#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_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	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_Exon	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_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_TranscriptID	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
SAMD9L	219285	hgsc.bcm.edu	37	7	92761121	92761121	+	Silent	SNP	A	A	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr7:92761121A>T	ENST00000318238.4	-	5	5380	c.4164T>A	c.(4162-4164)atT>atA	p.I1388I	SAMD9L_ENST00000411955.1_Silent_p.I1388I|SAMD9L_ENST00000437805.1_Silent_p.I1388I	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	1388					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)		p.I1388I(1)		central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			AACTCAGAATAATGTTGGCCA	0.388																																					p.I1388I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T4164A	7						.						175.0	171.0	172.0					7																	92761121		2203	4300	6503	92599057	SO:0001819	synonymous_variant	219285	exon5			AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"""Sterile alpha motif (SAM) domain containing"""	1349	protein-coding gene	gene with protein product		611170	"""chromosome 7 open reading frame 6"""	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.4164T>A	7.37:g.92761121A>T		Somatic		Capture	SOLID	Phase_I	92599057	NM_152703	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Silent	SNP	ENST00000318238.4	37	CCDS34681.1																																																																																				0.388	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703	
COL1A2	1278	hgsc.bcm.edu	37	7	94055738	94055738	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr7:94055738C>T	ENST00000297268.6	+	46	3472	c.3001C>T	c.(3001-3003)Cca>Tca	p.P1001S		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	1001					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)	p.P1001S(1)	COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	TTTATAGGGCCCACAAGGCAT	0.458										HNSCC(75;0.22)																											p.P1001S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3001T	7						.						35.0	30.0	32.0					7																	94055738		2203	4300	6503	93893674	SO:0001583	missense	1278	exon46			Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.3001C>T	7.37:g.94055738C>T	ENSP00000297268:p.Pro1001Ser	Somatic		Capture	SOLID	Phase_I	93893674	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	37	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	C	11.25	1.584218	0.28268	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.94793	-3.52	5.85	1.9	0.25705	.	0.111329	0.64402	D	0.000006	D	0.92675	0.7672	M	0.62088	1.915	0.45427	D	0.998401	B	0.19817	0.039	B	0.26416	0.069	D	0.87781	0.2612	10	0.56958	D	0.05	.	13.3614	0.60659	0.1166:0.5471:0.3364:0.0	.	1001	P08123	CO1A2_HUMAN	S	1001;1002	ENSP00000297268:P1001S	ENSP00000297268:P1001S	P	+	1	0	COL1A2	93893674	1.000000	0.71417	0.960000	0.40013	0.140000	0.21249	2.621000	0.46418	0.140000	0.18849	-0.955000	0.02649	CCA		0.458	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
TPX2	22974	hgsc.bcm.edu	37	20	30380610	30380610	+	Nonsense_Mutation	SNP	C	C	T	rs267605874		TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr20:30380610C>T	ENST00000300403.6	+	13	2014	c.1486C>T	c.(1486-1488)Cga>Tga	p.R496*	TPX2_ENST00000340513.4_Nonsense_Mutation_p.R532*	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated	496					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|regulation of mitotic spindle organization (GO:0060236)	axon hillock (GO:0043203)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|protein kinase binding (GO:0019901)	p.R496*(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			GAACAGAATTCGAATGCCCAC	0.418																																					p.R496X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1486T	20						.						149.0	137.0	141.0					20																	30380610		2203	4300	6503	29844271	SO:0001587	stop_gained	22974	exon13			AF098158	CCDS13190.1	20q11.2	2013-07-23	2013-07-23	2003-10-08	ENSG00000088325	ENSG00000088325			1249	protein-coding gene	gene with protein product		605917	"""chromosome 20 open reading frame 1"", ""TPX2, microtubule-associated, homolog (Xenopus laevis)"""	C20orf2, C20orf1		9207457, 10393424	Standard	NM_012112		Approved	p100, DIL-2	uc002wwp.1	Q9ULW0	OTTHUMG00000032190	ENST00000300403.6:c.1486C>T	20.37:g.30380610C>T	ENSP00000300403:p.Arg496*	Somatic		Capture	SOLID	Phase_I	29844271	NM_012112	Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Nonsense_Mutation	SNP	ENST00000300403.6	37	CCDS13190.1	.	.	.	.	.	.	.	.	.	.	C	39	7.440984	0.98286	.	.	ENSG00000088325	ENST00000300403;ENST00000340513	.	.	.	5.85	3.79	0.43588	.	0.068754	0.56097	D	0.000021	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.7504	13.8228	0.63333	0.2896:0.7104:0.0:0.0	.	.	.	.	X	496;532	.	ENSP00000300403:R496X	R	+	1	2	TPX2	29844271	0.996000	0.38824	0.950000	0.38849	0.040000	0.13550	3.314000	0.51943	1.449000	0.47699	0.650000	0.86243	CGA		0.418	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2		
ZBP1	81030	hgsc.bcm.edu	37	20	56185241	56185241	+	Missense_Mutation	SNP	C	C	A	rs61749015	byFrequency	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr20:56185241C>A	ENST00000371173.3	-	7	1234	c.1057G>T	c.(1057-1059)Gca>Tca	p.A353S	ZBP1_ENST00000395822.3_Missense_Mutation_p.A278S|ZBP1_ENST00000340462.4_Missense_Mutation_p.A330S|ZBP1_ENST00000343535.4_Missense_Mutation_p.A353S	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	353					innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|left-handed Z-DNA binding (GO:0003692)|RNA binding (GO:0003723)	p.A353S(1)		large_intestine(11)|lung(8)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	27	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)			CCAGACCCTGCGACTCCTCCT	0.597																																					p.A352S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1054T	20						.						113.0	111.0	112.0					20																	56185241		2203	4300	6503	55618647	SO:0001583	missense	81030	exon7			AJ300575	CCDS13461.1, CCDS54477.1, CCDS54478.1	20q13.31	2009-08-21	2002-07-25	2002-07-26	ENSG00000124256	ENSG00000124256			16176	protein-coding gene	gene with protein product	"""DNA-dependent activator of IRFs"""	606750	"""chromosome 20 open reading frame 183"""	C20orf183		11842111	Standard	NM_030776		Approved	dJ718J7.3, DLM1, DLM-1, DAI	uc002xyo.3	Q9H171	OTTHUMG00000032824	ENST00000371173.3:c.1057G>T	20.37:g.56185241C>A	ENSP00000360215:p.Ala353Ser	Somatic		Capture	SOLID	Phase_I	55618647	NM_001160417	A2A2F7|B3KVA1|F5GYT1|Q5JY39|Q9BYW4	Missense_Mutation	SNP	ENST00000371173.3	37	CCDS13461.1	.	.	.	.	.	.	.	.	.	.	C	7.338	0.620371	0.14193	.	.	ENSG00000124256	ENST00000371173;ENST00000395822;ENST00000340462;ENST00000357677;ENST00000343535	T;T;T;T	0.11712	3.12;2.75;3.11;3.1	3.75	-5.89	0.02282	.	2.268670	0.01814	N	0.033606	T	0.04724	0.0128	N	0.17082	0.46	0.09310	N	1	B;P;B	0.35226	0.156;0.491;0.156	B;B;B	0.25759	0.038;0.063;0.038	T	0.30995	-0.9959	10	0.09338	T	0.73	0.1142	7.639	0.28282	0.0:0.1598:0.1407:0.6995	.	353;278;353	A2RRL9;A2A2F7;Q9H171	.;.;ZBP1_HUMAN	S	353;278;330;353;353	ENSP00000360215:A353S;ENSP00000379167:A278S;ENSP00000344954:A330S;ENSP00000340584:A353S	ENSP00000344954:A330S	A	-	1	0	ZBP1	55618647	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.748000	0.04818	-1.274000	0.02421	-0.339000	0.08088	GCA		0.597	ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079849.1	NM_030776	
C20orf85	128602	hgsc.bcm.edu	37	20	56735809	56735809	+	Silent	SNP	C	C	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr20:56735809C>T	ENST00000371168.3	+	4	406	c.345C>T	c.(343-345)gaC>gaT	p.D115D		NM_178456.2	NP_848551.1	Q9H1P6	CT085_HUMAN	chromosome 20 open reading frame 85	115								p.D115D(1)		kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	13	all_epithelial(3;5.99e-14)|Lung NSC(12;0.000152)|all_lung(29;0.000518)|Melanoma(10;0.118)		BRCA - Breast invasive adenocarcinoma(13;5.53e-12)|Epithelial(14;7.42e-08)|all cancers(14;7.19e-07)			TAGAGCTCGACGATGCGATCA	0.602																																					p.D115D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C345T	20						.						68.0	54.0	59.0					20																	56735809		2203	4300	6503	56169215	SO:0001819	synonymous_variant	128602	exon4			AL354776	CCDS13465.1	20q13.32	2012-10-29			ENSG00000124237	ENSG00000124237			16216	protein-coding gene	gene with protein product	"""Low in Lung Cancer 1"""						Standard	NM_178456		Approved	bA196N14.1, LLC1	uc002xyv.3	Q9H1P6	OTTHUMG00000032836	ENST00000371168.3:c.345C>T	20.37:g.56735809C>T		Somatic		Capture	SOLID	Phase_I	56169215	NM_178456		Silent	SNP	ENST00000371168.3	37	CCDS13465.1																																																																																				0.602	C20orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079866.2	NM_178456	
SMARCA4	6597	hgsc.bcm.edu	37	19	11123782	11123782	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr19:11123782C>G	ENST00000429416.3	+	17	2713	c.2432C>G	c.(2431-2433)cCt>cGt	p.P811R	SMARCA4_ENST00000413806.3_Missense_Mutation_p.P811R|CTC-215O4.4_ENST00000587831.1_RNA|RN7SL192P_ENST00000584303.1_RNA|SMARCA4_ENST00000541122.2_Missense_Mutation_p.P811R|SMARCA4_ENST00000590574.1_Missense_Mutation_p.P811R|SMARCA4_ENST00000450717.3_Missense_Mutation_p.P811R|SMARCA4_ENST00000344626.4_Missense_Mutation_p.P811R|SMARCA4_ENST00000589677.1_Missense_Mutation_p.P811R|SMARCA4_ENST00000444061.3_Missense_Mutation_p.P811R|SMARCA4_ENST00000358026.2_Missense_Mutation_p.P811R	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	811	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|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)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.P811R(1)|p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				ATCATCGTGCCTCTCTCGTGA	0.567			"""F, N, Mis"""		NSCLC																																p.P811R			Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	.	.	2	Substitution - Missense(1)|Unknown(1)	large_intestine(1)|lung(1)	c.C2432G	19						.						140.0	72.0	95.0					19																	11123782		2203	4300	6503	10984782	SO:0001583	missense	6597	exon16			D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.2432C>G	19.37:g.11123782C>G	ENSP00000395654:p.Pro811Arg	Somatic		Capture	SOLID	Phase_I	10984782	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.571274	0.86542	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.97959	-4.63;-4.63;-4.63;-4.63;-4.63;-4.63;-4.63	4.73	4.73	0.59995	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.99149	0.9706	H	0.96489	3.83	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.99060	1.0830	10	0.87932	D	0	-17.178	16.6409	0.85098	0.0:1.0:0.0:0.0	.	811;811;811;811;811;811;811	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;A7E2E1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	R	811;811;875;811;811;811;811;811	ENSP00000395654:P811R;ENSP00000350720:P811R;ENSP00000343896:P811R;ENSP00000445036:P811R;ENSP00000392837:P811R;ENSP00000397783:P811R;ENSP00000414727:P811R	ENSP00000343896:P811R	P	+	2	0	SMARCA4	10984782	1.000000	0.71417	0.968000	0.41197	0.936000	0.57629	7.651000	0.83577	2.456000	0.83038	0.655000	0.94253	CCT		0.567	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	
