561000	0.74099	CGT		0.637	HOXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358869.2		
PTPRB	5787	hgsc.bcm.edu	37	12	70983905	70983905	+	Missense_Mutation	SNP	A	A	G			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:70983905A>G	ENST00000261266.5	-	6	1264	c.1235T>C	c.(1234-1236)cTc>cCc	p.L412P	PTPRB_ENST00000451516.2_Intron|PTPRB_ENST00000551525.1_Missense_Mutation_p.L629P|PTPRB_ENST00000550358.1_Missense_Mutation_p.L630P|PTPRB_ENST00000538708.1_Missense_Mutation_p.L412P|PTPRB_ENST00000550857.1_Intron|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000334414.6_Missense_Mutation_p.L630P	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	412	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.L412P(1)		breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			ATCATTGAAGAGTAGGATCCG	0.507											OREG0021990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - Missense(1)	lung(1)	12											131.0	131.0	131.0					12																	70983905		2010	4196	6206	69270172	SO:0001583	missense	5787			X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.1235T>C	12.37:g.70983905A>G	ENSP00000261266:p.Leu412Pro	1126	69270172	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	37	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	A	18.35	3.604596	0.66445	.	.	ENSG00000127329	ENST00000334414;ENST00000550358;ENST00000544694;ENST00000538708;ENST00000261266;ENST00000551525;ENST00000548122	T;T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3;0.3	5.63	5.63	0.86233	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.132141	0.51477	D	0.000086	T	0.80138	0.4568	M	0.88640	2.97	0.80722	D	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	1.0;1.0;1.0;1.0;1.0;1.0	D	0.84338	0.0525	10	0.87932	D	0	.	15.839	0.78831	1.0:0.0:0.0:0.0	.	412;509;629;630;412;630	F5H3G6;Q6ZR19;F8VSD5;P23467-3;P23467;F8VU56	.;.;.;.;PTPRB_HUMAN;.	P	630;630;630;412;412;629;509	ENSP00000334928:L630P;ENSP00000448058:L630P;ENSP00000438927:L412P;ENSP00000261266:L412P;ENSP00000448349:L629P;ENSP00000446982:L509P	ENSP00000261266:L412P	L	-	2	0	PTPRB	69270172	1.000000	0.71417	0.998000	0.56505	0.632000	0.37999	7.969000	0.87988	2.130000	0.65690	0.533000	0.62120	CTC		0.507	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
CEP290	80184	hgsc.bcm.edu	37	12	88474162	88474162	+	Missense_Mutation	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:88474162T>C	ENST00000552810.1	-	38	5366	c.5023A>G	c.(5023-5025)Aac>Gac	p.N1675D	CEP290_ENST00000309041.7_Missense_Mutation_p.N1677D|CEP290_ENST00000547691.2_Missense_Mutation_p.N735D|CEP290_ENST00000397838.3_Missense_Mutation_p.N735D	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1675					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						TCTTCATGGTTTTCTTGAAGC	0.363																																																	0			12											108.0	97.0	100.0					12																	88474162		1818	4077	5895	86998293	SO:0001583	missense	80184			AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"""Joubert syndrome 5"", ""nephrocystin-6"", ""cancer/testis antigen 87"", ""POC3 centriolar protein homolog (Chlamydomonas)"", ""Meckel syndrome, type 4"""	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.5023A>G	12.37:g.88474162T>C	ENSP00000448012:p.Asn1675Asp		86998293	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	T	6.754	0.507937	0.12883	.	.	ENSG00000198707	ENST00000547691;ENST00000552810;ENST00000309041;ENST00000397838	D;D;D;D	0.91843	-2.92;-2.92;-2.92;-2.92	4.35	4.35	0.52113	.	0.424145	0.27420	N	0.019448	D	0.84669	0.5523	N	0.24115	0.695	0.26288	N	0.978165	B	0.21309	0.054	B	0.20384	0.029	T	0.67879	-0.5556	10	0.11485	T	0.65	.	13.8052	0.63225	0.0:0.0:0.0:1.0	.	1675	O15078	CE290_HUMAN	D	735;1675;1677;735	ENSP00000446905:N735D;ENSP00000448012:N1675D;ENSP00000308021:N1677D;ENSP00000380938:N735D	ENSP00000308021:N1677D	N	-	1	0	CEP290	86998293	1.000000	0.71417	1.000000	0.80357	0.316000	0.28119	2.451000	0.44952	1.731000	0.51592	0.377000	0.23210	AAC		0.363	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	
CDK17	5128	hgsc.bcm.edu	37	12	96688840	96688840	+	Silent	SNP	G	G	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:96688840G>T	ENST00000261211.3	-	10	1537	c.934C>A	c.(934-936)Cga>Aga	p.R312R	CDK17_ENST00000553042.1_5'UTR|CDK17_ENST00000542666.1_Silent_p.R259R|CDK17_ENST00000543119.2_Silent_p.R312R	NM_001170464.2|NM_002595.4	NP_001163935.1|NP_002586.2	Q00537	CDK17_HUMAN	cyclin-dependent kinase 17	312	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)	p.R312G(2)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(6)|lung(11)|ovary(4)|prostate(2)|skin(1)	37						TTCAAGTCTCGATGCAATACC	0.343																																																	2	Substitution - Missense(2)	ovary(1)|lung(1)	12											137.0	129.0	132.0					12																	96688840		2203	4300	6503	95212971	SO:0001819	synonymous_variant	0				CCDS9061.1, CCDS53819.1	12q23.1	2011-11-08	2009-12-16	2009-12-16		ENSG00000059758		"""Cyclin-dependent kinases"""	8750	protein-coding gene	gene with protein product		603440	"""PCTAIRE protein kinase 2"""	PCTK2		9370357, 19884882	Standard	NM_001170464		Approved	PCTAIRE2	uc009ztk.3	Q00537		ENST00000261211.3:c.934C>A	12.37:g.96688840G>T			95212971	A8K1U6|B2RCQ2|Q8NEB8	Silent	SNP	ENST00000261211.3	37	CCDS9061.1																																																																																				0.343	CDK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408751.1	NM_002595	
RAD9B	144715	hgsc.bcm.edu	37	12	110960201	110960201	+	Silent	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:110960201T>C	ENST00000409778.3	+	8	927	c.903T>C	c.(901-903)tcT>tcC	p.S301S	RAD9B_ENST00000409246.1_Silent_p.S298S|RAD9B_ENST00000409300.1_Silent_p.S370S|RAD9B_ENST00000392672.4_Silent_p.S370S|RAD9B_ENST00000409425.1_Silent_p.S298S			Q6WBX8	RAD9B_HUMAN	RAD9 homolog B (S. pombe)	367					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)	checkpoint clamp complex (GO:0030896)|nucleoplasm (GO:0005654)				endometrium(1)|large_intestine(2)|lung(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	7						TGCCAGGGTCTCTGTGTCTCA	0.478																																																	0			12											65.0	50.0	55.0					12																	110960201		2203	4300	6503	109444584	SO:0001819	synonymous_variant	144715				CCDS9148.2, CCDS66469.1, CCDS73526.1, CCDS73527.1	12q24.13	2008-12-15	2008-12-15		ENSG00000151164	ENSG00000151164			21700	protein-coding gene	gene with protein product		608368					Standard	NM_152442		Approved	FLJ40346	uc001trf.4	Q6WBX8	OTTHUMG00000152952	ENST00000409778.3:c.903T>C	12.37:g.110960201T>C			109444584	Q5U5K0|Q6NVJ1|Q6ZVT7|Q8N7T9|Q96LI8	Silent	SNP	ENST00000409778.3	37																																																																																					0.478	RAD9B-009	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404634.1	NM_152442	
TCTN2	79867	hgsc.bcm.edu	37	12	124189172	124189172	+	Missense_Mutation	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr12:124189172T>C	ENST00000303372.5	+	15	1834	c.1706T>C	c.(1705-1707)cTc>cCc	p.L569P	TCTN2_ENST00000426174.2_Missense_Mutation_p.L568P|RP11-338K17.8_ENST00000538837.1_lincRNA	NM_001143850.2|NM_024809.4	NP_001137322.1|NP_079085.2	Q96GX1	TECT2_HUMAN	tectonic family member 2	569					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)		ATCCGCATCCTCATCTCGGAT	0.532																																																	0			12											84.0	67.0	73.0					12																	124189172		2203	4300	6503	122755125	SO:0001583	missense	79867			AK056924	CCDS9253.1, CCDS45007.1	12q24.31	2011-04-12	2007-08-20	2007-08-20	ENSG00000168778	ENSG00000168778		"""Tectonic proteins"""	25774	protein-coding gene	gene with protein product	"""Meckel syndrome, type 8"""	613846	"""chromosome 12 open reading frame 38"""	C12orf38		21462283	Standard	NM_024809		Approved	FLJ12975, TECT2, MKS8	uc001ufp.3	Q96GX1	OTTHUMG00000168700	ENST00000303372.5:c.1706T>C	12.37:g.124189172T>C	ENSP00000304941:p.Leu569Pro		122755125	A8K7Y8|B3KPW5|Q9H966	Missense_Mutation	SNP	ENST00000303372.5	37	CCDS9253.1	.	.	.	.	.	.	.	.	.	.	T	18.78	3.695957	0.68386	.	.	ENSG00000168778	ENST00000426174;ENST00000303372	D;D	0.86694	-2.16;-2.16	5.7	5.7	0.88788	.	0.229124	0.35615	N	0.003097	D	0.92770	0.7701	M	0.76574	2.34	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.72982	0.979;0.979	D	0.93250	0.6634	10	0.62326	D	0.03	-34.4659	14.8739	0.70481	0.0:0.0:0.0:1.0	.	568;569	A8K7Y8;Q96GX1	.;TECT2_HUMAN	P	568;569	ENSP00000395171:L568P;ENSP00000304941:L569P	ENSP00000304941:L569P	L	+	2	0	TCTN2	122755125	0.994000	0.37717	0.945000	0.38365	0.579000	0.36224	3.287000	0.51732	2.299000	0.77371	0.529000	0.55759	CTC		0.532	TCTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400652.1	NM_024809	
ATP10A	57194	hgsc.bcm.edu	37	15	25959334	25959334	+	Missense_Mutation	SNP	G	G	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr15:25959334G>A	ENST00000356865.6	-	10	1942	c.1831C>T	c.(1831-1833)Cgg>Tgg	p.R611W		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	611					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GTGAACCTCCGCAGGAAGTCT	0.592																																																	0			15											44.0	49.0	48.0					15																	25959334		2203	4300	6503	23510427	SO:0001583	missense	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.1831C>T	15.37:g.25959334G>A	ENSP00000349325:p.Arg611Trp		23510427	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	G	13.13	2.146206	0.37923	.	.	ENSG00000206190	ENST00000356865	T	0.11495	2.77	4.41	3.47	0.39725	HAD-like domain (1);	0.269079	0.37437	N	0.002095	T	0.27349	0.0671	L	0.57536	1.79	0.44345	D	0.99723	D	0.89917	1.0	D	0.70716	0.97	T	0.01819	-1.1267	10	0.72032	D	0.01	-30.2031	13.514	0.61530	0.0:0.0:0.8427:0.1573	.	611	O60312	AT10A_HUMAN	W	611	ENSP00000349325:R611W	ENSP00000349325:R611W	R	-	1	2	ATP10A	23510427	0.994000	0.37717	0.045000	0.18777	0.098000	0.18820	2.859000	0.48364	1.043000	0.40175	0.655000	0.94253	CGG		0.592	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
PAGE2	203569	hgsc.bcm.edu	37	X	55117792	55117792	+	Missense_Mutation	SNP	A	A	G			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chrX:55117792A>G	ENST00000374968.4	+	4	325	c.221A>G	c.(220-222)gAa>gGa	p.E74G	PAGE2_ENST00000374965.1_Missense_Mutation_p.E57G	NM_207339.2	NP_997222.1	Q7Z2X7	PAGE2_HUMAN	P antigen family, member 2 (prostate associated)	74										endometrium(1)|large_intestine(2)|lung(1)|ovary(2)	6						TTTCAACAGGAACTGGCTCTG	0.398																																																	0			X											76.0	80.0	79.0					X																	55117792		2171	4290	6461	55134517	SO:0001583	missense	203569			BC054022	CCDS14367.1	Xp11.22	2009-06-17			ENSG00000234068	ENSG00000234068			31804	protein-coding gene	gene with protein product		300738	"""G antigen, family C, 2"""	GAGEC2		9724777	Standard	NM_207339		Approved	MGC62094, PAGE-2, CT16.4		Q7Z2X7	OTTHUMG00000021648	ENST00000374968.4:c.221A>G	X.37:g.55117792A>G	ENSP00000364107:p.Glu74Gly		55134517	Q5JRK7|Q5JRK8	Missense_Mutation	SNP	ENST00000374968.4	37	CCDS14367.1	.	.	.	.	.	.	.	.	.	.	a	4.669	0.124320	0.08931	.	.	ENSG00000234068	ENST00000374968;ENST00000374965	T;T	0.26373	1.74;1.74	1.13	-0.159	0.13379	.	.	.	.	.	T	0.32585	0.0834	M	0.84433	2.695	0.09310	N	1	P	0.36683	0.565	B	0.40825	0.341	T	0.34030	-0.9845	9	0.87932	D	0	.	3.9312	0.09286	0.6225:0.3775:0.0:0.0	.	74	Q7Z2X7	GGEE2_HUMAN	G	74;57	ENSP00000364107:E74G;ENSP00000364104:E57G	ENSP00000364104:E57G	E	+	2	0	PAGE2	55134517	0.016000	0.18221	0.001000	0.08648	0.013000	0.08279	0.408000	0.21065	-0.109000	0.12044	-1.716000	0.00709	GAA		0.398	PAGE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056857.1	NM_207339	