ZNF333	84449	hgsc.bcm.edu	37	19	14829212	14829212	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr19:14829212A>C	ENST00000292530.6	+	12	1164	c.1073A>C	c.(1072-1074)aAa>aCa	p.K358T	ZNF333_ENST00000540689.2_Intron|ZNF333_ENST00000536363.1_Missense_Mutation_p.K249T	NM_032433.2	NP_115809.1	Q96JL9	ZN333_HUMAN	zinc finger protein 333	358					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K358T(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|prostate(1)	21						GTGCCCGAGAAAATCCGTAGT	0.433																																					p.K358T	NSCLC(60;75 1281 16985 25154 29885)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1073C	19						.						84.0	84.0	84.0					19																	14829212		2203	4300	6503	14690212	SO:0001583	missense	84449	exon12				CCDS12316.1, CCDS74298.1	19p13	2013-01-08				ENSG00000160961		"""Zinc fingers, C2H2-type"", ""-"""	15624	protein-coding gene	gene with protein product		611811				12151103	Standard	XM_005260098		Approved	KIAA1806	uc002mzn.3	Q96JL9		ENST00000292530.6:c.1073A>C	19.37:g.14829212A>C	ENSP00000292530:p.Lys358Thr	Somatic		Capture	SOLID	Phase_I	14690212	NM_032433	Q6P2E6|Q86WS6|Q8TDL0	Missense_Mutation	SNP	ENST00000292530.6	37	CCDS12316.1	.	.	.	.	.	.	.	.	.	.	A	13.92	2.379679	0.42207	.	.	ENSG00000160961	ENST00000536363;ENST00000292530	T;T	0.07327	4.64;3.2	3.24	1.06	0.20224	.	.	.	.	.	T	0.07908	0.0198	L	0.48935	1.535	0.27678	N	0.946523	B	0.26081	0.141	B	0.29942	0.109	T	0.35226	-0.9797	9	0.72032	D	0.01	.	2.5565	0.04761	0.4917:0.2665:0.2418:0.0	.	358	Q96JL9	ZN333_HUMAN	T	249;358	ENSP00000439749:K249T;ENSP00000292530:K358T	ENSP00000292530:K358T	K	+	2	0	ZNF333	14690212	0.207000	0.23482	0.134000	0.22075	0.169000	0.22640	1.074000	0.30703	0.433000	0.26313	0.477000	0.44152	AAA		0.433	ZNF333-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466496.1	NM_032433	
LSM14A	26065	hgsc.bcm.edu	37	19	34710449	34710449	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr19:34710449G>A	ENST00000433627.5	+	7	1010	c.935G>A	c.(934-936)aGa>aAa	p.R312K	LSM14A_ENST00000544216.3_Missense_Mutation_p.R312K|LSM14A_ENST00000540746.2_Missense_Mutation_p.R271K	NM_001114093.1	NP_001107565.1	Q8ND56	LS14A_HUMAN	LSM14A, SCD6 homolog A (S. cerevisiae)	312	DFDF. {ECO:0000255|PROSITE- ProRule:PRU00845}.				cytoplasmic mRNA processing body assembly (GO:0033962)|multicellular organismal development (GO:0007275)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of translation (GO:0006417)|RIG-I signaling pathway (GO:0039529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|intracellular membrane-bounded organelle (GO:0043231)	double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)	p.R312K(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(7)|skin(1)	22	Esophageal squamous(110;0.162)					GAGATTGACAGAGAGTTTCAT	0.323																																					p.R312K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G935A	19						.						57.0	64.0	62.0					19																	34710449		2203	4300	6503	39402289	SO:0001583	missense	26065	exon7			AL834398	CCDS12435.1, CCDS46040.1	19q13.12	2010-01-27	2006-12-21	2006-01-24		ENSG00000257103			24489	protein-coding gene	gene with protein product		610677	"""chromosome 19 open reading frame 13"", ""family with sequence similarity 61, member A"", ""LSM14 homolog A (SCD6, S. cerevisiae)"""	C19orf13, FAM61A		12477932	Standard	NM_015578		Approved	DKFZP434D1335, RAP55A, RAP55	uc002nva.4	Q8ND56		ENST00000433627.5:c.935G>A	19.37:g.34710449G>A	ENSP00000413964:p.Arg312Lys	Somatic		Capture	SOLID	Phase_I	39402289	NM_001114093	B4DTG6|Q76LX7|Q96AR3|Q96K73|Q96SN5|Q9UFR3	Missense_Mutation	SNP	ENST00000433627.5	37	CCDS46040.1	.	.	.	.	.	.	.	.	.	.	g	11.62	1.693934	0.30052	.	.	ENSG00000257103	ENST00000544216;ENST00000433627;ENST00000540746	T;T;T	0.25579	1.83;1.82;1.79	5.79	5.79	0.91817	DFDF motif (1);	0.045544	0.85682	D	0.000000	T	0.10423	0.0255	N	0.01482	-0.84	0.50632	D	0.999883	B;B;B	0.25351	0.015;0.021;0.124	B;B;B	0.22601	0.04;0.014;0.015	T	0.22661	-1.0210	10	0.02654	T	1	-16.5346	20.0371	0.97565	0.0:0.0:1.0:0.0	.	271;312;312	B4DTG6;Q8ND56;Q8ND56-2	.;LS14A_HUMAN;.	K	312;312;271	ENSP00000446271:R312K;ENSP00000413964:R312K;ENSP00000446451:R271K	ENSP00000314768:R312K	R	+	2	0	LSM14A	39402289	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.099000	0.57755	2.734000	0.93682	0.655000	0.94253	AGA		0.323	LSM14A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451576.3	NM_015578	
RYR1	6261	hgsc.bcm.edu	37	19	38958285	38958285	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr19:38958285C>T	ENST00000359596.3	+	25	3214	c.3214C>T	c.(3214-3216)Cgc>Tgc	p.R1072C	RYR1_ENST00000360985.3_Missense_Mutation_p.R1072C|RYR1_ENST00000355481.4_Missense_Mutation_p.R1072C			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1072	6 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				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)	p.R1072C(1)		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)	TGACCGGGTGCGCATCTTCCG	0.572																																					p.R1072C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3214T	19						.						103.0	97.0	99.0					19																	38958285		2203	4300	6503	43650125	SO:0001583	missense	6261	exon25			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.3214C>T	19.37:g.38958285C>T	ENSP00000352608:p.Arg1072Cys	Somatic		Capture	SOLID	Phase_I	43650125	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	c	11.60	1.686114	0.29962	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.97688	-4.49;-4.49;-4.49	2.92	2.92	0.33932	B30.2/SPRY domain (1);	0.000000	0.64402	U	0.000016	D	0.98604	0.9533	M	0.85462	2.755	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.99053	1.0828	10	0.87932	D	0	.	14.736	0.69416	0.0:1.0:0.0:0.0	.	1072;1072	P21817-2;P21817	.;RYR1_HUMAN	C	1072	ENSP00000352608:R1072C;ENSP00000347667:R1072C;ENSP00000354254:R1072C	ENSP00000347667:R1072C	R	+	1	0	RYR1	43650125	1.000000	0.71417	1.000000	0.80357	0.604000	0.37047	5.533000	0.67160	1.966000	0.57179	0.154000	0.16183	CGC		0.572	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
GTF2F1	2962	hgsc.bcm.edu	37	19	6389580	6389580	+	Silent	SNP	C	C	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr19:6389580C>T	ENST00000394456.5	-	4	665	c.201G>A	c.(199-201)gcG>gcA	p.A67A	CTB-180A7.6_ENST00000599584.1_RNA|GTF2F1_ENST00000429701.2_Silent_p.A39A	NM_002096.2	NP_002087.2	P35269	T2FA_HUMAN	general transcription factor IIF, polypeptide 1, 74kDa	67					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cell junction (GO:0030054)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	catalytic activity (GO:0003824)|DNA binding (GO:0003677)|phosphatase activator activity (GO:0019211)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.A67A(2)		breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(4)	16						ACTCACTGCCCGCGCCCGATT	0.617																																					p.A67A												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.G201A	19						.						136.0	142.0	140.0					19																	6389580		2203	4300	6503	6340580	SO:0001819	synonymous_variant	2962	exon4				CCDS12165.1	19p13.3	2010-03-23	2002-08-29		ENSG00000125651	ENSG00000125651		"""General transcription factors"""	4652	protein-coding gene	gene with protein product		189968	"""general transcription factor IIF, polypeptide 1 (74kD subunit)"""			1734284	Standard	NM_002096		Approved	TFIIF, BTF4, RAP74, TF2F1	uc002meq.2	P35269	OTTHUMG00000168087	ENST00000394456.5:c.201G>A	19.37:g.6389580C>T		Somatic		Capture	SOLID	Phase_I	6340580	NM_002096	B2RCS0|Q9BWN0	Silent	SNP	ENST00000394456.5	37	CCDS12165.1																																																																																				0.617	GTF2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398033.1	NM_002096	
ZNF536	9745	hgsc.bcm.edu	37	19	31039824	31039824	+	Missense_Mutation	SNP	G	G	A	rs200453890		TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr19:31039824G>A	ENST00000355537.3	+	4	3445	c.3298G>A	c.(3298-3300)Gtg>Atg	p.V1100M		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	1100					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)	p.V1100M(1)		NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					GACCGGCCACGTGGACCCTGC	0.537																																					p.V1100M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3298A	19						.						85.0	97.0	93.0					19																	31039824		2203	4300	6503	35731664	SO:0001583	missense	9745	exon4				CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"""Zinc fingers, C2H2-type"""	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.3298G>A	19.37:g.31039824G>A	ENSP00000347730:p.Val1100Met	Somatic		Capture	SOLID	Phase_I	35731664	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	37	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	G	0.001	-3.018703	0.00042	.	.	ENSG00000198597	ENST00000355537	T	0.06608	3.28	5.63	-2.28	0.06826	.	0.441463	0.25968	N	0.027152	T	0.01387	0.0045	N	0.01352	-0.895	0.25391	N	0.988523	B;B	0.10296	0.003;0.001	B;B	0.04013	0.001;0.0	T	0.46345	-0.9198	10	0.02654	T	1	-7.1098	6.1282	0.20192	0.6148:0.1552:0.23:0.0	.	1100;1100	A7E228;O15090	.;ZN536_HUMAN	M	1100	ENSP00000347730:V1100M	ENSP00000347730:V1100M	V	+	1	0	ZNF536	35731664	0.012000	0.17670	0.820000	0.32676	0.175000	0.22909	0.716000	0.25836	0.047000	0.15862	-0.150000	0.13652	GTG		0.537	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
FBXO27	126433	hgsc.bcm.edu	37	19	39516067	39516067	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr19:39516067C>T	ENST00000292853.4	-	6	955	c.836G>A	c.(835-837)cGa>cAa	p.R279Q	FBXO27_ENST00000509137.2_Missense_Mutation_p.R279Q|FBXO27_ENST00000600828.1_Missense_Mutation_p.R278Q	NM_178820.3	NP_849142.1	Q8NI29	FBX27_HUMAN	F-box protein 27	279	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.					SCF ubiquitin ligase complex (GO:0019005)	glycoprotein binding (GO:0001948)	p.R279Q(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|urinary_tract(2)	17	all_cancers(60;3.79e-07)|all_lung(34;1.26e-07)|Lung NSC(34;1.46e-07)|all_epithelial(25;4.69e-07)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			CAGACGGACTCGCACGATCAC	0.592																																					p.R279Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G836A	19						.						117.0	101.0	107.0					19																	39516067		2203	4300	6503	44207907	SO:0001583	missense	126433	exon6			AF436061	CCDS12527.1	19q13.2	2008-02-05	2004-06-15			ENSG00000161243		"""F-boxes /  ""other"""""	18753	protein-coding gene	gene with protein product		609099	"""F-box only protein 27"""			126433	Standard	NM_178820		Approved	Fbg5, Fbx27	uc002okh.3	Q8NI29		ENST00000292853.4:c.836G>A	19.37:g.39516067C>T	ENSP00000292853:p.Arg279Gln	Somatic		Capture	SOLID	Phase_I	44207907	NM_178820	Q96C87	Missense_Mutation	SNP	ENST00000292853.4	37	CCDS12527.1	.	.	.	.	.	.	.	.	.	.	C	10.94	1.492398	0.26774	.	.	ENSG00000161243	ENST00000292853;ENST00000509137	T;T	0.30714	1.52;1.52	3.5	-1.17	0.09648	Galactose-binding domain-like (1);F-box associated (FBA) domain (2);	1.393200	0.05198	N	0.504332	T	0.22085	0.0532	L	0.32530	0.975	0.09310	N	1	B	0.16166	0.016	B	0.14578	0.011	T	0.26643	-1.0097	10	0.30078	T	0.28	-10.0559	6.5604	0.22483	0.0:0.5557:0.0:0.4443	.	279	Q8NI29	FBX27_HUMAN	Q	279	ENSP00000292853:R279Q;ENSP00000437662:R279Q	ENSP00000292853:R279Q	R	-	2	0	FBXO27	44207907	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-2.279000	0.01159	-0.098000	0.12285	-0.424000	0.05967	CGA		0.592	FBXO27-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463281.1		
ENPP2	5168	hgsc.bcm.edu	37	8	120581481	120581481	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr8:120581481G>C	ENST00000075322.6	-	21	2105	c.2047C>G	c.(2047-2049)Cct>Gct	p.P683A	ENPP2_ENST00000427067.2_Missense_Mutation_p.P704A|ENPP2_ENST00000522826.1_Missense_Mutation_p.P708A|ENPP2_ENST00000522167.1_Missense_Mutation_p.P318A|ENPP2_ENST00000259486.6_Missense_Mutation_p.P735A	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	683					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.P735A(1)		breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TTACAAGGAGGAAAGAGGAAT	0.438																																					p.P708A	Melanoma(20;305 879 2501 4818 31020)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2122G	8						.						165.0	158.0	160.0					8																	120581481		2203	4300	6503	120650662	SO:0001583	missense	5168	exon22			D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"""autotaxin"""	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.2047C>G	8.37:g.120581481G>C	ENSP00000075322:p.Pro683Ala	Somatic		Capture	SOLID	Phase_I	120650662	NM_001130863	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Missense_Mutation	SNP	ENST00000075322.6	37	CCDS34936.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.469906	0.84533	.	.	ENSG00000136960	ENST00000259486;ENST00000427067;ENST00000522167;ENST00000522826;ENST00000075322	T;T;T;T;T	0.52983	0.64;0.64;0.64;0.64;0.64	5.37	5.37	0.77165	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.000000	0.85682	D	0.000000	T	0.72252	0.3437	M	0.81179	2.53	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	1.0;1.0;0.999;0.999;0.999	T	0.76192	-0.3049	10	0.87932	D	0	.	19.1242	0.93375	0.0:0.0:1.0:0.0	.	221;708;683;735;318	B4DJD3;E9PHP7;Q13822;Q13822-2;E5RIA2	.;.;ENPP2_HUMAN;.;.	A	735;704;318;708;683	ENSP00000259486:P735A;ENSP00000403315:P704A;ENSP00000429476:P318A;ENSP00000428291:P708A;ENSP00000075322:P683A	ENSP00000075322:P683A	P	-	1	0	ENPP2	120650662	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	9.010000	0.93611	2.519000	0.84933	0.655000	0.94253	CCT		0.438	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1		