ATRX	546	hgsc.bcm.edu	37	X	76937492	76937492	+	Missense_Mutation	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chrX:76937492C>T	ENST00000373344.5	-	9	3470	c.3256G>A	c.(3256-3258)Gca>Aca	p.A1086T	ATRX_ENST00000395603.3_Missense_Mutation_p.A1048T|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1086					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						CTACCATATGCTCCATTCTTA	0.363			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																																	Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	1	Unknown(1)	bone(1)	X											145.0	160.0	155.0					X																	76937492		2202	4290	6492	76824148	SO:0001583	missense	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.3256G>A	X.37:g.76937492C>T	ENSP00000362441:p.Ala1086Thr		76824148	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	C	7.002	0.555044	0.13436	.	.	ENSG00000085224	ENST00000373344;ENST00000395603;ENST00000400862	D;D	0.91740	-2.89;-2.9	5.56	-0.0726	0.13739	.	1.224500	0.05574	N	0.571506	T	0.78071	0.4226	N	0.04508	-0.205	0.09310	N	1	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.06405	0.001;0.002;0.0;0.001	T	0.66304	-0.5957	10	0.14252	T	0.57	-0.6494	2.337	0.04250	0.1131:0.3352:0.32:0.2317	.	1086;1018;1048;1086	A4LAA3;P46100-6;P46100-4;P46100	.;.;.;ATRX_HUMAN	T	1086;1048;1013	ENSP00000362441:A1086T;ENSP00000378967:A1048T	ENSP00000362441:A1086T	A	-	1	0	ATRX	76824148	0.000000	0.05858	0.078000	0.20375	0.923000	0.55619	-2.055000	0.01397	0.132000	0.18615	-0.305000	0.09177	GCA		0.363	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489	
SLITRK4	139065	hgsc.bcm.edu	37	X	142718503	142718503	+	Missense_Mutation	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chrX:142718503T>C	ENST00000381779.4	-	2	647	c.422A>G	c.(421-423)aAt>aGt	p.N141S	SLITRK4_ENST00000356928.1_Missense_Mutation_p.N141S|SLITRK4_ENST00000338017.4_Missense_Mutation_p.N141S	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	141						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					CTTGATTAAATTGTAGTCAGC	0.368																																																	0			X											82.0	82.0	82.0					X																	142718503		2203	4300	6503	142546169	SO:0001583	missense	139065			BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.422A>G	X.37:g.142718503T>C	ENSP00000371198:p.Asn141Ser		142546169	Q5JXG3|Q8TCM8|Q96DL3	Missense_Mutation	SNP	ENST00000381779.4	37	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.986423	0.53934	.	.	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	T;T;T	0.72615	-0.67;-0.67;-0.67	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	D	0.84933	0.5582	M	0.85945	2.785	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87364	0.2346	10	0.87932	D	0	-12.0771	13.1529	0.59500	0.0:0.0:0.0:1.0	.	141	Q8IW52	SLIK4_HUMAN	S	141	ENSP00000371198:N141S;ENSP00000349400:N141S;ENSP00000336627:N141S	ENSP00000336627:N141S	N	-	2	0	SLITRK4	142546169	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	1.788000	0.52465	0.486000	0.48141	AAT		0.368	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078	
PASD1	139135	hgsc.bcm.edu	37	X	150840856	150840856	+	Nonsense_Mutation	SNP	A	A	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chrX:150840856A>T	ENST00000370357.4	+	14	1884	c.1639A>T	c.(1639-1641)Aag>Tag	p.K547*		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	547	Lys-rich.					nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					Acaggagcggaagaagtggca	0.532																																																	0			X											52.0	52.0	52.0					X																	150840856		2203	4300	6503	150591512	SO:0001587	stop_gained	139135			AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"""cancer/testis antigen 63"""					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.1639A>T	X.37:g.150840856A>T	ENSP00000359382:p.Lys547*		150591512	Q3MNE0|Q69HD7|Q8N7X9	Nonsense_Mutation	SNP	ENST00000370357.4	37	CCDS35431.1	.	.	.	.	.	.	.	.	.	.	A	18.38	3.610478	0.66558	.	.	ENSG00000166049	ENST00000370357	.	.	.	0.681	-1.36	0.09085	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	.	.	.	.	.	.	.	X	547	.	ENSP00000359382:K547X	K	+	1	0	PASD1	150591512	0.001000	0.12720	0.001000	0.08648	0.009000	0.06853	0.095000	0.15127	-1.213000	0.02617	-0.749000	0.03505	AAG		0.532	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493	
L1CAM	3897	hgsc.bcm.edu	37	X	153135086	153135086	+	Missense_Mutation	SNP	G	G	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chrX:153135086G>A	ENST00000370060.1	-	11	1345	c.1156C>T	c.(1156-1158)Cgt>Tgt	p.R386C	L1CAM_ENST00000361981.3_Missense_Mutation_p.R381C|L1CAM_ENST00000538883.1_Missense_Mutation_p.R388C|L1CAM_ENST00000370057.3_Missense_Mutation_p.R386C|L1CAM_ENST00000370055.1_Missense_Mutation_p.R381C|L1CAM_ENST00000543994.1_Missense_Mutation_p.R388C|L1CAM_ENST00000361699.4_Missense_Mutation_p.R386C	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	386	Ig-like C2-type 4.		R -> C (in HSAS). {ECO:0000269|PubMed:9744477}.		axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)	p.R386C(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					AGGGCGCCACGCTGAATCCGG	0.622																																																	1	Substitution - Missense(1)	endometrium(1)	X	GRCh37	CM981152	L1CAM	M							86.0	71.0	76.0					X																	153135086		2202	4299	6501	152788280	SO:0001583	missense	3897			M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	6470	protein-coding gene	gene with protein product		308840	"""antigen identified by monoclonal antibody R1"""	HSAS1, SPG1, HSAS, MASA, MIC5, S10			Standard	NM_001278116		Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.1156C>T	X.37:g.153135086G>A	ENSP00000359077:p.Arg386Cys		152788280	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Missense_Mutation	SNP	ENST00000370060.1	37	CCDS14733.1	.	.	.	.	.	.	.	.	.	.	G	15.91	2.972345	0.53614	.	.	ENSG00000198910	ENST00000370060;ENST00000543994;ENST00000370057;ENST00000538883;ENST00000361981;ENST00000370055;ENST00000361699	T;T;T;T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27	5.6	1.45	0.22620	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.420400	0.04316	N	0.349796	T	0.71307	0.3324	L	0.43152	1.355	0.09310	N	1	D;D;D	0.57571	0.98;0.961;0.969	B;B;P	0.58172	0.237;0.319;0.834	T	0.53947	-0.8366	10	0.72032	D	0.01	.	5.7768	0.18283	0.088:0.4315:0.3758:0.1048	.	381;386;386	G3XAF4;P32004-2;P32004	.;.;L1CAM_HUMAN	C	386;388;386;388;381;381;386	ENSP00000359077:R386C;ENSP00000438430:R388C;ENSP00000359074:R386C;ENSP00000439645:R388C;ENSP00000354712:R381C;ENSP00000359072:R381C;ENSP00000355380:R386C	ENSP00000355380:R386C	R	-	1	0	L1CAM	152788280	0.001000	0.12720	0.000000	0.03702	0.886000	0.51366	0.156000	0.16382	0.101000	0.17610	0.483000	0.47432	CGT		0.622	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003	
TMLHE	55217	hgsc.bcm.edu	37	X	154754254	154754254	+	Missense_Mutation	SNP	A	A	G			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chrX:154754254A>G	ENST00000334398.3	-	3	366	c.221T>C	c.(220-222)gTc>gCc	p.V74A	TMLHE-AS1_ENST00000452506.1_RNA|TMLHE_ENST00000369439.4_Missense_Mutation_p.V74A	NM_018196.3	NP_060666.1	Q9NVH6	TMLH_HUMAN	trimethyllysine hydroxylase, epsilon	74					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of oxidoreductase activity (GO:0051354)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|trimethyllysine dioxygenase activity (GO:0050353)			breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	20	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Succinic acid(DB00139)|Vitamin C(DB00126)	TCGAAGCCAGACGTAATCAAA	0.428																																																	0			X											156.0	135.0	143.0					X																	154754254		2202	4300	6502	154407448	SO:0001583	missense	55217			AF373407, X97513	CCDS14768.1, CCDS55547.1	Xq28	2006-07-14			ENSG00000185973	ENSG00000185973			18308	protein-coding gene	gene with protein product	"""butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 2"""	300777				8908511, 11431483	Standard	NM_018196		Approved	TMLH, FLJ10727, BBOX2, XAP130	uc004fnn.3	Q9NVH6	OTTHUMG00000022674	ENST00000334398.3:c.221T>C	X.37:g.154754254A>G	ENSP00000335261:p.Val74Ala		154407448	A8K6M9|B4E3R3|Q5TZB5|Q6IA90|Q8TBT0	Missense_Mutation	SNP	ENST00000334398.3	37	CCDS14768.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.054643	0.75960	.	.	ENSG00000185973	ENST00000334398;ENST00000369439	D;T	0.83914	-1.78;-1.25	3.81	3.81	0.43845	Domain of unknown function, DUF971 (1);	0.000000	0.85682	D	0.000000	D	0.88945	0.6575	M	0.76574	2.34	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.998;0.998	D	0.87759	0.2597	10	0.39692	T	0.17	-10.9097	10.2175	0.43177	1.0:0.0:0.0:0.0	.	74;74;74	Q9NVH6-2;A8K6M9;Q9NVH6	.;.;TMLH_HUMAN	A	74	ENSP00000335261:V74A;ENSP00000358447:V74A	ENSP00000335261:V74A	V	-	2	0	TMLHE	154407448	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.698000	0.84413	1.476000	0.48215	0.417000	0.27973	GTC		0.428	TMLHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058817.1	NM_018196	
GRIA2	2891	hgsc.bcm.edu	37	4	158284035	158284035	+	Missense_Mutation	SNP	G	G	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr4:158284035G>A	ENST00000264426.9	+	15	2770	c.2491G>A	c.(2491-2493)Gct>Act	p.A831T	GRIA2_ENST00000296526.7_Missense_Mutation_p.A831T|GRIA2_ENST00000449365.1_Missense_Mutation_p.A784T|GRIA2_ENST00000507898.1_Missense_Mutation_p.A784T|GRIA2_ENST00000393815.2_Missense_Mutation_p.A784T|AC079233.1_ENST00000578227.1_RNA	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	831					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.A831T(2)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	AATGCTGGTGGCTTTGATTGA	0.468																																																	2	Substitution - Missense(2)	lung(2)	4											150.0	135.0	140.0					4																	158284035		2203	4300	6503	158503485	SO:0001583	missense	2891				CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.2491G>A	4.37:g.158284035G>A	ENSP00000264426:p.Ala831Thr		158503485	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	37	CCDS43274.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.4|24.4	4.532538|4.532538	0.85812|0.85812	.|.	.|.	ENSG00000120251|ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365|ENST00000510854	T;T;T;T;T|.	0.15718|.	2.4;2.4;2.44;2.44;2.4|.	6.08|6.08	6.08|6.08	0.98989|0.98989	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.83857|0.83857	0.5345|0.5345	M|M	0.84948|0.84948	2.725|2.725	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;0.999;0.997|.	D;D;D|.	0.87578|.	0.998;0.998;0.98|.	D|D	0.83604|0.83604	0.0130|0.0130	10|5	0.87932|.	D|.	0|.	.|.	20.6721|20.6721	0.99693|0.99693	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	831;831;784|.	P42262;P42262-2;A8MT92|.	GRIA2_HUMAN;.;.|.	T|D	784;784;831;831;784|161	ENSP00000426845:A784T;ENSP00000377403:A784T;ENSP00000296526:A831T;ENSP00000264426:A831T;ENSP00000389837:A784T|.	ENSP00000264426:A831T|.	A|G	+|+	1|2	0|0	GRIA2|GRIA2	158503485|158503485	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.869000|9.869000	0.99810|0.99810	2.894000|2.894000	0.99253|0.99253	0.591000|0.591000	0.81541|0.81541	GCT|GGC		0.468	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2		
RAPGEF2	9693	hgsc.bcm.edu	37	4	160264556	160264556	+	Splice_Site	SNP	G	G	A	rs201720107		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr4:160264556G>A	ENST00000264431.4	+	16	3190	c.2771G>A	c.(2770-2772)cGg>cAg	p.R924Q		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	924	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		TTCAGGACTCGGTGAGTATGT	0.398																																																	0			4						G	GLN/ARG	1,3877		0,1,1938	101.0	98.0	99.0		2771	4.9	1.0	4		99	1,8275		0,1,4137	yes	missense-near-splice	RAPGEF2	NM_014247.2	43	0,2,6075	AA,AG,GG		0.0121,0.0258,0.0165	possibly-damaging	924/1500	160264556	2,12152	1939	4138	6077	160484006	SO:0001630	splice_region_variant	9693			AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"""Rap GEP"""	609530	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 1"""	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.2771+1G>A	4.37:g.160264556G>A			160484006	D3DP27	Missense_Mutation	SNP	ENST00000264431.4	37	CCDS43277.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.359615	0.82353	2.58E-4	1.21E-4	ENSG00000109756	ENST00000264431	T	0.38560	1.13	5.73	4.89	0.63831	Guanine-nucleotide dissociation stimulator CDC25 (2);Ras guanine nucleotide exchange factor, domain (1);	0.043792	0.85682	D	0.000000	T	0.42086	0.1187	L	0.55481	1.735	0.80722	D	1	P	0.42078	0.77	B	0.40659	0.336	T	0.36625	-0.9740	10	0.46703	T	0.11	.	14.6849	0.69042	0.0697:0.0:0.9303:0.0	.	924	Q9Y4G8	RPGF2_HUMAN	Q	924	ENSP00000264431:R924Q	ENSP00000264431:R924Q	R	+	2	0	RAPGEF2	160484006	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.864000	0.99589	1.425000	0.47237	0.491000	0.48974	CGG		0.398	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247	Missense_Mutation
TENM3	55714	hgsc.bcm.edu	37	4	183713469	183713469	+	Missense_Mutation	SNP	G	G	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr4:183713469G>A	ENST00000511685.1	+	26	5767	c.5644G>A	c.(5644-5646)Gaa>Aaa	p.E1882K	TENM3_ENST00000406950.2_Missense_Mutation_p.E1882K			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1882					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GTACATCTTCGAATACGATAT	0.498																																																	0			4											95.0	97.0	96.0					4																	183713469		2044	4180	6224	183950463	SO:0001583	missense	55714			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.5644G>A	4.37:g.183713469G>A	ENSP00000424226:p.Glu1882Lys		183950463	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.725012	0.89298	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.86694	-2.16;-2.16	5.18	5.18	0.71444	.	.	.	.	.	D	0.83852	0.5344	M	0.71581	2.175	0.80722	D	1	P	0.44006	0.824	B	0.22386	0.039	D	0.87245	0.2269	9	0.62326	D	0.03	.	18.8905	0.92399	0.0:0.0:1.0:0.0	.	1882	Q9P273	TEN3_HUMAN	K	1882	ENSP00000424226:E1882K;ENSP00000385276:E1882K	ENSP00000385276:E1882K	E	+	1	0	ODZ3	183950463	1.000000	0.71417	0.964000	0.40570	0.983000	0.72400	9.623000	0.98386	2.688000	0.91661	0.591000	0.81541	GAA		0.498	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
FAT1	2195	hgsc.bcm.edu	37	4	187629652	187629652	+	Missense_Mutation	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr4:187629652T>C	ENST00000441802.2	-	2	1539	c.1330A>G	c.(1330-1332)Aaa>Gaa	p.K444E		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	444	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GTGGACGCTTTTCTGTCACTT	0.413										HNSCC(5;0.00058)																											Colon(197;1040 2055 4143 4984 49344)												0			4											216.0	211.0	212.0					4																	187629652		1890	4126	6016	187866646	SO:0001583	missense	2195			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.1330A>G	4.37:g.187629652T>C	ENSP00000406229:p.Lys444Glu		187866646		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	T	2.482	-0.319416	0.05386	.	.	ENSG00000083857	ENST00000441802;ENST00000260147;ENST00000509647	D;T	0.81996	-1.56;0.14	5.35	4.15	0.48705	Cadherin (3);Cadherin-like (1);	0.280194	0.44285	D	0.000478	T	0.73892	0.3645	L	0.37561	1.115	0.37357	D	0.911062	B	0.33120	0.398	B	0.37144	0.242	T	0.68887	-0.5290	10	0.06099	T	0.92	.	12.7126	0.57098	0.0:0.0:0.1372:0.8628	.	444	Q14517	FAT1_HUMAN	E	444	ENSP00000406229:K444E;ENSP00000423736:K444E	ENSP00000260147:K444E	K	-	1	0	FAT1	187866646	1.000000	0.71417	0.391000	0.26233	0.795000	0.44927	4.030000	0.57260	1.013000	0.39391	0.459000	0.35465	AAA		0.413	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
TRIML2	205860	hgsc.bcm.edu	37	4	189018291	189018291	+	Missense_Mutation	SNP	A	A	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr4:189018291A>T	ENST00000512729.1	-	6	893	c.519T>A	c.(517-519)caT>caA	p.H173Q	TRIML2_ENST00000326754.3_Missense_Mutation_p.H198Q	NM_173553.1	NP_775824.1	Q8N7C3	TRIMM_HUMAN	tripartite motif family-like 2	173					protein ubiquitination (GO:0016567)|response to retinoic acid (GO:0032526)		ligase activity (GO:0016874)			central_nervous_system(2)|kidney(1)|large_intestine(7)|lung(25)|prostate(3)|urinary_tract(1)	39		all_cancers(14;3.11e-44)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)		CGGGCTCCAGATGCTCAAGCA	0.493																																																	0			4											126.0	122.0	123.0					4																	189018291		2203	4300	6503	189255285	SO:0001583	missense	205860			AK098667	CCDS3850.1	4q35.2	2014-02-12	2007-12-14		ENSG00000179046	ENSG00000179046			26378	protein-coding gene	gene with protein product	"""SPRY domain containing 6"""						Standard	NM_173553		Approved	FLJ25801, SPRYD6	uc003izl.2	Q8N7C3	OTTHUMG00000160225	ENST00000512729.1:c.519T>A	4.37:g.189018291A>T	ENSP00000422581:p.His173Gln		189255285	B7Z6J6	Missense_Mutation	SNP	ENST00000512729.1	37	CCDS3850.1	.	.	.	.	.	.	.	.	.	.	A	6.722	0.502008	0.12822	.	.	ENSG00000179046	ENST00000512729;ENST00000326754	T;T	0.57595	3.63;0.39	4.51	-0.315	0.12746	.	0.766357	0.11596	N	0.548211	T	0.27489	0.0675	N	0.08118	0	0.09310	N	1	B;B	0.18461	0.028;0.004	B;B	0.16722	0.016;0.004	T	0.20338	-1.0278	10	0.22706	T	0.39	.	7.6956	0.28592	0.4367:0.0:0.5633:0.0	.	198;173	B7ZLC3;Q8N7C3	.;TRIMM_HUMAN	Q	173;198	ENSP00000422581:H173Q;ENSP00000317498:H198Q	ENSP00000317498:H198Q	H	-	3	2	TRIML2	189255285	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.489000	0.22387	-0.038000	0.13624	-0.937000	0.02696	CAT		0.493	TRIML2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359733.1	NM_173553	
FAM179A	165186	hgsc.bcm.edu	37	2	29259556	29259556	+	Silent	SNP	C	C	G			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr2:29259556C>G	ENST00000379558.4	+	18	2919	c.2568C>G	c.(2566-2568)ctC>ctG	p.L856L	FAM179A_ENST00000465300.1_3'UTR|FAM179A_ENST00000403861.2_Silent_p.L801L	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	856										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CAGACAACCTCAACTCCAAGA	0.582																																																	0			2											118.0	87.0	98.0					2																	29259556		2203	4300	6503	29113060	SO:0001819	synonymous_variant	165186			AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.2568C>G	2.37:g.29259556C>G			29113060	Q6ZUF5	Silent	SNP	ENST00000379558.4	37	CCDS1769.2																																																																																				0.582	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
DQX1	165545	hgsc.bcm.edu	37	2	74751165	74751165	+	Missense_Mutation	SNP	G	G	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr2:74751165G>T	ENST00000404568.3	-	4	920	c.701C>A	c.(700-702)cCc>cAc	p.P234H	DQX1_ENST00000495597.1_5'UTR|DQX1_ENST00000393951.2_Missense_Mutation_p.P234H	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1	234						nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)	p.P116L(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						CCAGTAGATGGGGGAAGGTCT	0.547																																																	1	Substitution - Missense(1)	ovary(1)	2											72.0	71.0	71.0					2																	74751165		2203	4300	6503	74604673	SO:0001583	missense	165545			AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"""DEAQ box polypeptide 1 (RNA-dependent ATPase)"""				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965	ENST00000404568.3:c.701C>A	2.37:g.74751165G>T	ENSP00000384621:p.Pro234His		74604673	Q6B017|Q8NAM8	Missense_Mutation	SNP	ENST00000404568.3	37	CCDS1949.2	.	.	.	.	.	.	.	.	.	.	G	4.240	0.043452	0.08196	.	.	ENSG00000144045	ENST00000393951;ENST00000404568;ENST00000451518	T;T;T	0.22743	3.31;3.31;1.94	5.38	1.22	0.21188	DEAD-like helicase (1);	0.695877	0.13971	N	0.350163	T	0.16811	0.0404	L	0.50333	1.59	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.27191	-1.0081	10	0.87932	D	0	-20.0491	3.6203	0.08093	0.4228:0.0:0.4066:0.1706	.	234	Q8TE96	DQX1_HUMAN	H	234;234;116	ENSP00000377523:P234H;ENSP00000384621:P234H;ENSP00000392969:P116H	ENSP00000377523:P234H	P	-	2	0	DQX1	74604673	0.004000	0.15560	0.003000	0.11579	0.020000	0.10135	1.354000	0.34056	0.160000	0.19432	0.609000	0.83330	CCC		0.547	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637	
CNNM4	26504	hgsc.bcm.edu	37	2	97427829	97427829	+	Missense_Mutation	SNP	G	G	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr2:97427829G>T	ENST00000377075.2	+	1	1191	c.1093G>T	c.(1093-1095)Gcc>Tcc	p.A365S		NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	365					biomineral tissue development (GO:0031214)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	20						GATCCAGGGTGCCCTGGAACT	0.512																																																	0			2											85.0	75.0	79.0					2																	97427829		2203	4300	6503	96791556	SO:0001583	missense	26504			AB046812	CCDS2024.2	2q11.2	2014-08-08	2014-08-07		ENSG00000158158	ENSG00000158158			105	protein-coding gene	gene with protein product		607805	"""cyclin M4"""	ACDP4		21393841, 24194943	Standard	XM_005263914		Approved	KIAA1592	uc002swx.3	Q6P4Q7	OTTHUMG00000130532	ENST00000377075.2:c.1093G>T	2.37:g.97427829G>T	ENSP00000366275:p.Ala365Ser		96791556	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Missense_Mutation	SNP	ENST00000377075.2	37	CCDS2024.2	.	.	.	.	.	.	.	.	.	.	G	21.2	4.114536	0.77210	.	.	ENSG00000158158	ENST00000377075	T	0.77229	-1.08	5.19	4.28	0.50868	.	0.063550	0.64402	N	0.000009	D	0.91338	0.7268	H	0.96142	3.775	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.93422	0.6778	10	0.87932	D	0	-4.6656	13.6727	0.62436	0.0:0.0:0.8438:0.1561	.	365	Q6P4Q7	CNNM4_HUMAN	S	365	ENSP00000366275:A365S	ENSP00000366275:A365S	A	+	1	0	CNNM4	96791556	1.000000	0.71417	0.983000	0.44433	0.962000	0.63368	9.807000	0.99171	1.119000	0.41883	0.655000	0.94253	GCC		0.512	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184	