OR6N1	128372	hgsc.bcm.edu	37	1	158735897	158735897	+	Silent	SNP	C	C	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr1:158735897C>T	ENST00000335094.2	-	1	595	c.576G>A	c.(574-576)acG>acA	p.T192T		NM_001005185.1	NP_001005185.1	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N, member 1	192						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T192T(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_hematologic(112;0.0378)					CATTTATAGACGTATCAGTGC	0.463																																					p.T192T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G576A	1						.						106.0	111.0	109.0					1																	158735897		2203	4300	6503	157002521	SO:0001819	synonymous_variant	128372	exon1			BK004199	CCDS30905.1	1q23.1	2012-08-09			ENSG00000197403	ENSG00000197403		"""GPCR / Class A : Olfactory receptors"""	15034	protein-coding gene	gene with protein product							Standard	NM_001005185		Approved		uc010piq.2	Q8NGY5	OTTHUMG00000022774	ENST00000335094.2:c.576G>A	1.37:g.158735897C>T		Somatic		Capture	SOLID	Phase_I	157002521	NM_001005185	Q5VUU8|Q96R35	Silent	SNP	ENST00000335094.2	37	CCDS30905.1																																																																																				0.463	OR6N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059067.1	NM_001005185	
SMG7	9887	hgsc.bcm.edu	37	1	183514071	183514071	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr1:183514071C>T	ENST00000347615.2	+	16	2113	c.1994C>T	c.(1993-1995)cCg>cTg	p.P665L	SMG7_ENST00000456731.2_Missense_Mutation_p.P577L|SMG7_ENST00000367537.3_Missense_Mutation_p.P648L|SMG7_ENST00000508461.1_Missense_Mutation_p.P623L|SMG7_ENST00000507469.1_Missense_Mutation_p.P619L|SMG7_ENST00000515829.2_Missense_Mutation_p.P619L	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor	665	Gln/Pro-rich.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)	p.P665L(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						GAAGGGTTTCCGCCCCCAACA	0.438																																					p.P623L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1868T	1						.						85.0	90.0	88.0					1																	183514071		2203	4300	6503	181780694	SO:0001583	missense	9887	exon15			D87437	CCDS1355.1, CCDS41445.1, CCDS41445.2, CCDS53444.1, CCDS53445.1	1q25	2013-07-02	2013-07-02	2006-02-16	ENSG00000116698	ENSG00000116698			16792	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog C (S. cerevisiae)"""	610964	"""chromosome 1 open reading frame 16"", ""smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C1orf16		14636577, 15721257	Standard	NM_173156		Approved	KIAA0250, EST1C, SGA56M, SMG-7	uc001gqf.3	Q92540	OTTHUMG00000035221	ENST00000347615.2:c.1994C>T	1.37:g.183514071C>T	ENSP00000340766:p.Pro665Leu	Somatic		Capture	SOLID	Phase_I	181780694	NM_001174061	B4DRB2|E9PCI0|E9PEH2|Q5T1Q0|Q6PIE0|Q7Z7H9|Q8IXC1|Q8IXC2	Missense_Mutation	SNP	ENST00000347615.2	37	CCDS1355.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.218021	0.79352	.	.	ENSG00000116698	ENST00000456731;ENST00000367537;ENST00000508461;ENST00000419169;ENST00000347615;ENST00000507469;ENST00000515829	T;T;T;T;T;T;T	0.60797	0.16;0.16;0.16;0.16;0.16;0.16;0.16	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.68439	0.3001	L	0.29908	0.895	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	0.87578	0.998;0.997;0.997;0.998;0.998;0.997	T	0.69942	-0.5008	10	0.59425	D	0.04	-11.3529	19.7629	0.96329	0.0:1.0:0.0:0.0	.	623;648;577;619;665;619	E9PCI0;E9PD50;E9PCE5;Q92540-2;Q92540;E9PEH2	.;.;.;.;SMG7_HUMAN;.	L	577;648;623;577;665;619;619	ENSP00000407629:P577L;ENSP00000356507:P648L;ENSP00000426915:P623L;ENSP00000388390:P577L;ENSP00000340766:P665L;ENSP00000425133:P619L;ENSP00000421358:P619L	ENSP00000340766:P665L	P	+	2	0	SMG7	181780694	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	7.123000	0.77176	2.666000	0.90696	0.561000	0.74099	CCG		0.438	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1	NM_014837	
RCC1	1104	hgsc.bcm.edu	37	1	28858687	28858687	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr1:28858687A>G	ENST00000373833.6	+	7	551	c.266A>G	c.(265-267)tAt>tGt	p.Y89C	RCC1_ENST00000398958.2_Missense_Mutation_p.Y89C|RCC1_ENST00000373831.3_Missense_Mutation_p.Y120C|RCC1_ENST00000429051.1_3'UTR|RCC1_ENST00000373832.1_Missense_Mutation_p.Y89C			P18754	RCC1_HUMAN	regulator of chromosome condensation 1	89					chromosome segregation (GO:0007059)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|positive regulation of Ran GTPase activity (GO:0032853)|regulation of mitosis (GO:0007088)|spindle assembly (GO:0051225)|viral process (GO:0016032)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|nucleosomal DNA binding (GO:0031492)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)	p.Y89C(1)		breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;0.000318)|all_lung(284;0.000434)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.00989)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|KIRC - Kidney renal clear cell carcinoma(1967;0.0101)|BRCA - Breast invasive adenocarcinoma(304;0.022)|READ - Rectum adenocarcinoma(331;0.0649)		GCACAGGTCTATTCCTTCGGC	0.562																																					p.Y89C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A266G	1						.						75.0	63.0	67.0					1																	28858687		2203	4300	6503	28731274	SO:0001583	missense	751867	exon4			X12654	CCDS323.1, CCDS41295.1	1p35.3	2008-08-18	2005-05-09	2005-05-09	ENSG00000180198	ENSG00000180198			1913	protein-coding gene	gene with protein product		179710	"""chromosome condensation 1"""	CHC1		7851910	Standard	NM_001048199		Approved		uc001bqf.2	P18754	OTTHUMG00000003645	ENST00000373833.6:c.266A>G	1.37:g.28858687A>G	ENSP00000362939:p.Tyr89Cys	Somatic		Capture	SOLID	Phase_I	28731274	NM_001269	Q16269|Q6NT97	Missense_Mutation	SNP	ENST00000373833.6	37	CCDS323.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.039998	0.75732	.	.	ENSG00000180198	ENST00000398958;ENST00000427469;ENST00000434290;ENST00000373833;ENST00000419074;ENST00000373832;ENST00000373831;ENST00000411533;ENST00000430407	D;D;D;D;D;D;D;D;D	0.91180	-2.8;-2.8;-2.8;-2.8;-2.8;-2.8;-2.8;-2.8;-2.8	5.53	5.53	0.82687	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.97052	0.9037	H	0.97440	4.005	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	D	0.98342	1.0539	10	0.87932	D	0	-13.3	14.5222	0.67859	1.0:0.0:0.0:0.0	.	120;106;89	P18754-2;E9PAT9;P18754	.;.;RCC1_HUMAN	C	89;89;97;89;89;89;120;106;89	ENSP00000381931:Y89C;ENSP00000402740:Y89C;ENSP00000405258:Y97C;ENSP00000362939:Y89C;ENSP00000402260:Y89C;ENSP00000362938:Y89C;ENSP00000362937:Y120C;ENSP00000413644:Y106C;ENSP00000394650:Y89C	ENSP00000362937:Y120C	Y	+	2	0	RCC1	28731274	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	9.297000	0.96120	2.107000	0.64212	0.529000	0.55759	TAT		0.562	RCC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010323.3	NM_001269	
PTPRF	5792	hgsc.bcm.edu	37	1	44019168	44019168	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr1:44019168C>T	ENST00000359947.4	+	4	437	c.97C>T	c.(97-99)Cct>Tct	p.P33S	PTPRF_ENST00000438120.1_Missense_Mutation_p.P33S|PTPRF_ENST00000372414.3_Missense_Mutation_p.P33S|PTPRF_ENST00000372413.3_Missense_Mutation_p.P33S	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	33	Ig-like C2-type 1.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.P23S(1)		NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TCCAGGCAAACCTGTCTTCAT	0.552																																					p.P33S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C97T	1						.						262.0	250.0	254.0					1																	44019168		2203	4300	6503	43791755	SO:0001583	missense	5792	exon4			Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.97C>T	1.37:g.44019168C>T	ENSP00000353030:p.Pro33Ser	Somatic		Capture	SOLID	Phase_I	43791755	NM_130440	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Missense_Mutation	SNP	ENST00000359947.4	37	CCDS489.2	.	.	.	.	.	.	.	.	.	.	C	24.2	4.510384	0.85389	.	.	ENSG00000142949	ENST00000359947;ENST00000438120;ENST00000372414;ENST00000372413;ENST00000437607	T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18	4.89	4.89	0.63831	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.34002	N	0.004350	D	0.85725	0.5763	H	0.95365	3.66	0.80722	D	1	D;P;P;D	0.89917	1.0;0.485;0.938;1.0	D;B;B;D	0.91635	0.996;0.153;0.43;0.999	D	0.90379	0.4386	10	0.87932	D	0	.	18.4352	0.90643	0.0:1.0:0.0:0.0	.	33;33;33;33	Q5T020;P10586-2;P10586;Q5T019	.;.;PTPRF_HUMAN;.	S	33	ENSP00000353030:P33S;ENSP00000398822:P33S;ENSP00000361491:P33S;ENSP00000361490:P33S;ENSP00000413306:P33S	ENSP00000353030:P33S	P	+	1	0	PTPRF	43791755	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	2.405000	0.81733	0.655000	0.94253	CCT		0.552	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
USH2A	7399	hgsc.bcm.edu	37	1	215990450	215990450	+	Silent	SNP	G	G	A	rs73090721	byFrequency	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	.			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr1:215990450G>A	ENST00000307340.3	-	48	9845	c.9459C>T	c.(9457-9459)tgC>tgT	p.C3153C	USH2A_ENST00000366943.2_Silent_p.C3153C	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3153	Fibronectin type-III 18. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.C3153C(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GAGTTTTAGCGCATGGATACC	0.428										HNSCC(13;0.011)			G|||	29	0.00579073	0.0212	0.0014	5008	,	,		14177	0.0		0.0	False		,,,				2504	0.0				p.C3153C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C9459T	1						.	G		60,4346	58.1+/-94.6	2,56,2145	142.0	133.0	136.0		9459	3.4	0.4	1	dbSNP_130	136	2,8596	1.2+/-3.3	0,2,4297	no	coding-synonymous	USH2A	NM_206933.2		2,58,6442	AA,AG,GG		0.0233,1.3618,0.4768		3153/5203	215990450	62,12942	2203	4299	6502	214057073	SO:0001819	synonymous_variant	7399	exon48			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.9459C>T	1.37:g.215990450G>A		Somatic		Capture	SOLID	Phase_I	214057073	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																				0.428	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
LUZP2	338645	hgsc.bcm.edu	37	11	24759822	24759822	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr11:24759822G>T	ENST00000336930.6	+	4	373	c.307G>T	c.(307-309)Gag>Tag	p.E103*	LUZP2_ENST00000533227.1_Nonsense_Mutation_p.E17*|LUZP2_ENST00000531187.1_3'UTR			Q86TE4	LUZP2_HUMAN	leucine zipper protein 2	103						extracellular region (GO:0005576)		p.E103*(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(11)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	32						GGAGACATCAGAGAAAGCAGA	0.363																																					p.E103X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G307T	11						.						84.0	86.0	85.0					11																	24759822		2203	4300	6503	24716398	SO:0001587	stop_gained	338645	exon4			AL832641	CCDS31446.1, CCDS58128.1	11p14.3	2005-09-18			ENSG00000187398	ENSG00000187398			23206	protein-coding gene	gene with protein product		608178				12856284	Standard	NM_001009909		Approved		uc001mqs.3	Q86TE4	OTTHUMG00000166109	ENST00000336930.6:c.307G>T	11.37:g.24759822G>T	ENSP00000336817:p.Glu103*	Somatic		Capture	SOLID	Phase_I	24716398	NM_001009909	A2RUB8|E9PN53|Q6UXE7|Q6ZS65	Nonsense_Mutation	SNP	ENST00000336930.6	37	CCDS31446.1	.	.	.	.	.	.	.	.	.	.	G	35	5.441489	0.96187	.	.	ENSG00000187398	ENST00000336930;ENST00000529015;ENST00000533227	.	.	.	5.77	5.77	0.91146	.	0.117966	0.56097	D	0.000040	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-7.6861	17.4594	0.87616	0.0:0.0:1.0:0.0	.	.	.	.	X	103;103;17	.	ENSP00000336817:E103X	E	+	1	0	LUZP2	24716398	1.000000	0.71417	0.989000	0.46669	0.920000	0.55202	7.689000	0.84165	2.725000	0.93324	0.655000	0.94253	GAG		0.363	LUZP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387861.1	NM_001009909	