PDE1A	5136	hgsc.bcm.edu	37	2	183053745	183053745	+	Missense_Mutation	SNP	A	A	G			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr2:183053745A>G	ENST00000410103.1	-	12	1299	c.1216T>C	c.(1216-1218)Tgt>Cgt	p.C406R	PDE1A_ENST00000456212.1_Missense_Mutation_p.C406R|PDE1A_ENST00000331935.6_Missense_Mutation_p.C406R|PDE1A_ENST00000536095.1_Missense_Mutation_p.C302R|PDE1A_ENST00000435564.1_Missense_Mutation_p.C406R|PDE1A_ENST00000358139.2_Missense_Mutation_p.C406R|PDE1A_ENST00000351439.5_Missense_Mutation_p.C390R|PDE1A_ENST00000346717.4_Missense_Mutation_p.C372R|PDE1A_ENST00000409365.1_Missense_Mutation_p.C390R	NM_001003683.2	NP_001003683.1	P54750	PDE1A_HUMAN	phosphodiesterase 1A, calmodulin-dependent	406	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of smooth muscle cell apoptotic process (GO:0034391)|regulation of smooth muscle cell proliferation (GO:0048660)|signal transduction (GO:0007165)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity (GO:0048101)|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			endometrium(5)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(2)	35			OV - Ovarian serous cystadenocarcinoma(117;0.061)		Bepridil(DB01244)|Caffeine(DB00201)|Felodipine(DB01023)|Nicardipine(DB00622)	TTCCGATCACAAAGTGGGGAA	0.418																																																	0			2											182.0	189.0	187.0					2																	183053745		2203	4300	6503	182761990	SO:0001583	missense	5136				CCDS2285.1, CCDS33344.1, CCDS58741.1, CCDS74612.1	2q32.1	2008-03-18			ENSG00000115252	ENSG00000115252	3.1.4.17	"""Phosphodiesterases"""	8774	protein-coding gene	gene with protein product		171890				8557689, 11342109	Standard	NM_005019		Approved		uc010zfq.2	P54750	OTTHUMG00000132596	ENST00000410103.1:c.1216T>C	2.37:g.183053745A>G	ENSP00000387037:p.Cys406Arg		182761990	D3DPG5|Q86VZ0|Q9C0K8|Q9C0K9|Q9C0L0|Q9C0L1|Q9C0L2|Q9C0L3|Q9C0L4|Q9UFX3	Missense_Mutation	SNP	ENST00000410103.1	37	CCDS33344.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.271533	0.80469	.	.	ENSG00000115252	ENST00000435564;ENST00000346717;ENST00000536095;ENST00000409365;ENST00000331935;ENST00000351439;ENST00000410103;ENST00000358139;ENST00000456212	D;D;D;D;D;D;D;D;D	0.83335	-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71	5.6	5.6	0.85130	5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.045414	0.85682	D	0.000000	D	0.94142	0.8121	H	0.96996	3.92	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;0.999;1.0;0.999	D	0.95903	0.8917	10	0.87932	D	0	.	15.2579	0.73599	1.0:0.0:0.0:0.0	.	302;372;406;390;406	B7Z3A7;P54750-3;P54750;P54750-2;P54750-4	.;.;PDE1A_HUMAN;.;.	R	406;372;302;390;406;390;406;406;406	ENSP00000410309:C406R;ENSP00000329112:C372R;ENSP00000439938:C302R;ENSP00000386767:C390R;ENSP00000331574:C406R;ENSP00000309269:C390R;ENSP00000387037:C406R;ENSP00000350858:C406R;ENSP00000408874:C406R	ENSP00000331574:C406R	C	-	1	0	PDE1A	182761990	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.542000	0.90647	2.254000	0.74563	0.482000	0.46254	TGT		0.418	PDE1A-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334356.1		
SGOL2	151246	hgsc.bcm.edu	37	2	201437640	201437640	+	Silent	SNP	A	A	G			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr2:201437640A>G	ENST00000357799.4	+	7	2669	c.2571A>G	c.(2569-2571)caA>caG	p.Q857Q		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	857					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						AAAATCTACAAGTCACAAATG	0.294																																																	0			2											85.0	84.0	84.0					2																	201437640		1805	4067	5872	201145885	SO:0001819	synonymous_variant	151246			AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.2571A>G	2.37:g.201437640A>G			201145885	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Silent	SNP	ENST00000357799.4	37	CCDS42796.1																																																																																				0.294	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524	
FRMPD1	22844	hgsc.bcm.edu	37	9	37737192	37737192	+	Missense_Mutation	SNP	C	C	G			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr9:37737192C>G	ENST00000539465.1	+	14	2094	c.1501C>G	c.(1501-1503)Ctc>Gtc	p.L501V	FRMPD1_ENST00000541302.1_Missense_Mutation_p.L370V|FRMPD1_ENST00000536622.1_Missense_Mutation_p.L323V|RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Missense_Mutation_p.L501V			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	501						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		CTCCATTTTCCTCTGGCCTGG	0.527																																																	0			9											108.0	96.0	100.0					9																	37737192		2203	4300	6503	37727192	SO:0001583	missense	22844			AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.1501C>G	9.37:g.37737192C>G	ENSP00000444411:p.Leu501Val		37727192	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	C	9.992	1.231053	0.22626	.	.	ENSG00000070601	ENST00000377765;ENST00000539465;ENST00000536622;ENST00000541302	T;T;T;T	0.11277	2.79;2.79;2.79;2.79	5.45	3.48	0.39840	.	0.403653	0.26542	N	0.023797	T	0.07324	0.0185	N	0.22421	0.69	0.23743	N	0.996967	B;B	0.14438	0.004;0.01	B;B	0.12837	0.002;0.008	T	0.34502	-0.9826	10	0.16420	T	0.52	-3.577	12.1514	0.54051	0.3089:0.6911:0.0:0.0	.	370;501	B4DZC8;Q5SYB0	.;FRPD1_HUMAN	V	501;501;323;370	ENSP00000366995:L501V;ENSP00000444411:L501V;ENSP00000437762:L323V;ENSP00000444804:L370V	ENSP00000366995:L501V	L	+	1	0	FRMPD1	37727192	0.962000	0.33011	1.000000	0.80357	0.973000	0.67179	1.955000	0.40372	1.290000	0.44636	0.591000	0.81541	CTC		0.527	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907	
TPTE2	93492	hgsc.bcm.edu	37	13	20025364	20025364	+	Splice_Site	SNP	T	T	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr13:20025364T>A	ENST00000400230.2	-	11	787	c.743A>T	c.(742-744)gAa>gTa	p.E248V	TPTE2_ENST00000382978.1_Splice_Site_p.E208V|TPTE2_ENST00000390680.2_Splice_Site_p.E171V|TPTE2_ENST00000400103.2_Splice_Site_p.E137V|TPTE2_ENST00000255310.6_Splice_Site_p.E171V|TPTE2_ENST00000457266.2_Splice_Site_p.E137V|TPTE2_ENST00000382975.4_Splice_Site_p.E208V|TPTE2_ENST00000382977.4_Splice_Site_p.E248V			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	248	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		CCGCACAACTTCCTAAAAAAG	0.333																																																	0			13											98.0	87.0	91.0					13																	20025364		2203	4300	6503	18923364	SO:0001630	splice_region_variant	93492			AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.742-1A>T	13.37:g.20025364T>A			18923364	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Missense_Mutation	SNP	ENST00000400230.2	37	CCDS45014.1	.	.	.	.	.	.	.	.	.	.	t	12.17	1.857568	0.32791	.	.	ENSG00000132958	ENST00000382978;ENST00000400103;ENST00000400230;ENST00000255310;ENST00000390680;ENST00000382977;ENST00000382975;ENST00000457266;ENST00000343548;ENST00000419256	T;T;T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48	2.63	2.63	0.31362	Phosphatase tensin type (1);	0.118680	0.56097	D	0.000029	T	0.48169	0.1485	M	0.86178	2.8	0.58432	D	0.999994	P;D;D	0.57257	0.929;0.979;0.965	P;P;P	0.57620	0.824;0.788;0.542	T	0.51426	-0.8707	9	.	.	.	-28.2763	7.1515	0.25614	0.0:0.0:0.0:1.0	.	137;171;248	A8MX64;Q6XPS3-3;Q6XPS3	.;.;TPTE2_HUMAN	V	208;137;248;171;171;248;208;137;248;117	ENSP00000372438:E208V;ENSP00000382974:E137V;ENSP00000383089:E248V;ENSP00000255310:E171V;ENSP00000375098:E171V;ENSP00000372437:E248V;ENSP00000372435:E208V;ENSP00000442218:E137V	.	E	-	2	0	TPTE2	18923364	1.000000	0.71417	0.987000	0.45799	0.146000	0.21551	5.681000	0.68175	1.460000	0.47911	0.163000	0.16589	GAA		0.333	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254	Missense_Mutation
PABPC3	5042	hgsc.bcm.edu	37	13	25671195	25671195	+	Missense_Mutation	SNP	A	A	G	rs201411821		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr13:25671195A>G	ENST00000281589.3	+	1	896	c.859A>G	c.(859-861)Agg>Ggg	p.R287G		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	287					mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		GAAGCAAGATAGGATCACCAG	0.398																																																	0			13											186.0	178.0	181.0					13																	25671195		2203	4300	6503	24569195	SO:0001583	missense	5042			AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.859A>G	13.37:g.25671195A>G	ENSP00000281589:p.Arg287Gly		24569195	Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	37	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	A	10.48	1.362072	0.24684	.	.	ENSG00000151846	ENST00000281589	T	0.31247	1.5	0.875	0.875	0.19130	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.45126	U	0.000389	T	0.35451	0.0932	M	0.91354	3.2	0.44711	D	0.997704	B	0.33135	0.399	B	0.32677	0.15	T	0.31336	-0.9947	10	0.87932	D	0	.	3.6845	0.08323	0.5912:0.4087:0.0:1.0E-4	.	287	Q9H361	PABP3_HUMAN	G	287	ENSP00000281589:R287G	ENSP00000281589:R287G	R	+	1	2	PABPC3	24569195	1.000000	0.71417	0.990000	0.47175	0.729000	0.41735	2.714000	0.47202	0.632000	0.30432	0.260000	0.18958	AGG		0.398	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979	
NBEA	26960	hgsc.bcm.edu	37	13	36229754	36229754	+	Missense_Mutation	SNP	G	G	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr13:36229754G>A	ENST00000400445.3	+	54	8701	c.8167G>A	c.(8167-8169)Gtc>Atc	p.V2723I	NBEA_ENST00000379922.3_Missense_Mutation_p.V301I|NBEA_ENST00000537702.1_Missense_Mutation_p.V516I|NBEA_ENST00000540320.1_Missense_Mutation_p.V2723I|NBEA_ENST00000379939.2_Missense_Mutation_p.V2720I|NBEA_ENST00000310336.4_Missense_Mutation_p.V2723I	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2723					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TTGGGATGTGGTCACTTGCTT	0.483																																																	0			13											216.0	222.0	220.0					13																	36229754		2087	4225	6312	35127754	SO:0001583	missense	26960			AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"""A-kinase anchor proteins"", ""WD repeat domain containing"""	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.8167G>A	13.37:g.36229754G>A	ENSP00000383295:p.Val2723Ile		35127754	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	35	5.544882	0.96488	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518;ENST00000402346;ENST00000537702;ENST00000379922	T;T;T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25;-0.25;-0.25	6.06	6.06	0.98353	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.80003	0.4544	L	0.60904	1.88	0.80722	D	1	B;D;D	0.71674	0.149;0.998;0.957	B;D;P	0.67231	0.386;0.95;0.859	T	0.77294	-0.2641	10	0.46703	T	0.11	.	20.6208	0.99490	0.0:0.0:1.0:0.0	.	2723;301;2720	Q8NFP9;Q8NFP9-2;Q5T321	NBEA_HUMAN;.;.	I	2723;2723;2720;2723;1350;301;516;301	ENSP00000440951:V2723I;ENSP00000383295:V2723I;ENSP00000369271:V2720I;ENSP00000308534:V2723I;ENSP00000440233:V516I;ENSP00000369254:V301I	ENSP00000308534:V2723I	V	+	1	0	NBEA	35127754	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	9.694000	0.98686	2.882000	0.98803	0.655000	0.94253	GTC		0.483	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