CD44	960	hgsc.bcm.edu	37	11	35198189	35198189	+	Silent	SNP	T	T	C			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr11:35198189T>C	ENST00000428726.2	+	2	258	c.135T>C	c.(133-135)tcT>tcC	p.S45S	CD44_ENST00000433354.2_Silent_p.S45S|CD44_ENST00000526025.1_Silent_p.S45S|CD44_ENST00000278386.6_Silent_p.S45S|CD44_ENST00000449691.2_Silent_p.S45S|CD44_ENST00000352818.4_Silent_p.S45S|CD44_ENST00000437706.2_Silent_p.S45S|CD44_ENST00000434472.2_Silent_p.S45S|CD44_ENST00000263398.6_Silent_p.S45S|CD44_ENST00000360158.4_Silent_p.S45S|CD44_ENST00000433892.2_Silent_p.S45S|CD44_ENST00000415148.2_Silent_p.S45S|CD44_ENST00000526669.2_Silent_p.S45S	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	45	Link. {ECO:0000255|PROSITE- ProRule:PRU00323}.				blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)	p.S45S(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	ACAGCATCTCTCGGACGGAGG	0.478																																					p.S45S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T135C	11						.						51.0	49.0	50.0					11																	35198189		2202	4298	6500	35154765	SO:0001819	synonymous_variant	960	exon2			M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"""CD molecules"", ""Blood group antigens"", ""Proteoglycans / Cell surface : Other"""	1681	protein-coding gene	gene with protein product	"""hematopoietic cell E- and L-selectin ligand"", ""chondroitin sulfate proteoglycan 8"""	107269	"""CD44 antigen (homing function and Indian blood group system)"""	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.135T>C	11.37:g.35198189T>C		Somatic		Capture	SOLID	Phase_I	35154765	NM_001001389	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Silent	SNP	ENST00000428726.2	37	CCDS7897.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.999|9.999	1.232989|1.232989	0.22626|0.22626	.|.	.|.	ENSG00000026508|ENSG00000026508	ENST00000527889|ENST00000442151	.|T	.|0.11604	.|2.76	5.85|5.85	-11.7|-11.7	0.00046|0.00046	.|.	.|0.129124	.|0.48286	.|D	.|0.000189	T|T	0.09642|0.09642	0.0237|0.0237	.|.	.|.	.|.	0.38674|0.38674	D|D	0.952371|0.952371	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.60870|0.60870	-0.7177|-0.7177	4|7	.|0.87932	.|D	.|0	-26.4353|-26.4353	2.1532|2.1532	0.03805|0.03805	0.152:0.3277:0.2089:0.3114|0.152:0.3277:0.2089:0.3114	.|.	.|.	.|.	.|.	P|P	1|45	.|ENSP00000398099:S45P	.|ENSP00000398099:S45P	L|S	+|+	2|1	0|0	CD44|CD44	35154765|35154765	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.979000|0.979000	0.70002|0.70002	-5.839000|-5.839000	0.00095|0.00095	-3.882000|-3.882000	0.00095|0.00095	0.459000|0.459000	0.35465|0.35465	CTC|TCG		0.478	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610	
GUCY1A2	2977	hgsc.bcm.edu	37	11	106558445	106558445	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr11:106558445G>A	ENST00000526355.2	-	8	2497	c.2029C>T	c.(2029-2031)Cgg>Tgg	p.R677W	GUCY1A2_ENST00000347596.2_Missense_Mutation_p.R698W|GUCY1A2_ENST00000282249.2_Missense_Mutation_p.R708W	NM_000855.2	NP_000846.1	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	677					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|positive regulation of cGMP biosynthetic process (GO:0030828)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)	p.R677W(1)		breast(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(18)|liver(1)|lung(32)|ovary(1)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	74		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)	Isosorbide Mononitrate(DB01020)|Nitric Oxide(DB00435)	TCACGAGACCGCGGAATGAAT	0.423																																					p.R677W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2029T	11						.						100.0	103.0	102.0					11																	106558445		2201	4298	6499	106063655	SO:0001583	missense	2977	exon8			X63282	CCDS8335.1, CCDS58170.1	11q21-q22	2008-03-18			ENSG00000152402	ENSG00000152402	4.6.1.2		4684	protein-coding gene	gene with protein product		601244		GUC1A2		1683630	Standard	NM_000855		Approved	GC-SA2	uc001pjg.2	P33402	OTTHUMG00000166296	ENST00000526355.2:c.2029C>T	11.37:g.106558445G>A	ENSP00000431245:p.Arg677Trp	Somatic		Capture	SOLID	Phase_I	106063655	NM_000855	A1L4C4|B7ZLT5	Missense_Mutation	SNP	ENST00000526355.2	37	CCDS8335.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.725974	0.89298	.	.	ENSG00000152402	ENST00000526355;ENST00000282249;ENST00000347596	D;D;D	0.85955	-2.05;-1.69;-2.05	5.52	5.52	0.82312	Adenylyl cyclase class-3/4/guanylyl cyclase (3);	0.000000	0.42053	U	0.000778	D	0.96303	0.8794	H	0.99404	4.55	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97953	1.0333	10	0.87932	D	0	.	18.7903	0.91971	0.0:0.0:1.0:0.0	.	698;708;677	B7ZLT5;P33402-2;P33402	.;.;GCYA2_HUMAN	W	677;708;698	ENSP00000431245:R677W;ENSP00000282249:R708W;ENSP00000344874:R698W	ENSP00000282249:R708W	R	-	1	2	GUCY1A2	106063655	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.340000	0.97038	2.762000	0.94881	0.467000	0.42956	CGG		0.423	GUCY1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389003.2		
KPNA5	3841	hgsc.bcm.edu	37	6	117047749	117047749	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr6:117047749C>G	ENST00000368564.1	+	12	1365	c.1217C>G	c.(1216-1218)aCt>aGt	p.T406S	KPNA5_ENST00000356348.1_Missense_Mutation_p.T406S			O15131	IMA6_HUMAN	karyopherin alpha 5 (importin alpha 6)	403					cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)	p.T406S(1)		breast(6)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212)		TGGGCTATAACTAATGCAACA	0.338																																					p.T406S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1217G	6						.						86.0	90.0	89.0					6																	117047749		2203	4300	6503	117154442	SO:0001583	missense	3841	exon12			AF005361	CCDS5111.1	6q22.2	2013-02-14			ENSG00000196911	ENSG00000196911		"""Importins"", ""Armadillo repeat containing"""	6398	protein-coding gene	gene with protein product		604545				9395085	Standard	NM_002269		Approved	SRP6, IPOA6	uc003pxh.3	O15131	OTTHUMG00000015448	ENST00000368564.1:c.1217C>G	6.37:g.117047749C>G	ENSP00000357552:p.Thr406Ser	Somatic		Capture	SOLID	Phase_I	117154442	NM_002269	B2RAI5|Q86X23	Missense_Mutation	SNP	ENST00000368564.1	37	CCDS5111.1	.	.	.	.	.	.	.	.	.	.	C	12.42	1.931625	0.34096	.	.	ENSG00000196911	ENST00000368564;ENST00000356348	T;T	0.63580	-0.05;-0.05	5.53	5.53	0.82687	Armadillo-like helical (1);Armadillo-type fold (1);	0.135964	0.47852	D	0.000217	T	0.48409	0.1498	N	0.21508	0.67	0.49687	D	0.999815	P	0.39696	0.683	P	0.53861	0.736	T	0.48387	-0.9040	10	0.02654	T	1	.	19.507	0.95121	0.0:1.0:0.0:0.0	.	403	O15131	IMA5_HUMAN	S	406	ENSP00000357552:T406S;ENSP00000348704:T406S	ENSP00000348704:T406S	T	+	2	0	KPNA5	117154442	1.000000	0.71417	1.000000	0.80357	0.793000	0.44817	7.507000	0.81676	2.617000	0.88574	0.485000	0.47835	ACT		0.338	KPNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041967.1	NM_002269	
SUPT6H	6830	hgsc.bcm.edu	37	17	27010748	27010748	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr17:27010748C>T	ENST00000314616.6	+	17	2426	c.2143C>T	c.(2143-2145)Cgg>Tgg	p.R715W	SUPT6H_ENST00000347486.4_Missense_Mutation_p.R715W	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	715	Interaction with KDM6A. {ECO:0000250}.|Interaction with PAAF1.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R715W(1)		NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					GGCCATCGAACGGGCTTTACA	0.498																																					p.R715W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2143T	17						.						74.0	73.0	74.0					17																	27010748		2203	4300	6503	24034875	SO:0001583	missense	6830	exon17			U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"""SH2 domain containing"""	11470	protein-coding gene	gene with protein product		601333	"""suppressor of Ty (S.cerevisiae) 6 homolog"""			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.2143C>T	17.37:g.27010748C>T	ENSP00000319104:p.Arg715Trp	Somatic		Capture	SOLID	Phase_I	24034875	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	37	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.998760	0.74818	.	.	ENSG00000109111	ENST00000314616	T	0.40756	1.02	5.39	5.39	0.77823	Tex-like domain (1);	0.060685	0.64402	D	0.000003	T	0.57740	0.2074	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	P	0.58391	0.838	T	0.53585	-0.8418	10	0.36615	T	0.2	-1.2919	19.2162	0.93780	0.0:1.0:0.0:0.0	.	715	Q7KZ85	SPT6H_HUMAN	W	715	ENSP00000319104:R715W	ENSP00000319104:R715W	R	+	1	2	SUPT6H	24034875	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.930000	0.48924	2.557000	0.86248	0.650000	0.86243	CGG		0.498	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
ACACA	31	hgsc.bcm.edu	37	17	35687262	35687262	+	Silent	SNP	T	T	C			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr17:35687262T>C	ENST00000394406.2	-	3	268	c.78A>G	c.(76-78)gaA>gaG	p.E26E	ACACA_ENST00000416895.1_Silent_p.E26E|ACACA_ENST00000353139.5_Silent_p.E63E|ACACA_ENST00000588142.1_Silent_p.E26E	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	26					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)	p.E63E(1)		NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	CTGAGTTATCTTCAGACACAG	0.483																																					p.E63E	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A189G	17						.						157.0	146.0	150.0					17																	35687262		2203	4300	6503	32761375	SO:0001819	synonymous_variant	31	exon3			U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 1"""	200350	"""acetyl-Coenzyme A carboxylase alpha"""	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.78A>G	17.37:g.35687262T>C		Somatic		Capture	SOLID	Phase_I	32761375	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Silent	SNP	ENST00000394406.2	37	CCDS11317.1																																																																																				0.483	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836	
DHX8	1659	hgsc.bcm.edu	37	17	41584439	41584439	+	Silent	SNP	C	C	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	.			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr17:41584439C>T	ENST00000262415.3	+	13	1869	c.1797C>T	c.(1795-1797)acC>acT	p.T599T	DHX8_ENST00000540306.1_Silent_p.T599T	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	599	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.T599T(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		CACAGATCACCCAGTACCTGG	0.502																																					p.T599T	NSCLC(56;1548 1661 49258 49987)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1797T	17						.						89.0	81.0	83.0					17																	41584439		2203	4300	6503	38939965	SO:0001819	synonymous_variant	1659	exon13			D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"""DEAH-boxes"""	2749	protein-coding gene	gene with protein product		600396	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"""	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.1797C>T	17.37:g.41584439C>T		Somatic		Capture	SOLID	Phase_I	38939965	NM_004941		Silent	SNP	ENST00000262415.3	37	CCDS11464.1																																																																																				0.502	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1		
TP53	7157	hgsc.bcm.edu	37	17	7577022	7577022	+	Nonsense_Mutation	SNP	G	G	A	rs121913344		TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr17:7577022G>A	ENST00000269305.4	-	8	1105	c.916C>T	c.(916-918)Cga>Tga	p.R306*	TP53_ENST00000359597.4_Nonsense_Mutation_p.R306*|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Nonsense_Mutation_p.R306*|TP53_ENST00000445888.2_Nonsense_Mutation_p.R306*|TP53_ENST00000455263.2_Nonsense_Mutation_p.R306*|TP53_ENST00000413465.2_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	306	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.		R -> P (in LFS; germline mutation and in a sporadic cancer; somatic mutation).|R -> Q (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.R306*(133)|p.0?(8)|p.?(3)|p.R306fs*39(2)|p.K305fs*1(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)	TGCTTACCTCGCTTAGTGCTC	0.562	R306*(HCC1937_BREAST)|R306*(JURLMK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R306*(MFE296_ENDOMETRIUM)|R306*(MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R306*(RCM1_LARGE_INTESTINE)	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)																											p.R306X	Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53,large_intestine,rectum,Substitution - Nonsense,0	.	147	Substitution - Nonsense(133)|Whole gene deletion(8)|Unknown(3)|Deletion - Frameshift(2)|Insertion - Frameshift(1)	large_intestine(39)|breast(21)|upper_aerodigestive_tract(15)|ovary(11)|central_nervous_system(10)|oesophagus(10)|stomach(8)|lung(8)|endometrium(6)|bone(4)|pancreas(3)|haematopoietic_and_lymphoid_tissue(3)|biliary_tract(3)|kidney(2)|NS(2)|urinary_tract(1)|liver(1)	c.C916T	17	GRCh37	CM971506	TP53	M	rs121913344	.						120.0	106.0	110.0					17																	7577022		2203	4300	6503	7517747	SO:0001587	stop_gained	7157	exon8	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.916C>T	17.37:g.7577022G>A	ENSP00000269305:p.Arg306*	Somatic		Capture	SOLID	Phase_I	7517747	NM_001126114	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	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.782988	0.90282	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	.	.	.	5.26	3.21	0.36854	.	1.348720	0.05032	N	0.474808	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.4785	0.44678	0.0:0.0:0.6334:0.3666	.	.	.	.	X	306;306;306;306;306;295;174	.	ENSP00000269305:R306X	R	-	1	2	TP53	7517747	1.000000	0.71417	0.970000	0.41538	0.345000	0.29048	2.280000	0.43443	0.735000	0.32537	0.561000	0.74099	CGA		0.562	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
RNF157	114804	hgsc.bcm.edu	37	17	74161623	74161623	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr17:74161623T>C	ENST00000269391.6	-	7	764	c.632A>G	c.(631-633)tAt>tGt	p.Y211C	RNF157_ENST00000319945.6_Missense_Mutation_p.Y211C	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157	211							zinc ion binding (GO:0008270)	p.Y821C(1)		breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	25			LUSC - Lung squamous cell carcinoma(166;0.187)			ATGGCCAAAATACTCTGAAAG	0.463																																					p.Y211C	GBM(186;507 2120 27388 27773 52994)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A632G	17						.						158.0	144.0	149.0					17																	74161623		2203	4300	6503	71673218	SO:0001583	missense	114804	exon7			AK091467	CCDS32740.1	17q25.3	2004-02-27			ENSG00000141576	ENSG00000141576		"""RING-type (C3HC4) zinc fingers"""	29402	protein-coding gene	gene with protein product						11572484	Standard	NM_052916		Approved	KIAA1917	uc002jqz.3	Q96PX1	OTTHUMG00000132627	ENST00000269391.6:c.632A>G	17.37:g.74161623T>C	ENSP00000269391:p.Tyr211Cys	Somatic		Capture	SOLID	Phase_I	71673218	NM_052916	Q8NB72|Q96N56	Missense_Mutation	SNP	ENST00000269391.6	37	CCDS32740.1	.	.	.	.	.	.	.	.	.	.	T	13.88	2.368075	0.42003	.	.	ENSG00000141576	ENST00000269391;ENST00000319945;ENST00000301610	T;T	0.27890	1.64;1.64	5.27	5.27	0.74061	.	0.046616	0.85682	D	0.000000	T	0.23492	0.0568	N	0.22421	0.69	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.09377	0.003;0.004	T	0.02705	-1.1121	10	0.41790	T	0.15	.	15.4731	0.75456	0.0:0.0:0.0:1.0	.	211;211	Q96PX1-2;Q96PX1	.;RN157_HUMAN	C	211;211;173	ENSP00000269391:Y211C;ENSP00000321837:Y211C	ENSP00000269391:Y211C	Y	-	2	0	RNF157	71673218	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	5.756000	0.68757	2.099000	0.63709	0.533000	0.62120	TAT		0.463	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255874.2	XM_290732	
CYYR1	116159	hgsc.bcm.edu	37	21	27852646	27852646	+	Silent	SNP	C	C	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr21:27852646C>T	ENST00000299340.4	-	3	622	c.279G>A	c.(277-279)gcG>gcA	p.A93A	AP001597.1_ENST00000414486.1_RNA|CYYR1_ENST00000400043.3_Silent_p.A93A|CYYR1_ENST00000435845.2_3'UTR|AP001597.1_ENST00000357401.3_RNA	NM_052954.2	NP_443186.1	Q96J86	CYYR1_HUMAN	cysteine/tyrosine-rich 1	93						integral component of membrane (GO:0016021)		p.A93A(1)		large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	15						CCACGCGGGTCGCCCTGTGGT	0.498																																					p.A93A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G279A	21						.						140.0	126.0	130.0					21																	27852646		2203	4300	6503	26774517	SO:0001819	synonymous_variant	116159	exon3			AY061853	CCDS13578.1	21q21.2	2014-07-04	2005-07-24		ENSG00000166265	ENSG00000166265			16274	protein-coding gene	gene with protein product			"""cysteine and tyrosine-rich 1"""	C21orf95		12036297, 12062809, 24981926	Standard	NM_052954		Approved		uc002ymd.3	Q96J86	OTTHUMG00000078689	ENST00000299340.4:c.279G>A	21.37:g.27852646C>T		Somatic		Capture	SOLID	Phase_I	26774517	NM_052954	A0A059TD09|A8MTU9|B2R845|Q53ER3|Q5JPD0|Q96NV7|R9QAJ4|W8CQB3	Silent	SNP	ENST00000299340.4	37	CCDS13578.1																																																																																				0.498	CYYR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171654.2	NM_052954	
SCAF4	57466	hgsc.bcm.edu	37	21	33073309	33073309	+	Splice_Site	SNP	T	T	A			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr21:33073309T>A	ENST00000286835.7	-	7	1158	c.776A>T	c.(775-777)aAg>aTg	p.K259M	SCAF4_ENST00000399804.1_Splice_Site_p.K259M|SCAF4_ENST00000434667.3_Splice_Site_p.K244M	NM_020706.2	NP_065757.1	O95104	SFR15_HUMAN	SR-related CTD-associated factor 4	259						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.K259M(1)		NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(11)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						GAAATATACCTTGTCAAATGC	0.408																																					p.K244M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A731T	21						.						143.0	147.0	146.0					21																	33073309		2203	4300	6503	31995180	SO:0001630	splice_region_variant	57466	exon6			AB032998	CCDS33537.1, CCDS46644.1, CCDS54482.1	21q22.1	2013-02-12	2011-01-10	2011-01-10	ENSG00000156304	ENSG00000156304		"""RNA binding motif (RRM) containing"""	19304	protein-coding gene	gene with protein product			"""splicing factor, arginine/serine-rich 15"""	SFRS15		10574461	Standard	NM_020706		Approved	KIAA1172, DKFZp434E098, SRA4	uc002ypd.2	O95104	OTTHUMG00000084903	ENST00000286835.7:c.777+1A>T	21.37:g.33073309T>A		Somatic		Capture	SOLID	Phase_I	31995180	NM_001145444	C9JLZ0|Q0P5W8|Q6P1M5|Q8N3I8|Q9UFM1|Q9ULP8	Missense_Mutation	SNP	ENST00000286835.7	37	CCDS33537.1	.	.	.	.	.	.	.	.	.	.	T	19.97	3.925975	0.73327	.	.	ENSG00000156304	ENST00000434667;ENST00000286835;ENST00000399804	T;T;T	0.60171	0.22;0.21;0.3	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.75354	0.3838	M	0.70275	2.135	0.50632	D	0.999888	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.997;0.997;0.999;0.997	T	0.77945	-0.2397	10	0.87932	D	0	-20.6794	15.2117	0.73230	0.0:0.0:0.0:1.0	.	244;259;259;259	C9JLZ0;Q0P607;O95104-2;O95104	.;.;.;SFR15_HUMAN	M	244;259;259	ENSP00000402377:K244M;ENSP00000286835:K259M;ENSP00000382703:K259M	ENSP00000286835:K259M	K	-	2	0	SCAF4	31995180	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	6.496000	0.73670	2.326000	0.78906	0.533000	0.62120	AAG		0.408	SCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000192659.1	XM_047889	Missense_Mutation
PAXBP1	94104	hgsc.bcm.edu	37	21	34134572	34134572	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr21:34134572G>A	ENST00000331923.4	-	4	895	c.706C>T	c.(706-708)Cga>Tga	p.R236*	PAXBP1_ENST00000472588.1_5'UTR|PAXBP1_ENST00000290178.4_Nonsense_Mutation_p.R236*	NM_016631.3	NP_057715.2	Q9Y5B6	PAXB1_HUMAN	PAX3 and PAX7 binding protein 1	236					muscle organ development (GO:0007517)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of satellite cell proliferation (GO:0014842)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R236*(1)									CCCAATTCTCGGGCCATTTGG	0.428																																					p.R236X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C706T	21						.						74.0	73.0	74.0					21																	34134572		2203	4300	6503	33056443	SO:0001587	stop_gained	94104	exon4			AF231920	CCDS13619.1, CCDS33541.1	21q22.11	2014-01-23	2013-01-08	2013-01-08	ENSG00000159086	ENSG00000159086			13579	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 105"", ""GC-rich sequence DNA-binding factor candidate"""		"""chromosome 21 open reading frame 66"", ""GC-rich sequence DNA-binding factor 1"""	C21orf66, GCFC1		11707072, 22862948	Standard	NM_016631		Approved	GCFC, fSAP105	uc002yqn.3	Q9Y5B6	OTTHUMG00000064980	ENST00000331923.4:c.706C>T	21.37:g.34134572G>A	ENSP00000328992:p.Arg236*	Somatic		Capture	SOLID	Phase_I	33056443	NM_013329	D3DSE7|Q96DU8|Q9NYQ0	Nonsense_Mutation	SNP	ENST00000331923.4	37	CCDS13619.1	.	.	.	.	.	.	.	.	.	.	G	33	5.200282	0.94997	.	.	ENSG00000159086	ENST00000331923;ENST00000290178	.	.	.	5.81	4.92	0.64577	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.7078	15.7977	0.78424	0.0:0.0:0.8625:0.1375	.	.	.	.	X	236	.	ENSP00000290178:R236X	R	-	1	2	GCFC1	33056443	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	5.946000	0.70234	1.427000	0.47276	0.557000	0.71058	CGA		0.428	PAXBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139563.1	NM_013329	
IGSF6	10261	hgsc.bcm.edu	37	16	21655620	21655620	+	Silent	SNP	G	G	A			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr16:21655620G>A	ENST00000268389.4	-	3	586	c.525C>T	c.(523-525)ctC>ctT	p.L175L	RNU6-196P_ENST00000384315.1_RNA|METTL9_ENST00000396014.4_Intron|RNU6-1005P_ENST00000384519.1_RNA|METTL9_ENST00000358154.3_Intron	NM_005849.3	NP_005840.2	O95976	IGSF6_HUMAN	immunoglobulin superfamily, member 6	175					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)	integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)	p.L175L(1)		endometrium(1)|large_intestine(1)|lung(4)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(48;0.066)		CTTTGGAGAGGAGTATGAAGG	0.428																																					p.L175L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C525T	16						.						118.0	110.0	113.0					16																	21655620		2199	4300	6499	21563121	SO:0001819	synonymous_variant	10261	exon3			AJ223183	CCDS10599.1	16p12.2	2013-01-11			ENSG00000140749	ENSG00000140749		"""Immunoglobulin superfamily / V-set domain containing"""	5953	protein-coding gene	gene with protein product		606222				9809579	Standard	NM_005849		Approved	DORA	uc002djg.2	O95976	OTTHUMG00000090709	ENST00000268389.4:c.525C>T	16.37:g.21655620G>A		Somatic		Capture	SOLID	Phase_I	21563121	NM_005849	Q8WWD8	Silent	SNP	ENST00000268389.4	37	CCDS10599.1																																																																																				0.428	IGSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207400.1		
HYDIN	54768	hgsc.bcm.edu	37	16	71101253	71101253	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr16:71101253G>T	ENST00000393567.2	-	15	2165	c.2015C>A	c.(2014-2016)gCa>gAa	p.A672E	HYDIN_ENST00000538248.1_Missense_Mutation_p.A699E|HYDIN_ENST00000393550.2_Missense_Mutation_p.A687E|HYDIN_ENST00000541601.1_Missense_Mutation_p.A689E|HYDIN_ENST00000288168.10_Missense_Mutation_p.A689E|HYDIN_ENST00000543639.1_5'Flank|HYDIN_ENST00000448691.1_Missense_Mutation_p.A672E|HYDIN_ENST00000321489.5_Missense_Mutation_p.A672E|HYDIN_ENST00000448089.2_Missense_Mutation_p.A672E	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	672					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.A672E(3)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				CACCACGAGTGCCAGCTCGTA	0.532																																					p.A672E												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.C2015A	16						.						77.0	65.0	69.0					16																	71101253		2198	4300	6498	69658754	SO:0001583	missense	54768	exon15			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.2015C>A	16.37:g.71101253G>T	ENSP00000377197:p.Ala672Glu	Somatic		Capture	SOLID	Phase_I	69658754	NM_032821	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.09|16.09	3.024197|3.024197	0.54683|0.54683	.|.	.|.	ENSG00000157423|ENSG00000157423	ENST00000393567;ENST00000316490;ENST00000448089;ENST00000448691;ENST00000321489;ENST00000538248;ENST00000541601;ENST00000288168;ENST00000393550|ENST00000542890	T;T;T;T;T;T;T;T|.	0.06371|.	3.31;3.31;3.31;3.31;3.31;3.31;3.31;3.31|.	4.99|4.99	4.99|4.99	0.66335|0.66335	.|.	0.000000|.	0.32703|.	U|.	0.005751|.	T|T	0.67822|0.67822	0.2934|0.2934	L|L	0.48642|0.48642	1.525|1.525	0.47994|0.47994	D|D	0.99956|0.99956	P;P;B;P;D|.	0.89917|.	0.875;0.875;0.34;0.875;1.0|.	P;P;B;P;D|.	0.87578|.	0.729;0.729;0.108;0.547;0.998|.	T|T	0.65413|0.65413	-0.6174|-0.6174	10|5	0.06365|.	T|.	0.9|.	.|.	17.1332|17.1332	0.86732|0.86732	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	699;689;689;672;672|.	B4DRN4;F5H6V3;F8WD03;Q4G0P3-5;F8WD23|.	.;.;.;.;.|.	E|N	672;672;672;672;672;699;689;689;687|74	ENSP00000377197:A672E;ENSP00000398544:A672E;ENSP00000394826:A672E;ENSP00000314736:A672E;ENSP00000444970:A699E;ENSP00000437341:A689E;ENSP00000288168:A689E;ENSP00000377181:A687E|.	ENSP00000288168:A689E|.	A|H	-|-	2|1	0|0	HYDIN|HYDIN	69658754|69658754	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.864000|0.864000	0.49448|0.49448	6.181000|6.181000	0.71988|0.71988	2.332000|2.332000	0.79248|0.79248	0.603000|0.603000	0.83216|0.83216	GCA|CAC		0.532	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