FREM2	341640	hgsc.bcm.edu	37	13	39454504	39454504	+	Missense_Mutation	SNP	A	A	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr13:39454504A>T	ENST00000280481.7	+	24	9306	c.9090A>T	c.(9088-9090)agA>agT	p.R3030S		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	3030					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TTGGCAAAAGAAGTGTGGAGT	0.488																																																	0			13											107.0	100.0	103.0					13																	39454504		2203	4300	6503	38352504	SO:0001583	missense	341640			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.9090A>T	13.37:g.39454504A>T	ENSP00000280481:p.Arg3030Ser		38352504	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	A	17.57	3.421842	0.62622	.	.	ENSG00000150893	ENST00000280481	T	0.27402	1.67	5.89	-1.66	0.08265	.	0.000000	0.85682	D	0.000000	T	0.50343	0.1610	M	0.87682	2.9	0.58432	D	0.999995	D	0.71674	0.998	D	0.65987	0.94	T	0.52830	-0.8523	10	0.87932	D	0	.	7.5545	0.27817	0.521:0.1135:0.3655:0.0	.	3030	Q5SZK8	FREM2_HUMAN	S	3030	ENSP00000280481:R3030S	ENSP00000280481:R3030S	R	+	3	2	FREM2	38352504	0.998000	0.40836	0.938000	0.37757	0.356000	0.29392	0.784000	0.26816	-0.188000	0.10499	0.460000	0.39030	AGA		0.488	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
RB1	5925	hgsc.bcm.edu	37	13	49037913	49037913	+	Missense_Mutation	SNP	A	A	G			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr13:49037913A>G	ENST00000267163.4	+	21	2291	c.2153A>G	c.(2152-2154)gAc>gGc	p.D718G		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	718	Domain B.|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.?(10)|p.I703_E737del(2)|p.C712_A727del(1)		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)"""	AAGAATATAGACCTTAAATTC	0.299		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"""	28	Whole gene deletion(15)|Unknown(10)|Deletion - In frame(3)	bone(10)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|lung(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|ovary(1)|prostate(1)|liver(1)	13											113.0	118.0	116.0					13																	49037913		2203	4292	6495	47935914	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.2153A>G	13.37:g.49037913A>G	ENSP00000267163:p.Asp718Gly		47935914	A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.796854	0.90453	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.92348	-3.02	6.07	6.07	0.98685	Retinoblastoma-associated protein, B-box (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	D	0.95723	0.8609	M	0.71296	2.17	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96024	0.9011	10	0.87932	D	0	-15.7516	16.6406	0.85098	1.0:0.0:0.0:0.0	.	718	P06400	RB_HUMAN	G	697;718	ENSP00000267163:D718G	ENSP00000267163:D718G	D	+	2	0	RB1	47935914	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.962000	0.93254	2.326000	0.78906	0.533000	0.62120	GAC		0.299	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		
MLNR	2862	hgsc.bcm.edu	37	13	49794957	49794957	+	Missense_Mutation	SNP	C	C	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr13:49794957C>A	ENST00000218721.1	+	1	484	c.484C>A	c.(484-486)Ctc>Atc	p.L162I	MLNR_ENST00000398307.1_Missense_Mutation_p.L162I	NM_001507.1	NP_001498.1	O43193	MTLR_HUMAN	motilin receptor	162					digestion (GO:0007586)|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)|growth hormone-releasing hormone receptor activity (GO:0016520)			endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)	14		all_lung(13;8.31e-06)|Lung NSC(96;0.000251)|Breast(56;0.0008)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;6.1e-09)		CATCGCTGTGCTCTGGGCCGT	0.721																																																	0			13											7.0	8.0	7.0					13																	49794957		2170	4257	6427	48692958	SO:0001583	missense	2862			AF034632	CCDS9414.1	13q14-q21	2012-08-08	2004-05-27	2004-05-28	ENSG00000102539	ENSG00000102539		"""GPCR / Class A : Motilin receptors"""	4495	protein-coding gene	gene with protein product		602885	"""G protein-coupled receptor 38"""	GPR38		9441746	Standard	NM_001507		Approved		uc010tgj.2	O43193	OTTHUMG00000016909	ENST00000218721.1:c.484C>A	13.37:g.49794957C>A	ENSP00000218721:p.Leu162Ile		48692958		Missense_Mutation	SNP	ENST00000218721.1	37	CCDS9414.1	.	.	.	.	.	.	.	.	.	.	c	19.25	3.791343	0.70452	.	.	ENSG00000102539	ENST00000218721;ENST00000398307	T;T	0.70516	-0.49;-0.49	4.53	4.53	0.55603	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.67211	0.2869	N	0.11698	0.16	0.35328	D	0.785388	D	0.89917	1.0	D	0.87578	0.998	T	0.64275	-0.6446	10	0.02654	T	1	-18.536	15.7998	0.78443	0.0:1.0:0.0:0.0	.	162	O43193	MTLR_HUMAN	I	162	ENSP00000218721:L162I;ENSP00000381352:L162I	ENSP00000218721:L162I	L	+	1	0	MLNR	48692958	1.000000	0.71417	0.994000	0.49952	0.348000	0.29142	4.788000	0.62439	2.062000	0.61559	0.558000	0.71614	CTC		0.721	MLNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044897.1	NM_001507	
SLITRK5	26050	hgsc.bcm.edu	37	13	88328216	88328216	+	Silent	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr13:88328216T>C	ENST00000325089.6	+	2	792	c.573T>C	c.(571-573)agT>agC	p.S191S	SLITRK5_ENST00000400028.3_Intron	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	191					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					TTTTGTCCAGTTTACCCAACA	0.483																																																	0			13											85.0	86.0	86.0					13																	88328216		2203	4300	6503	87126217	SO:0001819	synonymous_variant	26050			AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"""leucine rich repeat containing 11"""	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.573T>C	13.37:g.88328216T>C			87126217	B3KNB8|B4DSH5|Q5VT81	Silent	SNP	ENST00000325089.6	37	CCDS9465.1																																																																																				0.483	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3		
NALCN	259232	hgsc.bcm.edu	37	13	101844369	101844369	+	Missense_Mutation	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr13:101844369C>T	ENST00000251127.6	-	14	1744	c.1663G>A	c.(1663-1665)Gga>Aga	p.G555R	NALCN_ENST00000376196.3_Missense_Mutation_p.G555R|NALCN_ENST00000470333.1_5'UTR	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	555					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TCCACCCATCCTTCCTGGGTG	0.433																																																	0			13											136.0	98.0	111.0					13																	101844369		2203	4300	6503	100642370	SO:0001583	missense	259232			AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"""Ion channels / Sodium leak channels, non-selective"""	19082	protein-coding gene	gene with protein product		611549	"""voltage gated channel like 1"""	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.1663G>A	13.37:g.101844369C>T	ENSP00000251127:p.Gly555Arg		100642370	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	37	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	C	31	5.099966	0.94197	.	.	ENSG00000102452	ENST00000251127;ENST00000376196	D;D	0.99888	-7.54;-7.54	5.48	5.48	0.80851	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99891	0.9948	M	0.83953	2.67	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.99;0.991	D	0.96510	0.9378	10	0.87932	D	0	.	19.7249	0.96160	0.0:1.0:0.0:0.0	.	555;555;555	F2Z323;B3KSZ6;Q8IZF0	.;.;NALCN_HUMAN	R	555	ENSP00000251127:G555R;ENSP00000365367:G555R	ENSP00000251127:G555R	G	-	1	0	NALCN	100642370	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.356000	0.79445	2.735000	0.93741	0.650000	0.86243	GGA		0.433	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867	
PTPLA	9200	hgsc.bcm.edu	37	10	17636294	17636294	+	Nonsense_Mutation	SNP	C	C	A	rs536952738	byFrequency	TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr10:17636294C>A	ENST00000361271.3	-	6	731	c.694G>T	c.(694-696)Gga>Tga	p.G232*		NM_014241.3	NP_055056.3	B0YJ81	HACD1_HUMAN	protein tyrosine phosphatase-like (proline instead of catalytic arginine), member A	232					fatty acid biosynthetic process (GO:0006633)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)|protein tyrosine phosphatase activity (GO:0004725)	p.G232*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|skin(1)	13						GAAAACATTCCTGTTTTCTTC	0.318																																																	1	Substitution - Nonsense(1)	lung(1)	10											71.0	72.0	72.0					10																	17636294		2203	4294	6497	17676300	SO:0001587	stop_gained	9200			AF114494	CCDS7121.1	10p14-p13	2008-08-01	2005-11-11		ENSG00000165996	ENSG00000165996			9639	protein-coding gene	gene with protein product	"""cementum attachment protein"""	610467	"""protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a"""			10644438	Standard	XM_005252641		Approved	CAP	uc001ipg.3	B0YJ81	OTTHUMG00000017750	ENST00000361271.3:c.694G>T	10.37:g.17636294C>A	ENSP00000355308:p.Gly232*		17676300	B0YJ80|Q6JIC5|Q96FW7|Q9HB93|Q9UHX2	Nonsense_Mutation	SNP	ENST00000361271.3	37	CCDS7121.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.148376	0.78001	.	.	ENSG00000165996	ENST00000361271	.	.	.	5.72	5.72	0.89469	.	0.105361	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-13.8521	20.2406	0.98372	0.0:1.0:0.0:0.0	.	.	.	.	X	232	.	ENSP00000355308:G232X	G	-	1	0	PTPLA	17676300	1.000000	0.71417	0.969000	0.41365	0.574000	0.36063	6.074000	0.71253	2.857000	0.98124	0.650000	0.86243	GGA		0.318	PTPLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047046.1	NM_014241	
NSUN6	221078	hgsc.bcm.edu	37	10	18937509	18937509	+	Silent	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr10:18937509T>C	ENST00000377304.4	-	2	559	c.141A>G	c.(139-141)tcA>tcG	p.S47S	RP11-139J15.7_ENST00000606425.1_Silent_p.S35S	NM_182543.2	NP_872349.1	Q8TEA1	NSUN6_HUMAN	NOP2/Sun domain family, member 6	47							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15						ATGGAGGATGTGACAGGTGCT	0.348																																																	0			10											214.0	202.0	206.0					10																	18937509		2203	4300	6503	18977515	SO:0001819	synonymous_variant	221078			BC035778	CCDS7130.1	10p13	2014-06-23	2009-11-23	2004-08-26	ENSG00000241058	ENSG00000241058		"""NOP2/Sun domain containing"""	23529	protein-coding gene	gene with protein product			"""NOL1/NOP2/Sun domain family 6"", ""NOL1/NOP2/Sun domain family, member 6"", ""ARL5B antisense RNA 1"""	NOPD1, ARL5B-AS1			Standard	XM_005252394		Approved	FLJ23743	uc010qcp.1	Q8TEA1	OTTHUMG00000017767	ENST00000377304.4:c.141A>G	10.37:g.18937509T>C			18977515	B0YJ54	Silent	SNP	ENST00000377304.4	37	CCDS7130.1																																																																																				0.348	NSUN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047083.1	NM_182543	
TSPAN14	81619	hgsc.bcm.edu	37	10	82269162	82269162	+	Missense_Mutation	SNP	A	A	G			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr10:82269162A>G	ENST00000429989.3	+	5	608	c.385A>G	c.(385-387)Agc>Ggc	p.S129G	TSPAN14_ENST00000372164.3_Missense_Mutation_p.S112G|TSPAN14_ENST00000341863.6_Intron|TSPAN14_ENST00000481124.1_Intron|TSPAN14_ENST00000372158.1_Missense_Mutation_p.S129G|TSPAN14_ENST00000372156.1_Missense_Mutation_p.S129G	NM_030927.2	NP_112189.2	Q8NG11	TSN14_HUMAN	tetraspanin 14	129					establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of Notch signaling pathway (GO:0045747)|protein maturation (GO:0051604)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	enzyme binding (GO:0019899)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7			Colorectal(32;0.229)			GTTCTTCGAGAGCAACATCAA	0.582																																																	0			10											111.0	95.0	100.0					10																	82269162		2203	4300	6503	82259142	SO:0001583	missense	81619			AF311903	CCDS7369.1, CCDS44448.1	10q23.1	2013-02-14	2005-03-21	2005-03-21	ENSG00000108219	ENSG00000108219		"""Tetraspanins"""	23303	protein-coding gene	gene with protein product			"""transmembrane 4 superfamily member 14"""	TM4SF14		11230166	Standard	NM_030927		Approved	DC-TM4F2, MGC11352	uc001kcj.4	Q8NG11	OTTHUMG00000018615	ENST00000429989.3:c.385A>G	10.37:g.82269162A>G	ENSP00000396270:p.Ser129Gly		82259142	A6NHE1|B4DHY6|D3DWD7|D3DWD8|Q567U7|Q9BU34|Q9H0U1	Missense_Mutation	SNP	ENST00000429989.3	37	CCDS7369.1	.	.	.	.	.	.	.	.	.	.	A	15.39	2.819668	0.50633	.	.	ENSG00000108219	ENST00000429989;ENST00000372157;ENST00000372164;ENST00000372158;ENST00000372156	D;D;D;D;D	0.87256	-2.23;-2.23;-2.23;-2.23;-2.23	5.45	5.45	0.79879	Tetraspanin, EC2 domain (1);	0.683157	0.15992	N	0.234765	T	0.76407	0.3983	N	0.10874	0.06	0.29256	N	0.871647	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.68228	-0.5464	10	0.34782	T	0.22	-32.0593	13.4682	0.61268	1.0:0.0:0.0:0.0	.	129;112	Q8NG11;Q8NG11-2	TSN14_HUMAN;.	G	129;99;112;129;129	ENSP00000396270:S129G;ENSP00000361230:S99G;ENSP00000361237:S112G;ENSP00000361231:S129G;ENSP00000361229:S129G	ENSP00000361229:S129G	S	+	1	0	TSPAN14	82259142	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.794000	0.62482	2.064000	0.61679	0.533000	0.62120	AGC		0.582	TSPAN14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049081.2	NM_030927	
PTEN	5728	hgsc.bcm.edu	37	10	89717628	89717628	+	Missense_Mutation	SNP	G	G	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr10:89717628G>T	ENST00000371953.3	+	7	2010	c.653G>T	c.(652-654)tGc>tTc	p.C218F	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	218	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.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.Q214fs*1(1)|p.?(1)|p.Q214fs*22(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)		TTTGTGGTCTGCCAGCTAAAG	0.408		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(10)|Complex - frameshift(1)|Deletion - In frame(1)|Unknown(1)	prostate(16)|central_nervous_system(10)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|endometrium(2)|urinary_tract(2)|soft_tissue(1)	10											127.0	110.0	116.0					10																	89717628		2203	4300	6503	89707608	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.653G>T	10.37:g.89717628G>T	ENSP00000361021:p.Cys218Phe		89707608	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	10.23	1.291817	0.23564	.	.	ENSG00000171862	ENST00000371953	D	0.84223	-1.82	5.67	4.77	0.60923	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.147938	0.64402	D	0.000005	T	0.65770	0.2723	N	0.08118	0	0.50467	D	0.99987	B	0.12013	0.005	B	0.15870	0.014	T	0.60068	-0.7335	9	.	.	.	-4.5893	5.4251	0.16421	0.2701:0.0:0.7299:0.0	.	218	P60484	PTEN_HUMAN	F	218	ENSP00000361021:C218F	.	C	+	2	0	PTEN	89707608	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.024000	0.76443	2.677000	0.91161	0.585000	0.79938	TGC		0.408	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
CUTC	51076	hgsc.bcm.edu	37	10	101502947	101502947	+	Silent	SNP	A	A	G			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr10:101502947A>G	ENST00000370476.5	+	4	360	c.231A>G	c.(229-231)ccA>ccG	p.P77P	CUTC_ENST00000493385.1_3'UTR	NM_015960.2	NP_057044.2	Q9NTM9	CUTC_HUMAN	cutC copper transporter	77			P -> L (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		copper ion homeostasis (GO:0055070)|copper ion transport (GO:0006825)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	copper ion binding (GO:0005507)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Colorectal(252;0.234)		Epithelial(162;3e-10)|all cancers(201;2.37e-08)		TTCAGATCCCAGTTTTTGTGA	0.398																																																	0			10											204.0	187.0	193.0					10																	101502947		2203	4300	6503	101492937	SO:0001819	synonymous_variant	51076			AF132966	CCDS7483.1	10q24.31	2013-07-31	2013-07-31		ENSG00000119929	ENSG00000119929			24271	protein-coding gene	gene with protein product		610101	"""cutC copper transporter homolog (E. coli)"""			16182249	Standard	NM_015960		Approved	CGI-32	uc001kqd.4	Q9NTM9	OTTHUMG00000018889	ENST00000370476.5:c.231A>G	10.37:g.101502947A>G			101492937	Q5TCZ8|Q9Y321	Silent	SNP	ENST00000370476.5	37	CCDS7483.1																																																																																				0.398	CUTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049811.1	NM_015960	
HSPA12A	259217	hgsc.bcm.edu	37	10	118441351	118441351	+	Silent	SNP	G	G	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr10:118441351G>T	ENST00000369209.3	-	8	977	c.873C>A	c.(871-873)acC>acA	p.T291T		NM_025015.2	NP_079291.2	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	291						extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	32				all cancers(201;0.0158)		CCACCAAAAAGGTCCGACTCT	0.478											OREG0020558	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					0			10											111.0	108.0	109.0					10																	118441351		1954	4138	6092	118431341	SO:0001819	synonymous_variant	259217			AB007877	CCDS41569.1	10q25.3	2011-09-02	2002-08-29		ENSG00000165868	ENSG00000165868		"""Heat shock proteins / HSP70"""	19022	protein-coding gene	gene with protein product		610701	"""heat shock 70kD protein 12A"""			12552099	Standard	NM_025015		Approved	FLJ13874, KIAA0417	uc001lct.3	O43301	OTTHUMG00000019107	ENST00000369209.3:c.873C>A	10.37:g.118441351G>T		1488	118431341		Silent	SNP	ENST00000369209.3	37	CCDS41569.1																																																																																				0.478	HSPA12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050530.1	NM_025015	
DOCK1	1793	hgsc.bcm.edu	37	10	128925984	128925984	+	Missense_Mutation	SNP	G	G	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr10:128925984G>T	ENST00000280333.6	+	27	2849	c.2740G>T	c.(2740-2742)Gtg>Ttg	p.V914L		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	914					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		TCTCCGGACCGTGAACCGAAC	0.478																																																	0			10											129.0	116.0	120.0					10																	128925984		1928	4110	6038	128815974	SO:0001583	missense	1793			D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"""DOwnstream of CrK"""	601403	"""dedicator of cyto-kinesis 1"""			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.2740G>T	10.37:g.128925984G>T	ENSP00000280333:p.Val914Leu		128815974	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	37		.	.	.	.	.	.	.	.	.	.	G	16.62	3.174629	0.57692	.	.	ENSG00000150760	ENST00000280333	T	0.55413	0.52	4.88	4.88	0.63580	.	0.077055	0.50627	D	0.000106	T	0.47637	0.1456	L	0.37697	1.125	0.54753	D	0.999989	B;B	0.21753	0.028;0.06	B;B	0.29663	0.063;0.105	T	0.37103	-0.9720	10	0.27785	T	0.31	.	18.4202	0.90587	0.0:0.0:1.0:0.0	.	914;914	B2RUU3;Q14185	.;DOCK1_HUMAN	L	914	ENSP00000280333:V914L	ENSP00000280333:V914L	V	+	1	0	DOCK1	128815974	1.000000	0.71417	0.962000	0.40283	0.963000	0.63663	5.118000	0.64673	2.416000	0.81992	0.557000	0.71058	GTG		0.478	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
ICE1	23379	hgsc.bcm.edu	37	5	5460921	5460921	+	Missense_Mutation	SNP	G	G	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr5:5460921G>A	ENST00000296564.7	+	13	1696	c.1474G>A	c.(1474-1476)Gat>Aat	p.D492N		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		492					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						TAGGGAGATGGATAAGTCAGT	0.438																																																	0			5											94.0	98.0	96.0					5																	5460921		1972	4152	6124	5513921	SO:0001583	missense	23379																														ENST00000296564.7:c.1474G>A	5.37:g.5460921G>A	ENSP00000296564:p.Asp492Asn		5513921	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	37	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	G	16.42	3.117346	0.56505	.	.	ENSG00000164151	ENST00000296564	T	0.13420	2.59	4.64	2.82	0.32997	.	0.623486	0.16171	N	0.226267	T	0.12944	0.0314	L	0.32530	0.975	0.09310	N	1	P	0.48016	0.904	P	0.46718	0.525	T	0.10245	-1.0638	10	0.52906	T	0.07	-6.7037	6.5835	0.22609	0.1:0.1821:0.7179:0.0	.	492	Q9Y2F5	K0947_HUMAN	N	492	ENSP00000296564:D492N	ENSP00000296564:D492N	D	+	1	0	KIAA0947	5513921	0.135000	0.22499	0.000000	0.03702	0.037000	0.13140	3.133000	0.50531	0.478000	0.27488	0.305000	0.20034	GAT		0.438	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1		
PIK3R1	5295	hgsc.bcm.edu	37	5	67589618	67589618	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr5:67589618C>T	ENST00000521381.1	+	11	1997	c.1381C>T	c.(1381-1383)Cga>Tga	p.R461*	PIK3R1_ENST00000336483.5_Nonsense_Mutation_p.R191*|PIK3R1_ENST00000396611.1_Nonsense_Mutation_p.R461*|PIK3R1_ENST00000523872.1_Nonsense_Mutation_p.R98*|PIK3R1_ENST00000521657.1_Nonsense_Mutation_p.R461*|PIK3R1_ENST00000320694.8_Nonsense_Mutation_p.R161*|PIK3R1_ENST00000274335.5_Nonsense_Mutation_p.R461*	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	461					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)|p.?(1)|p.F456_R461>S(1)|p.F456_R461del(1)|p.Q457_R461del(1)|p.R461*(1)|p.T454_D464del(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	AGAAAAAAGTCGAGAATATGA	0.279			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																														Rec	yes		5	5q13.1	5295	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""		"""E, O"""	7	Deletion - In frame(3)|Substitution - Nonsense(1)|Whole gene deletion(1)|Complex - deletion inframe(1)|Unknown(1)	endometrium(4)|large_intestine(2)|lung(1)	5											45.0	49.0	47.0					5																	67589618		2184	4265	6449	67625374	SO:0001587	stop_gained	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1381C>T	5.37:g.67589618C>T	ENSP00000428056:p.Arg461*		67625374	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Nonsense_Mutation	SNP	ENST00000521381.1	37	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079198	0.94050	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000320694;ENST00000521409;ENST00000336483;ENST00000519025;ENST00000523872	.	.	.	5.1	2.12	0.27331	.	0.185230	0.43110	D	0.000617	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.9788	17.5497	0.87872	0.3803:0.6197:0.0:0.0	.	.	.	.	X	461;461;461;461;161;98;191;134;98	.	ENSP00000274335:R461X	R	+	1	2	PIK3R1	67625374	0.959000	0.32827	0.987000	0.45799	0.824000	0.46624	0.433000	0.21477	0.405000	0.25532	-0.824000	0.03097	CGA		0.279	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504	