LAMA1	284217	hgsc.bcm.edu	37	18	6986298	6986298	+	Silent	SNP	C	C	T	rs201901346		TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr18:6986298C>T	ENST00000389658.3	-	37	5310	c.5217G>A	c.(5215-5217)ccG>ccA	p.P1739P		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1739	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.P1739P(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				ATTCTTCCAGCGGCTTCTGGT	0.433																																					p.P1739P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G5217A	18						.						97.0	91.0	93.0					18																	6986298		2203	4300	6503	6976298	SO:0001819	synonymous_variant	284217	exon37			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.5217G>A	18.37:g.6986298C>T		Somatic		Capture	SOLID	Phase_I	6976298	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																				0.433	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
UBA5	79876	hgsc.bcm.edu	37	3	132394105	132394105	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr3:132394105T>A	ENST00000356232.4	+	9	1898	c.826T>A	c.(826-828)Ttt>Att	p.F276I	UBA5_ENST00000473651.1_Missense_Mutation_p.F276I|UBA5_ENST00000493720.2_Missense_Mutation_p.F276I|UBA5_ENST00000494238.2_Missense_Mutation_p.F220I|UBA5_ENST00000264991.4_Missense_Mutation_p.F220I	NM_024818.3	NP_079094.1	Q9GZZ9	UBA5_HUMAN	ubiquitin-like modifier activating enzyme 5	276					protein ufmylation (GO:0071569)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|UFM1 activating enzyme activity (GO:0071566)	p.F276I(1)		breast(2)|endometrium(4)|kidney(4)|large_intestine(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						TCTGTTAAATTTTGGTACTGT	0.284																																					p.F220I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T658A	3						.						63.0	61.0	62.0					3																	132394105		2202	4300	6502	133876795	SO:0001583	missense	79876	exon9			AY253672	CCDS3076.1, CCDS3077.1	3q22	2007-11-30	2007-11-30	2007-11-30	ENSG00000081307	ENSG00000081307		"""Ubiquitin-like modifier activating enzymes"""	23230	protein-coding gene	gene with protein product	"""UBA5, ubiquitin-activating enzyme E1 homolog (yeast)"""	610552	"""ubiquitin-activating enzyme E1-domain containing 1"""	UBE1DC1		11230166, 15071506	Standard	NM_198329		Approved	FLJ23251	uc003epa.4	Q9GZZ9	OTTHUMG00000159759	ENST00000356232.4:c.826T>A	3.37:g.132394105T>A	ENSP00000348565:p.Phe276Ile	Somatic		Capture	SOLID	Phase_I	133876795	NM_198329	A6NJL3|D3DNC8|Q96ST1	Missense_Mutation	SNP	ENST00000356232.4	37	CCDS3076.1	.	.	.	.	.	.	.	.	.	.	T	18.22	3.575072	0.65878	.	.	ENSG00000081307	ENST00000264991;ENST00000356232;ENST00000493720;ENST00000473651;ENST00000494238	T;T;T;T;T	0.28454	1.61;1.61;1.61;1.61;1.61	5.78	5.78	0.91487	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.49218	0.1544	H	0.95043	3.615	0.80722	D	1	P;P	0.38729	0.644;0.503	B;B	0.38378	0.203;0.272	T	0.59563	-0.7431	10	0.24483	T	0.36	-21.3268	16.0928	0.81102	0.0:0.0:0.0:1.0	.	276;276	E7EWE1;Q9GZZ9	.;UBA5_HUMAN	I	220;276;276;276;220	ENSP00000264991:F220I;ENSP00000348565:F276I;ENSP00000417879:F276I;ENSP00000424984:F276I;ENSP00000418807:F220I	ENSP00000264991:F220I	F	+	1	0	UBA5	133876795	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.614000	0.82996	2.192000	0.70111	0.482000	0.46254	TTT		0.284	UBA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357187.2	NM_024818	
TGM4	7047	hgsc.bcm.edu	37	3	44929232	44929232	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr3:44929232C>T	ENST00000296125.4	+	3	313	c.245C>T	c.(244-246)aCg>aTg	p.T82M		NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	82					mating plug formation (GO:0042628)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.T82M(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(9)|lung(21)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	38				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)	GACCCGAGGACGCCCTCAGAC	0.617																																					p.T82M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C245T	3						.						87.0	80.0	82.0					3																	44929232		2203	4300	6503	44904236	SO:0001583	missense	7047	exon3			BC007003	CCDS2723.1	3p22-p21.33	2013-05-02	2013-05-02		ENSG00000163810	ENSG00000163810	2.3.2.13	"""Transglutaminases"""	11780	protein-coding gene	gene with protein product		600585	"""transglutaminase 4 (prostate)"""			7665178, 7916568	Standard	NM_003241		Approved	TGP	uc003coc.4	P49221	OTTHUMG00000133096	ENST00000296125.4:c.245C>T	3.37:g.44929232C>T	ENSP00000296125:p.Thr82Met	Somatic		Capture	SOLID	Phase_I	44904236	NM_003241	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	37	CCDS2723.1	.	.	.	.	.	.	.	.	.	.	C	10.34	1.322517	0.23994	.	.	ENSG00000163810	ENST00000296125	D	0.86956	-2.19	1.63	-1.54	0.08584	Immunoglobulin E-set (1);Transglutaminase, N-terminal (1);Immunoglobulin-like fold (1);	5.526840	0.02235	U	0.065237	D	0.86994	0.6067	L	0.46157	1.445	0.09310	N	1	P;D	0.71674	0.749;0.998	B;P	0.56088	0.34;0.791	T	0.72414	-0.4301	10	0.45353	T	0.12	.	2.042	0.03552	0.2551:0.3859:0.0:0.359	.	82;82	P49221;B4YUQ1	TGM4_HUMAN;.	M	82	ENSP00000296125:T82M	ENSP00000296125:T82M	T	+	2	0	TGM4	44904236	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.323000	0.07997	-0.542000	0.06249	-1.391000	0.01154	ACG		0.617	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241	
NCBP2	22916	hgsc.bcm.edu	37	3	196664484	196664484	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr3:196664484C>T	ENST00000321256.5	-	3	389	c.296G>A	c.(295-297)cGg>cAg	p.R99Q	NCBP2_ENST00000452404.2_Missense_Mutation_p.R81Q|NCBP2_ENST00000427641.2_Missense_Mutation_p.R46Q|NCBP2_ENST00000467803.1_5'UTR|NCBP2_ENST00000447325.1_Missense_Mutation_p.R29Q|NCBP2-AS1_ENST00000447775.1_RNA|NCBP2_ENST00000422610.1_Missense_Mutation_p.R29Q	NM_007362.3	NP_031388.2	P52298	NCBP2_HUMAN	nuclear cap binding protein subunit 2, 20kDa	99	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of RNA export from nucleus (GO:0046833)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|snRNA export from nucleus (GO:0006408)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|RNA cap binding (GO:0000339)	p.R99Q(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.42e-24)|all cancers(36;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(49;4.13e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00551)		ATTTATGTACCGCATGGCGTT	0.493																																					p.R99Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G296A	3						.						116.0	106.0	110.0					3																	196664484		2203	4300	6503	198148881	SO:0001583	missense	22916	exon3			D59253	CCDS3323.1, CCDS46986.1	3q29	2013-02-12	2002-08-29		ENSG00000114503	ENSG00000114503		"""RNA binding motif (RRM) containing"""	7659	protein-coding gene	gene with protein product		605133	"""nuclear cap binding protein subunit 2, 20kD"""			7478990, 7651522, 8682299	Standard	NM_001042540		Approved	NIP1, CBP20, Cbc2	uc003fxd.1	P52298	OTTHUMG00000155520	ENST00000321256.5:c.296G>A	3.37:g.196664484C>T	ENSP00000326806:p.Arg99Gln	Somatic		Capture	SOLID	Phase_I	198148881	NM_007362	B2RE91|B4DMK7|E9PAR5|Q14924|Q2TS50	Missense_Mutation	SNP	ENST00000321256.5	37	CCDS3323.1	.	.	.	.	.	.	.	.	.	.	C	35	5.451308	0.96205	.	.	ENSG00000114503	ENST00000447325;ENST00000321256;ENST00000427641;ENST00000452404;ENST00000422610;ENST00000411704	T;T;T;T;T;T	0.74209	-0.82;2.44;-0.82;2.44;-0.82;-0.82	4.96	4.96	0.65561	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.057701	0.64402	N	0.000003	T	0.71273	0.3320	N	0.25201	0.72	0.80722	D	1	P;P;P	0.51449	0.872;0.945;0.862	B;P;B	0.50314	0.082;0.637;0.133	T	0.73665	-0.3911	10	0.49607	T	0.09	.	17.7697	0.88487	0.0:1.0:0.0:0.0	.	81;46;99	P52298-2;E9PAR5;P52298	.;.;NCBP2_HUMAN	Q	29;99;46;81;29;29	ENSP00000413518:R29Q;ENSP00000326806:R99Q;ENSP00000397619:R46Q;ENSP00000412785:R81Q;ENSP00000394105:R29Q;ENSP00000389315:R29Q	ENSP00000326806:R99Q	R	-	2	0	NCBP2	198148881	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.510000	0.81708	2.767000	0.95098	0.655000	0.94253	CGG		0.493	NCBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340470.2	NM_007362	
LRP6	4040	hgsc.bcm.edu	37	12	12300408	12300408	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr12:12300408A>G	ENST00000261349.4	-	15	3365	c.3289T>C	c.(3289-3291)Ttt>Ctt	p.F1097L	LRP6_ENST00000543091.1_Missense_Mutation_p.F1097L	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1097	Beta-propeller 4.				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)	p.F1097L(1)		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)				CCACTGAAAAAGAGGACCTCC	0.458																																					p.F1097L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3289C	12						.						136.0	139.0	138.0					12																	12300408		2203	4300	6503	12191675	SO:0001583	missense	4040	exon15			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.3289T>C	12.37:g.12300408A>G	ENSP00000261349:p.Phe1097Leu	Somatic		Capture	SOLID	Phase_I	12191675	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.917648	0.92249	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.96136	-3.92;-3.92	5.69	5.69	0.88448	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	U	0.000010	D	0.96482	0.8852	L	0.45744	1.44	0.80722	D	1	D;D	0.65815	0.995;0.989	D;P	0.74674	0.984;0.904	D	0.96102	0.9070	10	0.39692	T	0.17	.	15.9477	0.79806	1.0:0.0:0.0:0.0	.	1097;1097	F5H7J9;O75581	.;LRP6_HUMAN	L	1097	ENSP00000261349:F1097L;ENSP00000442472:F1097L	ENSP00000261349:F1097L	F	-	1	0	LRP6	12191675	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.179000	0.69175	0.460000	0.39030	TTT		0.458	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1		
LMNTD1	160492	hgsc.bcm.edu	37	12	25671789	25671789	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr12:25671789C>T	ENST00000282881.6	-	7	1215	c.1066G>A	c.(1066-1068)Gct>Act	p.A356T	IFLTD1_ENST00000413632.2_Missense_Mutation_p.A337T|IFLTD1_ENST00000445693.1_Missense_Mutation_p.A293T|IFLTD1_ENST00000539744.1_Missense_Mutation_p.A259T|IFLTD1_ENST00000458174.2_Missense_Mutation_p.A377T	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		356					cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)	p.A356T(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					CTGCCTCCAGCGGTGGATGTA	0.522											OREG0031252	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.A293T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G877A	12						.						142.0	128.0	133.0					12																	25671789		2203	4300	6503	25563056	SO:0001583	missense	160492	exon6																														ENST00000282881.6:c.1066G>A	12.37:g.25671789C>T	ENSP00000282881:p.Ala356Thr	Somatic	780	Capture	SOLID	Phase_I	25563056	NM_001145727	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	37	CCDS8704.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.370|0.370	-0.934556|-0.934556	0.02340|0.02340	.|.	.|.	ENSG00000152936|ENSG00000152936	ENST00000282881;ENST00000539744;ENST00000458174;ENST00000445693;ENST00000413632;ENST00000539523|ENST00000543629	T;T;T;T;T;T|.	0.23552|.	2.71;2.73;2.7;2.69;2.49;1.9|.	4.95|4.95	-9.9|-9.9	0.00461|0.00461	.|.	.|.	.|.	.|.	.|.	T|T	0.13841|0.13841	0.0335|0.0335	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	B;B;B;B|.	0.24963|.	0.115;0.115;0.115;0.07|.	B;B;B;B|.	0.21708|.	0.036;0.036;0.036;0.016|.	T|T	0.12400|0.12400	-1.0549|-1.0549	9|5	0.10902|.	T|.	0.67|.	-17.3179|-17.3179	0.5601|0.5601	0.00677|0.00677	0.3233:0.132:0.1706:0.3741|0.3233:0.132:0.1706:0.3741	.|.	293;377;337;356|.	Q8N9Z9-3;Q8N9Z9-5;Q8N9Z9-4;Q8N9Z9|.	.;.;.;ILFT1_HUMAN|.	T|H	356;259;377;293;337;73|130	ENSP00000282881:A356T;ENSP00000443132:A259T;ENSP00000407353:A377T;ENSP00000407043:A293T;ENSP00000393150:A337T;ENSP00000438160:A73T|.	ENSP00000282881:A356T|.	A|R	-|-	1|2	0|0	IFLTD1|IFLTD1	25563056|25563056	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-4.124000|-4.124000	0.00290|0.00290	-2.959000|-2.959000	0.00290|0.00290	-0.964000|-0.964000	0.02622|0.02622	GCT|CGC		0.522	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1		