FAM81B	153643	hgsc.bcm.edu	37	5	94785910	94785910	+	Missense_Mutation	SNP	T	T	C			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr5:94785910T>C	ENST00000283357.5	+	10	1329	c.1283T>C	c.(1282-1284)aTg>aCg	p.M428T		NM_152548.2	NP_689761	Q96LP2	FA81B_HUMAN	family with sequence similarity 81, member B	428						nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_cancers(142;1.1e-06)|all_epithelial(76;1.48e-09)|all_lung(232;0.000696)|Lung NSC(167;0.000947)|Ovarian(225;0.00473)		all cancers(79;1.04e-16)		AAAACAAAGATGGATTTAGAG	0.338																																																	0			5											119.0	113.0	114.0					5																	94785910		1811	4074	5885	94811666	SO:0001583	missense	153643				CCDS43341.1	5q15	2008-02-05			ENSG00000153347	ENSG00000153347			26335	protein-coding gene	gene with protein product							Standard	NM_152548		Approved	FLJ25333	uc003kla.1	Q96LP2	OTTHUMG00000162837	ENST00000283357.5:c.1283T>C	5.37:g.94785910T>C	ENSP00000283357:p.Met428Thr		94811666		Missense_Mutation	SNP	ENST00000283357.5	37	CCDS43341.1	.	.	.	.	.	.	.	.	.	.	T	18.18	3.566118	0.65651	.	.	ENSG00000153347	ENST00000283357;ENST00000512365	T	0.19250	2.16	5.62	5.62	0.85841	.	0.238711	0.45126	D	0.000384	T	0.36799	0.0980	M	0.66939	2.045	0.27631	N	0.948026	D	0.56035	0.974	P	0.53861	0.736	T	0.26258	-1.0108	10	0.39692	T	0.17	-17.7928	14.7984	0.69894	0.0:0.0:0.0:1.0	.	428	Q96LP2	FA81B_HUMAN	T	428;103	ENSP00000283357:M428T	ENSP00000283357:M428T	M	+	2	0	FAM81B	94811666	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.291000	0.51764	2.133000	0.65898	0.482000	0.46254	ATG		0.338	FAM81B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370690.1	NM_152548	
PCDHA12	56137	hgsc.bcm.edu	37	5	140256833	140256833	+	Silent	SNP	G	G	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr5:140256833G>A	ENST00000398631.2	+	1	1776	c.1776G>A	c.(1774-1776)gcG>gcA	p.A592A	PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA7_ENST00000525929.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	592	Cadherin 6. {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)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGTGGTGGCGAAAGTGCGCG	0.697																																					Pancreas(113;759 1672 13322 24104 50104)												0			5											324.0	295.0	305.0					5																	140256833		2203	4299	6502	140237017	SO:0001819	synonymous_variant	56137			AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"""Cadherins / Protocadherins : Clustered"""	8666	other	complex locus constituent	"""KIAA0345-like 2"""	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.1776G>A	5.37:g.140256833G>A			140237017	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	37	CCDS47285.1																																																																																				0.697	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903	
PCDHGA10	56106	hgsc.bcm.edu	37	5	140794236	140794236	+	Silent	SNP	C	C	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr5:140794236C>T	ENST00000398610.2	+	1	1494	c.1494C>T	c.(1492-1494)gaC>gaT	p.D498D	PCDHGB4_ENST00000519479.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	498	Cadherin 5. {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)			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGCTGAAGACACCATCCAGG	0.527																																																	0			5											130.0	138.0	135.0					5																	140794236		2122	4277	6399	140774420	SO:0001819	synonymous_variant	56106				CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"""Cadherins / Protocadherins : Clustered"""	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.1494C>T	5.37:g.140794236C>T			140774420	Q9Y5E0	Silent	SNP	ENST00000398610.2	37	CCDS47292.1																																																																																				0.527	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913	
FLT4	2324	hgsc.bcm.edu	37	5	180045831	180045831	+	Silent	SNP	G	G	A			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr5:180045831G>A	ENST00000261937.6	-	21	3018	c.2940C>T	c.(2938-2940)gtC>gtT	p.V980V	FLT4_ENST00000424276.2_5'Flank|FLT4_ENST00000502649.1_Silent_p.V980V|FLT4_ENST00000393347.3_Silent_p.V980V	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	980	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GCGCGAAGAGGACCCTGTCGC	0.672																																					Colon(97;1075 1466 27033 27547 35871)												0			5											14.0	18.0	17.0					5																	180045831		2173	4278	6451	179978437	SO:0001819	synonymous_variant	2324			X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.2940C>T	5.37:g.180045831G>A			179978437	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Silent	SNP	ENST00000261937.6	37	CCDS4457.1																																																																																				0.672	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		
RPTN	126638	hgsc.bcm.edu	37	1	152129066	152129101	+	In_Frame_Del	DEL	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	-	rs369805852|rs78544048|rs375710188|rs368770198|rs200003389|rs117596468|rs76015112|rs199889562	byFrequency	TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr1:152129066_152129101delTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	ENST00000316073.3	-	3	538_573	c.474_509delTGGTCAGTCTGAGAAACAAGACAGAGATTCCCACCA	c.(472-510)catggtcagtctgagaaacaagacagagattcccaccac>cac	p.158_170HGQSEKQDRDSHH>H		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	158	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.G159_H170delGQSEKQDRDSHH(1)|p.S168>?(1)		breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						AGGCTGACTGTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCATGGTGGGAAT	0.492																																																	2	Complex(1)|Deletion - In frame(1)	stomach(1)|skin(1)	1																																								150395725	SO:0001651	inframe_deletion	126638			AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.474_509delTGGTCAGTCTGAGAAACAAGACAGAGATTCCCACCA	1.37:g.152129066_152129101delTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	ENSP00000317895:p.His158_His169del		150395690	B7ZBZ3	In_Frame_Del	DEL	ENST00000316073.3	37	CCDS41397.1																																																																																				0.492	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312	
PRKRA	8575	hgsc.bcm.edu	37	2	179315735	179315736	+	Frame_Shift_Del	DEL	GC	GC	-	rs141354030|rs79769305	byFrequency	TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	GC	GC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr2:179315735_179315736delGC	ENST00000325748.4	-	1	222_223	c.22_23delGC	c.(22-24)gccfs	p.A8fs	PRKRA_ENST00000432031.2_5'Flank|PRKRA_ENST00000438687.3_5'UTR|DFNB59_ENST00000409117.3_5'Flank|PRKRA_ENST00000487082.1_5'Flank|PRKRA_ENST00000470200.1_5'UTR|DFNB59_ENST00000375129.4_5'Flank	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator	8	Sufficient for self-association and interaction with TARBP2.				cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			CGGGGCCTCGGCGCGGTGCCTG	0.757														1193	0.238219	0.1649	0.3545	5008	,	,		12129	0.123		0.339	False		,,,				2504	0.2699				Melanoma(200;68 3001 23825 48764)												0			2								658,2174		225,208,983						-1.9	0.8		dbSNP_134	7	2206,4138		751,704,1717	no	frameshift	PRKRA	NM_003690.4		976,912,2700	A1A1,A1R,RR		34.773,23.2345,31.2119				2864,6312				179023982	SO:0001589	frameshift_variant	8575			AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"""protein activator of the interferon-induced protein kinase"""	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.22_23delGC	2.37:g.179315737_179315738delGC	ENSP00000318176:p.Ala8fs		179023981	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Frame_Shift_Del	DEL	ENST00000325748.4	37	CCDS2279.1																																																																																				0.757	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2	NM_003690	
ATR	545	hgsc.bcm.edu	37	3	142274740	142274740	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr3:142274740delT	ENST00000350721.4	-	10	2441	c.2320delA	c.(2320-2322)atafs	p.I774fs	ATR_ENST00000383101.3_Frame_Shift_Del_p.I710fs	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	774					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.I774fs*5(1)		NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						GGACTAGGTATTTTTTTTTTC	0.328								Other conserved DNA damage response genes																																									1	Deletion - Frameshift(1)	breast(1)	3											72.0	79.0	77.0					3																	142274740		2203	4300	6503	143757430	SO:0001589	frameshift_variant	390502			U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.2320delA	3.37:g.142274740delT	ENSP00000343741:p.Ile774fs		143757430	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Frame_Shift_Del	DEL	ENST00000350721.4	37	CCDS3124.1																																																																																				0.328	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388622	1388623	+	Frame_Shift_Ins	INS	-	-	CA	rs79704405|rs540461234|rs558358960	byFrequency	TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr4:1388622_1388623insCA	ENST00000324803.4	+	1	3283_3284	c.323_324insCA	c.(322-327)ctcacgfs	p.LT108fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	108					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.L108H(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			GCCCGCCTGCTCACGTGCCCAT	0.668														506	0.101038	0.0567	0.1427	5008	,	,		19207	0.0169		0.1759	False		,,,				2504	0.1411																1	Substitution - Missense(1)	pancreas(1)	4																																								1378623	SO:0001589	frameshift_variant	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.324_325dupCA	4.37:g.1388623_1388624dupCA	ENSP00000323978:p.Leu108fs		1378622	Q8NB03	Frame_Shift_Ins	INS	ENST00000324803.4	37	CCDS3349.1																																																																																				0.668	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
APC	324	hgsc.bcm.edu	37	5	112175772	112175772	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr5:112175772delA	ENST00000457016.1	+	16	4861	c.4481delA	c.(4480-4482)gaafs	p.E1494fs	APC_ENST00000257430.4_Frame_Shift_Del_p.E1494fs|APC_ENST00000508376.2_Frame_Shift_Del_p.E1494fs|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1494	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)|p.K1454fs*3(1)|p.T1493fs*17(1)|p.S1495fs*19(1)|p.K1192fs*3(1)|p.E1494fs*12(1)|p.E1494fs*11(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)		TTTGCCACGGAAAGTACTCCA	0.438		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"""	7	Deletion - Frameshift(3)|Complex - frameshift(2)|Unknown(1)|Insertion - Frameshift(1)	large_intestine(4)|thyroid(1)|soft_tissue(1)|skin(1)	5											70.0	72.0	71.0					5																	112175772		2201	4300	6501	112203671	SO:0001589	frameshift_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.4481delA	5.37:g.112175772delA	ENSP00000413133:p.Glu1494fs		112203671	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.438	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
KRTAP5-1	387264	hgsc.bcm.edu	37	11	1606121	1606150	+	In_Frame_Del	DEL	CCACAGCCACCCTTGGATCCCCCACAAGAG	CCACAGCCACCCTTGGATCCCCCACAAGAG	-	rs138363822|rs199501537|rs80025267|rs76191756	byFrequency	TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	CCACAGCCACCCTTGGATCCCCCACAAGAG	CCACAGCCACCCTTGGATCCCCCACAAGAG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:1606121_1606150delCCACAGCCACCCTTGGATCCCCCACAAGAG	ENST00000382171.2	-	1	363_392	c.330_359delCTCTTGTGGGGGATCCAAGGGTGGCTGTGG	c.(328-360)ggctcttgtgggggatccaagggtggctgtggt>ggt	p.110_120GSCGGSKGGCG>G	KRTAP5-AS1_ENST00000524947.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA|KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA	NM_001005922.1	NP_001005922.1	Q6L8H4	KRA51_HUMAN	keratin associated protein 5-1	110	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(3)|kidney(1)|lung(9)|skin(2)|upper_aerodigestive_tract(1)	16		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		ACAGCCGGAACCACAGCCACCCTTGGATCCCCCACAAGAGCCACAGCCCC	0.661																																																	0			11								2171,2035		609,953,541						-5.2	0.0			71	4129,4059		1127,1875,1092	no	coding	KRTAP5-1	NM_001005922.1		1736,2828,1633	A1A1,A1R,RR		49.5725,48.3833,49.169				6300,6094				1562726	SO:0001651	inframe_deletion	387264			AB126070	CCDS31330.1	11p15.5	2008-02-05			ENSG00000205869	ENSG00000205869		"""Keratin associated proteins"""	23596	protein-coding gene	gene with protein product		148022	"""keratin, cuticle, ultrahigh sulphur 1-like"""	KRN1L		15144888	Standard	NM_001005922		Approved	KRTAP5.1	uc001ltu.1	Q6L8H4	OTTHUMG00000057557	ENST00000382171.2:c.330_359delCTCTTGTGGGGGATCCAAGGGTGGCTGTGG	11.37:g.1606121_1606150delCCACAGCCACCCTTGGATCCCCCACAAGAG	ENSP00000371606:p.Gly110_Cys119del		1562697		In_Frame_Del	DEL	ENST00000382171.2	37	CCDS31330.1																																																																																				0.661	KRTAP5-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127922.1	NM_001005922	
ART5	116969	hgsc.bcm.edu	37	11	3661585	3661586	+	In_Frame_Ins	INS	-	-	TGG	rs80248801|rs3062849|rs397784566|rs33994425|rs72515796	byFrequency	TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:3661585_3661586insTGG	ENST00000397068.3	-	2	465_466	c.73_74insCCA	c.(73-75)atc>aCCAtc	p.24_25insT	TRPC2_ENST00000526541.1_RNA|ART5_ENST00000359918.4_In_Frame_Ins_p.24_25insT|ART5_ENST00000397067.3_In_Frame_Ins_p.24_25insT	NM_053017.3	NP_443750.2	Q96L15	NAR5_HUMAN	ADP-ribosyltransferase 5	24			P -> PT (in dbSNP:rs72515796). {ECO:0000269|PubMed:12070318, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		protein ADP-ribosylation (GO:0006471)	extracellular region (GO:0005576)|membrane (GO:0016020)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ nucleosidase activity (GO:0003953)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(6)|ovary(1)	11		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0336)|LUSC - Lung squamous cell carcinoma(625;0.19)		CAGGGGCAGGATGGGAACAGCC	0.569														4845	0.967452	0.8828	0.9914	5008	,	,		17488	1.0		0.999	False		,,,				2504	0.999																0			11							,	3654,406		1675,304,51					,	5.0	1.0		dbSNP_102	24	7782,12		3887,8,2	no	coding,coding	ART5	NM_053017.3,NM_001079536.1	,	5562,312,53	A1A1,A1R,RR		0.154,10.0,3.5262	,	,		11436,418				3618162	SO:0001652	inframe_insertion	116969			Y16835	CCDS7743.1, CCDS73242.1	11p15.4	2008-02-05			ENSG00000167311	ENSG00000167311			24049	protein-coding gene	gene with protein product		610625				11587854, 10448534	Standard	NM_001079536		Approved		uc001lyb.1	Q96L15	OTTHUMG00000011842	ENST00000397068.3:c.71_73dupCCA	11.37:g.3661586_3661588dupTGG	ENSP00000380258:p.Pro24_Ile25insThr		3618161	C9IYG7|Q6UX84|Q86W02	In_Frame_Ins	INS	ENST00000397068.3	37	CCDS7743.1																																																																																				0.569	ART5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032760.2	NM_053017	
NFRKB	4798	hgsc.bcm.edu	37	11	129735843	129735844	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	AG	AG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr11:129735843_129735844delAG	ENST00000446488.3	-	24	3669_3670	c.3566_3567delCT	c.(3565-3567)tctfs	p.S1189fs	NFRKB_ENST00000524746.1_Frame_Shift_Del_p.S1189fs|NFRKB_ENST00000304521.5_Frame_Shift_Del_p.S1189fs|NFRKB_ENST00000524794.1_Frame_Shift_Del_p.S1214fs	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	1189					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		GGCTGATCACAGAGAGGGGAAC	0.49																																																	0			11																																								129241054	SO:0001589	frameshift_variant	4798				CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"""INO80 complex subunits"""	7802	protein-coding gene	gene with protein product	"""nuclear factor related to kappa B binding protein"", ""DNA-binding protein R kappa B"", ""INO80 complex subunit G"""	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.3566_3567delCT	11.37:g.129735847_129735848delAG	ENSP00000400476:p.Ser1189fs		129241053	Q12869|Q15312|Q9H048	Frame_Shift_Del	DEL	ENST00000446488.3	37	CCDS44770.1																																																																																				0.490	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165	
UACA	55075	hgsc.bcm.edu	37	15	70991976	70991977	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	AT	AT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr15:70991976_70991977delAT	ENST00000322954.6	-	2	286_287	c.101_102delAT	c.(100-102)tatfs	p.Y34fs	UACA_ENST00000379983.2_Frame_Shift_Del_p.Y21fs|UACA_ENST00000539319.1_Frame_Shift_Del_p.Y34fs|UACA_ENST00000560441.1_Frame_Shift_Del_p.Y21fs	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	34					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						ATCGGTCATCATATTTATTCCA	0.356																																																	0			15																																								68779031	SO:0001589	frameshift_variant	55075			AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"""Ankyrin repeat domain containing"""	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.101_102delAT	15.37:g.70991978_70991979delAT	ENSP00000314556:p.Tyr34fs		68779030	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Frame_Shift_Del	DEL	ENST00000322954.6	37	CCDS10235.1																																																																																				0.356	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2		
KRT222	125113	hgsc.bcm.edu	37	17	38818271	38818272	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr17:38818271_38818272insT	ENST00000476049.1	-	2	162_163	c.121_122insA	c.(121-123)atgfs	p.M41fs	KRT222_ENST00000394052.3_Frame_Shift_Ins_p.M41fs			Q8N1A0	KT222_HUMAN	keratin 222	41						intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(2)|skin(1)	15						ATCTTTGTCCATTTTTTTGCTT	0.426																																																	0			17																																								36071798	SO:0001589	frameshift_variant	0			AK092967	CCDS11371.1	17q21.2	2013-06-25	2009-08-25	2009-08-25	ENSG00000213424	ENSG00000213424		"""-"""	28695	protein-coding gene	gene with protein product			"""keratin 222 pseudogene"""	KRT222P		16831889	Standard	NM_152349		Approved	KA21, MGC45562	uc002hvc.2	Q8N1A0	OTTHUMG00000133374	ENST00000476049.1:c.122dupA	17.37:g.38818278_38818278dupT	ENSP00000463483:p.Met41fs		36071797	Q7Z368	Frame_Shift_Ins	INS	ENST00000476049.1	37	CCDS11371.1																																																																																				0.426	KRT222-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000447539.1	NM_152349	
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-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	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	
TGIF1	7050	hgsc.bcm.edu	37	18	3452223	3452223	+	Frame_Shift_Del	DEL	T	T	-	rs11571510|rs557543525|rs202189171	byFrequency	TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr18:3452223delT	ENST00000330513.5	+	1	549	c.246delT	c.(244-246)cctfs	p.P85fs	TGIF1_ENST00000577543.1_Intron|TGIF1_ENST00000551402.1_Intron|TGIF1_ENST00000548489.2_Intron|TGIF1_ENST00000405385.3_Intron|TGIF1_ENST00000343820.5_Intron|TGIF1_ENST00000345133.5_Intron|TGIF1_ENST00000551541.1_Intron|TGIF1_ENST00000400167.2_5'Flank|TGIF1_ENST00000401449.1_Intron|TGIF1_ENST00000407501.2_Intron	NM_170695.2	NP_733796.2	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	85					determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nodal signaling pathway (GO:0038092)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.P83fs*51(1)		cervix(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	13	Esophageal squamous(4;0.0859)	Colorectal(8;0.0104)				GCGCCCCCCCTCCTCCACCGG	0.766													T|T|-|deletion	1280	0.255591	0.3419	0.2349	5008	,	,		10884	0.0109		0.4304	False		,,,				2504	0.226																1	Deletion - Frameshift(1)	large_intestine(1)	18											10.0	11.0	10.0					18																	3452223		2031	3818	5849	3442223	SO:0001589	frameshift_variant	7050			X89750	CCDS11832.1, CCDS11833.1, CCDS11834.1, CCDS11835.1	18p11.31	2011-06-20	2007-01-30	2007-01-30	ENSG00000177426	ENSG00000177426		"""Homeoboxes / TALE class"""	11776	protein-coding gene	gene with protein product		602630	"""TGFB-induced factor (TALE family homeobox)"""	HPE4, TGIF		8537382, 10835638	Standard	NM_173211		Approved		uc002klz.3	Q15583	OTTHUMG00000131511	ENST00000330513.5:c.246delT	18.37:g.3452223delT	ENSP00000327959:p.Pro85fs		3442223	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Frame_Shift_Del	DEL	ENST00000330513.5	37	CCDS11834.1																																																																																				0.766	TGIF1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254368.4	NM_170695	
KRTAP10-7	386675	hgsc.bcm.edu	37	21	46020656	46020670	+	In_Frame_Del	DEL	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG	-	rs36208679|rs60739860|rs373191083		TCGA-AH-6549-01A-11D-1826-10	TCGA-AH-6549-10A-01D-1826-10	CTGCTGCGCCCCCAG	CTGCTGCGCCCCCAG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	749f8e6a-864e-4ed2-879a-188d0f153e8d	db8dd0b1-6bbd-471c-be21-c24fd1f008e2	g.chr21:46020656_46020670delCTGCTGCGCCCCCAG	ENST00000380102.2	+	1	160_174	c.135_149delCTGCTGCGCCCCCAG	c.(133-150)ccctgctgcgcccccagc>ccc	p.CCAPS46del	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	46	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.S50_P54delSCCAP(1)		breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						GCGAGCCCCCCTGCTGCGCCCCCAGCTGCTGCGCC	0.698																																																	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	21							,	2258,1042		849,560,241					,	-0.7	1.0		dbSNP_126	22	6001,1123		2605,791,166	no	coding,intron	TSPEAR,KRTAP10-7	NM_198689.2,NM_144991.2	,	3454,1351,407	A1A1,A1R,RR		15.7636,31.5758,20.7694	,	,		8259,2165				44845098	SO:0001651	inframe_deletion	386675			AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"""Keratin associated proteins"""	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.135_149delCTGCTGCGCCCCCAG	21.37:g.46020656_46020670delCTGCTGCGCCCCCAG	ENSP00000369445:p.Cys46_Ser50del		44845084	Q0VDJ8|Q70LJ2	Frame_Shift_Del	DEL	ENST00000380102.2	37																																																																																					0.698	KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689	