RASAL1	8437	hgsc.bcm.edu	37	12	113545929	113545929	+	Silent	SNP	C	C	T	rs201065218	byFrequency	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr12:113545929C>T	ENST00000261729.5	-	15	1788	c.1473G>A	c.(1471-1473)gcG>gcA	p.A491A	RASAL1_ENST00000418411.2_5'UTR|RASAL1_ENST00000548055.1_Silent_p.A491A|RASAL1_ENST00000446861.3_Silent_p.A491A|RASAL1_ENST00000546530.1_Silent_p.A492A			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	491	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)	p.A491A(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						TCTGGGGGTCCGCGTGTTGGT	0.542													C|||	5	0.000998403	0.0023	0.0	5008	,	,		17375	0.0		0.0	False		,,,				2504	0.002				p.A491A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1473A	12						.						59.0	53.0	55.0					12																	113545929		2203	4300	6503	112030312	SO:0001819	synonymous_variant	8437	exon15			AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"""Pleckstrin homology (PH) domain containing"""	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.1473G>A	12.37:g.113545929C>T		Somatic		Capture	SOLID	Phase_I	112030312	NM_004658	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Silent	SNP	ENST00000261729.5	37	CCDS9165.1																																																																																				0.542	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658	
NIPA2	81614	hgsc.bcm.edu	37	15	23006736	23006736	+	Missense_Mutation	SNP	C	C	T	rs373772836		TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr15:23006736C>T	ENST00000337451.3	-	8	1180	c.568G>A	c.(568-570)Gcg>Acg	p.A190T	NIPA2_ENST00000398013.3_Missense_Mutation_p.A190T|NIPA2_ENST00000398014.2_Missense_Mutation_p.A190T|NIPA2_ENST00000359727.4_Missense_Mutation_p.A171T|NIPA2_ENST00000539711.2_Missense_Mutation_p.A171T	NM_030922.6	NP_112184.4	Q8N8Q9	NIPA2_HUMAN	non imprinted in Prader-Willi/Angelman syndrome 2	190						early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	magnesium ion transmembrane transporter activity (GO:0015095)	p.A171T(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(4)|skin(1)	15		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;1.48e-06)|Epithelial(43;1.44e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000353)		ACTGAAAACGCGCCGATTACA	0.517																																					p.A190T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G568A	15						.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	71.0	65.0	67.0		568,568,511,511,568,568	5.5	0.8	15		67	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense	NIPA2	NM_001008860.2,NM_001008892.2,NM_001008894.2,NM_001184888.1,NM_001184889.1,NM_030922.6	58,58,58,58,58,58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	190/361,190/361,171/342,171/342,190/361,190/361	23006736	1,13005	2203	4300	6503	20558177	SO:0001583	missense	81614	exon7			AY732242	CCDS73693.1, CCDS73694.1	15q11.2	2008-02-05			ENSG00000140157	ENSG00000140157			17044	protein-coding gene	gene with protein product		608146				14508708	Standard	NM_001008860		Approved		uc001yuz.3	Q8N8Q9	OTTHUMG00000129101	ENST00000337451.3:c.568G>A	15.37:g.23006736C>T	ENSP00000337618:p.Ala190Thr	Somatic		Capture	SOLID	Phase_I	20558177	NM_001008860	F8W7Y8|Q96F03|Q9BVS2	Missense_Mutation	SNP	ENST00000337451.3	37	CCDS10010.1	.	.	.	.	.	.	.	.	.	.	C	15.66	2.899265	0.52227	0.0	1.16E-4	ENSG00000140157	ENST00000337451;ENST00000398014;ENST00000359727;ENST00000539711;ENST00000398013	D;D;D	0.91180	-2.8;-2.8;-2.8	5.54	5.54	0.83059	.	0.045801	0.85682	D	0.000000	D	0.89739	0.6802	L	0.49350	1.555	0.80722	D	1	B;P	0.43578	0.301;0.811	B;B	0.41466	0.103;0.358	D	0.90634	0.4569	10	0.72032	D	0.01	-6.2548	19.8379	0.96666	0.0:1.0:0.0:0.0	.	171;190	F8W7Y8;Q8N8Q9	.;NIPA2_HUMAN	T	190;190;171;190;171	ENSP00000337618:A190T;ENSP00000381096:A190T;ENSP00000352762:A171T	ENSP00000337618:A190T	A	-	1	0	NIPA2	20558177	1.000000	0.71417	0.814000	0.32528	0.008000	0.06430	7.713000	0.84693	2.765000	0.95021	0.655000	0.94253	GCG		0.517	NIPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251137.1	NM_030922	
FBXW7	55294	hgsc.bcm.edu	37	4	153244092	153244092	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr4:153244092G>A	ENST00000281708.4	-	12	3294	c.2065C>T	c.(2065-2067)Cgg>Tgg	p.R689W	FBXW7_ENST00000603548.1_Missense_Mutation_p.R689W|FBXW7_ENST00000603841.1_Missense_Mutation_p.R689W|RP11-461L13.3_ENST00000603766.1_lincRNA|FBXW7_ENST00000263981.5_Missense_Mutation_p.R609W|FBXW7_ENST00000393956.3_Missense_Mutation_p.R513W|FBXW7_ENST00000296555.5_Missense_Mutation_p.R571W	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	689					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R689W(10)|p.R450W(3)|p.R609W(3)|p.R571W(1)|p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				GTCCCATTCCGACTCCCAACT	0.478			"""Mis, N, D, F"""		"""colorectal, endometrial, T-ALL"""																																p.R609W			Rec	yes		4	4q31.3	55294	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"""		"""E, L"""	FBXW7,large_intestine,colon,Substitution - Missense,0	.	18	Substitution - Missense(17)|Unknown(1)	large_intestine(11)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)	c.C1825T	4						.						172.0	167.0	168.0					4																	153244092		2203	4300	6503	153463542	SO:0001583	missense	55294	exon11			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	16712	protein-coding gene	gene with protein product	"""archipelago homolog (Drosophila)"""	606278	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"", ""F-box and WD repeat domain containing 7"""			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.2065C>T	4.37:g.153244092G>A	ENSP00000281708:p.Arg689Trp	Somatic		Capture	SOLID	Phase_I	153463542	NM_018315	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	G	10.88	1.475565	0.26511	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.18657	2.2;2.2;2.2;2.2	5.67	5.67	0.87782	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.50188	0.1601	M	0.82923	2.615	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.53892	-0.8374	10	0.87932	D	0	-15.04	14.5904	0.68359	0.0:0.0:0.854:0.146	.	513;689;571;609	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	W	689;571;609;513	ENSP00000281708:R689W;ENSP00000296555:R571W;ENSP00000263981:R609W;ENSP00000377528:R513W	ENSP00000263981:R609W	R	-	1	2	FBXW7	153463542	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.906000	0.56340	2.681000	0.91329	0.655000	0.94253	CGG		0.478	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1		
MAP2	4133	hgsc.bcm.edu	37	2	210559909	210559909	+	Silent	SNP	A	A	G			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr2:210559909A>G	ENST00000360351.4	+	7	3521	c.3015A>G	c.(3013-3015)tcA>tcG	p.S1005S	MAP2_ENST00000199940.6_Intron|MAP2_ENST00000447185.1_Silent_p.S1001S|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000392194.1_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1005					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)	p.S1005S(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	AAGATTTGTCAATACCAACAG	0.428																																					p.S1005S	Pancreas(27;423 979 28787 29963)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A3015G	2						.						89.0	86.0	87.0					2																	210559909		2203	4300	6503	210268154	SO:0001819	synonymous_variant	4133	exon7				CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"""A-kinase anchor proteins"""	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.3015A>G	2.37:g.210559909A>G		Somatic		Capture	SOLID	Phase_I	210268154	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Silent	SNP	ENST00000360351.4	37	CCDS2384.1																																																																																				0.428	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538	
CAD	790	hgsc.bcm.edu	37	2	27448699	27448699	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr2:27448699G>A	ENST00000403525.1	+	12	1891	c.1747G>A	c.(1747-1749)Gcc>Acc	p.A583T	CAD_ENST00000264705.4_Missense_Mutation_p.A583T			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)	p.A583T(1)		NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCAGCTTTTGCCCATACCAG	0.577																																					p.A583T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1747A	2						.						112.0	105.0	108.0					2																	27448699		2203	4300	6503	27302203	SO:0001583	missense	790	exon12			D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.1747G>A	2.37:g.27448699G>A	ENSP00000384510:p.Ala583Thr	Somatic		Capture	SOLID	Phase_I	27302203	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	37		.	.	.	.	.	.	.	.	.	.	G	20.9	4.069487	0.76301	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	D;D	0.97161	-4.27;-4.27	5.65	5.65	0.86999	ATP-grasp fold (1);ATP-grasp fold, subdomain 1 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);	0.097389	0.64402	D	0.000001	D	0.96503	0.8859	L	0.58969	1.84	0.53688	D	0.999971	P;B	0.48640	0.913;0.053	P;B	0.49528	0.614;0.048	D	0.96088	0.9059	10	0.59425	D	0.04	4.0728	12.7162	0.57117	0.0797:0.0:0.9203:0.0	.	583;583	F8VPD4;P27708	.;PYR1_HUMAN	T	583	ENSP00000264705:A583T;ENSP00000384510:A583T	ENSP00000264705:A583T	A	+	1	0	CAD	27302203	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	7.546000	0.82137	2.683000	0.91414	0.456000	0.33151	GCC		0.577	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1		
CCDC88A	55704	hgsc.bcm.edu	37	2	55616020	55616020	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr2:55616020T>C	ENST00000436346.1	-	3	1008	c.167A>G	c.(166-168)aAt>aGt	p.N56S	CCDC88A_ENST00000336838.6_Missense_Mutation_p.N56S|CCDC88A_ENST00000263630.8_Missense_Mutation_p.N56S|CCDC88A_ENST00000413716.2_Missense_Mutation_p.N56S	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	56					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)	p.N56S(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						CAATTTAGGATTACTGTAAGA	0.214																																					p.N56S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A167G	2						.						58.0	61.0	60.0					2																	55616020		2202	4281	6483	55469524	SO:0001583	missense	55704	exon3			AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"""Galpha-interacting vesicle-associated protein"", ""Akt-phosphorylation enhancer"", ""girdin"", ""girders of actin filaments"""	609736	"""KIAA1212"""	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.167A>G	2.37:g.55616020T>C	ENSP00000410608:p.Asn56Ser	Somatic		Capture	SOLID	Phase_I	55469524	NM_001135597	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Missense_Mutation	SNP	ENST00000436346.1	37		.	.	.	.	.	.	.	.	.	.	T	23.9	4.468176	0.84533	.	.	ENSG00000115355	ENST00000336838;ENST00000263630;ENST00000436346;ENST00000413716	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.97	5.97	0.96955	.	0.000000	0.47455	U	0.000226	T	0.63271	0.2497	M	0.66939	2.045	0.80722	D	1	P;D;D	0.69078	0.872;0.997;0.997	P;D;D	0.70716	0.81;0.967;0.97	T	0.65894	-0.6057	10	0.72032	D	0.01	-23.0439	16.1075	0.81236	0.0:0.0:0.0:1.0	.	56;56;56	B7ZM78;Q3V6T2-2;Q3V6T2-3	.;.;.	S	56	ENSP00000338728:N56S;ENSP00000263630:N56S;ENSP00000410608:N56S;ENSP00000404431:N56S	ENSP00000263630:N56S	N	-	2	0	CCDC88A	55469524	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.867000	0.69597	2.285000	0.76669	0.528000	0.53228	AAT		0.214	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571	
SPRED2	200734	hgsc.bcm.edu	37	2	65540828	65540828	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr2:65540828G>A	ENST00000356388.4	-	6	1253	c.1064C>T	c.(1063-1065)tCg>tTg	p.S355L	SPRED2_ENST00000443619.2_Missense_Mutation_p.S352L	NM_181784.2	NP_861449.2	Q7Z698	SPRE2_HUMAN	sprouty-related, EVH1 domain containing 2	355	SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|regulation of protein deacetylation (GO:0090311)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|stem cell factor receptor binding (GO:0005173)	p.S355L(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(7)|ovary(2)|upper_aerodigestive_tract(3)	34						CTCGGGGTCCGACATACAGTG	0.607																																					p.S355L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1064T	2						.						93.0	88.0	90.0					2																	65540828		2203	4300	6503	65394332	SO:0001583	missense	200734	exon6			AF052178	CCDS33211.1, CCDS46308.1	2p14	2003-06-02			ENSG00000198369	ENSG00000198369			17722	protein-coding gene	gene with protein product		609292					Standard	NM_181784		Approved	Spred-2, FLJ21897, FLJ31917	uc002sdr.4	Q7Z698	OTTHUMG00000152737	ENST00000356388.4:c.1064C>T	2.37:g.65540828G>A	ENSP00000348753:p.Ser355Leu	Somatic		Capture	SOLID	Phase_I	65394332	NM_181784	A1L3V4|B7Z5K7|D6W5F7|E9PEP0|Q2NKX6	Missense_Mutation	SNP	ENST00000356388.4	37	CCDS33211.1	.	.	.	.	.	.	.	.	.	.	G	35	5.440206	0.96168	.	.	ENSG00000198369	ENST00000356388;ENST00000443619;ENST00000452315	T;T;T	0.65549	-0.16;-0.16;-0.16	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.82999	0.5159	M	0.87682	2.9	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.85473	0.1174	10	0.87932	D	0	-11.3638	19.6373	0.95740	0.0:0.0:1.0:0.0	.	352;355	E9PEP0;Q7Z698	.;SPRE2_HUMAN	L	355;352;370	ENSP00000348753:S355L;ENSP00000393697:S352L;ENSP00000390595:S370L	ENSP00000348753:S355L	S	-	2	0	SPRED2	65394332	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.636000	0.89361	0.655000	0.94253	TCG		0.607	SPRED2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327632.1		
ABCA12	26154	hgsc.bcm.edu	37	2	215819945	215819945	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr2:215819945T>A	ENST00000272895.7	-	43	6593	c.6374A>T	c.(6373-6375)aAg>aTg	p.K2125M	AC072062.1_ENST00000607412.1_RNA|ABCA12_ENST00000389661.4_Missense_Mutation_p.K1807M	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	2125					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.K2125M(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		AGGCTTTTCCTTGGAAAGAAA	0.358																																					p.K2125M	Ovarian(66;664 1488 5121 34295)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A6374T	2						.						73.0	67.0	69.0					2																	215819945		2203	4300	6503	215528190	SO:0001583	missense	26154	exon43			AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"""ATP binding cassette transporters / subfamily A"""	14637	protein-coding gene	gene with protein product		607800	"""ichthyosis congenita II, lamellar ichthyosis B"""	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.6374A>T	2.37:g.215819945T>A	ENSP00000272895:p.Lys2125Met	Somatic		Capture	SOLID	Phase_I	215528190	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	T	14.57	2.574051	0.45902	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.83419	-1.72;-1.72	5.97	5.97	0.96955	.	0.076494	0.56097	D	0.000030	D	0.84343	0.5451	L	0.29908	0.895	0.80722	D	1	D;B	0.64830	0.994;0.257	D;B	0.64410	0.925;0.103	D	0.85149	0.0985	10	0.54805	T	0.06	.	11.5185	0.50536	0.1337:0.0:0.0:0.8663	.	2125;1807	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	M	2125;1807	ENSP00000272895:K2125M;ENSP00000374312:K1807M	ENSP00000272895:K2125M	K	-	2	0	ABCA12	215528190	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.363000	0.44178	2.285000	0.76669	0.528000	0.53228	AAG		0.358	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076	
GLIS3	169792	hgsc.bcm.edu	37	9	4118717	4118717	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr9:4118717A>T	ENST00000324333.10	-	3	489	c.296T>A	c.(295-297)cTt>cAt	p.L99H	GLIS3_ENST00000381971.3_Missense_Mutation_p.L254H	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	99	Ser-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|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)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.L99H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		CCCGGGAGGAAGGCTAAGGAG	0.547																																					p.L99H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T296A	9						.						160.0	144.0	150.0					9																	4118717		2203	4300	6503	4108717	SO:0001583	missense	169792	exon3			BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"""Zinc fingers, C2H2-type"""	28510	protein-coding gene	gene with protein product		610192	"""zinc finger protein 515"""	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000324333.10:c.296T>A	9.37:g.4118717A>T	ENSP00000325494:p.Leu99His	Somatic		Capture	SOLID	Phase_I	4108717	NM_152629	B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000324333.10	37	CCDS6451.1	.	.	.	.	.	.	.	.	.	.	A	18.08	3.544948	0.65198	.	.	ENSG00000107249	ENST00000324333;ENST00000381971	T;T	0.14266	2.52;2.52	5.59	5.59	0.84812	.	0.147317	0.25674	N	0.029054	T	0.27205	0.0667	M	0.65498	2.005	0.25821	N	0.98429	D;D	0.63880	0.993;0.988	P;P	0.53360	0.724;0.533	T	0.14254	-1.0479	10	0.87932	D	0	.	12.8398	0.57794	0.8643:0.1357:0.0:0.0	.	254;99	Q8NEA6-2;Q8NEA6	.;GLIS3_HUMAN	H	99;254	ENSP00000325494:L99H;ENSP00000371398:L254H	ENSP00000325494:L99H	L	-	2	0	GLIS3	4108717	1.000000	0.71417	0.998000	0.56505	0.964000	0.63967	5.890000	0.69774	2.128000	0.65567	0.533000	0.62120	CTT		0.547	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629	
TUBA3C	7278	hgsc.bcm.edu	37	13	19748092	19748092	+	Missense_Mutation	SNP	G	G	A	rs150743792	byFrequency	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr13:19748092G>A	ENST00000400113.3	-	5	1368	c.1264C>T	c.(1264-1266)Cgc>Tgc	p.R422C		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	422					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.R422G(1)|p.R422C(1)		NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		AGGTCCTCGCGGGCCTCAGAG	0.582													G|||	2	0.000399361	0.0	0.0	5008	,	,		16782	0.001		0.0	False		,,,				2504	0.001				p.R422C												.	.	2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	c.C1264T	13						.	G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	135.0	134.0	134.0		1264	1.2	1.0	13	dbSNP_134	134	1,8599	1.2+/-3.3	0,1,4299	no	missense	TUBA3C	NM_006001.2	180	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	422/451	19748092	2,13004	2203	4300	6503	18646092	SO:0001583	missense	7278	exon5			AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"""Tubulins"""	12408	protein-coding gene	gene with protein product		602528	"""tubulin, alpha 2"""	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.1264C>T	13.37:g.19748092G>A	ENSP00000382982:p.Arg422Cys	Somatic		Capture	SOLID	Phase_I	18646092	NM_006001	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Missense_Mutation	SNP	ENST00000400113.3	37	CCDS9284.1	.	.	.	.	.	.	.	.	.	.	g	6.710	0.499778	0.12762	2.27E-4	1.16E-4	ENSG00000198033	ENST00000400113	D	0.85339	-1.97	1.21	1.21	0.21127	.	0.000000	0.42964	U	0.000632	D	0.86965	0.6060	.	.	.	0.50171	D	0.999854	.	.	.	.	.	.	D	0.86309	0.1685	7	0.87932	D	0	.	8.3447	0.32266	0.0:0.0:1.0:0.0	.	.	.	.	C	422	ENSP00000382982:R422C	ENSP00000382982:R422C	R	-	1	0	TUBA3C	18646092	1.000000	0.71417	0.991000	0.47740	0.219000	0.24729	3.313000	0.51935	0.976000	0.38417	0.184000	0.17185	CGC		0.582	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001	
PGBD3	267004	hgsc.bcm.edu	37	10	50723608	50723608	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr10:50723608C>T	ENST00000374127.3	-	2	1754	c.1553G>A	c.(1552-1554)cGt>cAt	p.R518H	ERCC6-PGBD3_ENST00000515869.1_Missense_Mutation_p.R986H|PGBD3_ENST00000603152.1_Missense_Mutation_p.R986H|ERCC6_ENST00000355832.5_Intron|PGBD3_ENST00000508005.2_Missense_Mutation_p.R518H|ERCC6-PGBD3_ENST00000447839.2_Missense_Mutation_p.R986H	NM_170753.2	NP_736609.2	Q8N328	PGBD3_HUMAN	piggyBac transposable element derived 3	518								p.R518H(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(16)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	33						GCATACCACACGTCGACGAAA	0.438																																					p.R518H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1553A	10						.						152.0	133.0	139.0					10																	50723608		2203	4300	6503	50393614	SO:0001583	missense	267004	exon2			AK074682	CCDS7230.1	10q11	2011-03-24			ENSG00000243251	ENSG00000243251			19400	protein-coding gene	gene with protein product							Standard	NM_170753		Approved	FLJ90201		Q8N328	OTTHUMG00000018193	ENST00000374127.3:c.1553G>A	10.37:g.50723608C>T	ENSP00000363242:p.Arg518His	Somatic		Capture	SOLID	Phase_I	50393614	NM_170753	B3KQC4|Q5W0M0|Q6PIH0	Missense_Mutation	SNP	ENST00000374127.3	37	CCDS7230.1	.	.	.	.	.	.	.	.	.	.	C	11.61	1.691288	0.30052	.	.	ENSG00000243251;ENSG00000243251;ENSG00000258838;ENSG00000258838	ENST00000374127;ENST00000508005;ENST00000515869;ENST00000447839	T;T;T;T	0.14640	2.49;2.49;3.36;3.36	0.706	-0.329	0.12686	.	.	.	.	.	T	0.06917	0.0176	N	0.08118	0	0.09310	N	1	D;D	0.60160	0.987;0.987	B;P	0.47299	0.102;0.543	T	0.29366	-1.0014	8	0.16420	T	0.52	-26.3944	.	.	.	.	986;518	E7EV46;Q8N328	.;PGBD3_HUMAN	H	518;518;986;986	ENSP00000363242:R518H;ENSP00000426963:R518H;ENSP00000423550:R986H;ENSP00000387966:R986H	ENSP00000387966:R986H	R	-	2	0	PGBD3;RP11-123B3.6	50393614	0.906000	0.30813	0.001000	0.08648	0.969000	0.65631	-0.064000	0.11636	-0.170000	0.10816	0.491000	0.48974	CGT		0.438	PGBD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047988.1		
KCNMA1	3778	hgsc.bcm.edu	37	10	78704719	78704719	+	Missense_Mutation	SNP	G	G	A	rs201192736		TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr10:78704719G>A	ENST00000286628.8	-	23	2713	c.2714C>T	c.(2713-2715)aCg>aTg	p.T905M	RP11-443A13.5_ENST00000600782.1_RNA|KCNMA1_ENST00000372440.1_Missense_Mutation_p.T847M|RP11-443A13.5_ENST00000598613.1_RNA|KCNMA1_ENST00000404857.1_Missense_Mutation_p.T888M|KCNMA1_ENST00000406533.3_Missense_Mutation_p.T909M|KCNMA1_ENST00000286627.5_Missense_Mutation_p.T847M|RP11-443A13.5_ENST00000426234.1_RNA|RP11-443A13.5_ENST00000608791.1_RNA|RP11-443A13.5_ENST00000458661.2_RNA|KCNMA1_ENST00000354353.5_Missense_Mutation_p.T908M|KCNMA1_ENST00000372443.1_Missense_Mutation_p.T847M|KCNMA1_ENST00000404771.3_Missense_Mutation_p.T905M	NM_001161352.1	NP_001154824.1	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	905					blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)	p.T847M(1)		breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	ACTTAATGGCGTACCCTTTGG	0.453																																					p.T888M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2663T	10						.						88.0	74.0	79.0					10																	78704719		2203	4300	6503	78374725	SO:0001583	missense	3778	exon23			U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6284	protein-coding gene	gene with protein product	"""BK channel alpha subunit"""	600150		SLO		7987297, 16382103	Standard	NM_002247		Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286628.8:c.2714C>T	10.37:g.78704719G>A	ENSP00000286628:p.Thr905Met	Somatic		Capture	SOLID	Phase_I	78374725	NM_001161353	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	Missense_Mutation	SNP	ENST00000286628.8	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.5|22.5	4.303418|4.303418	0.81136|0.81136	.|.	.|.	ENSG00000156113|ENSG00000156113	ENST00000372403|ENST00000372440;ENST00000372408;ENST00000372437;ENST00000457953;ENST00000404771;ENST00000372443;ENST00000286627;ENST00000286628;ENST00000406533;ENST00000354353;ENST00000404857;ENST00000412708	.|T;T;T;T;T;T;T;T;T	.|0.51574	.|0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7;0.7	5.74|5.74	5.74|5.74	0.90152|0.90152	.|NAD(P)-binding domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.52240|0.52240	0.1722|0.1722	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D;D;D	.|0.76494	.|0.999;0.992;0.996;0.998;0.996;0.978;0.999;0.996	.|D;P;P;P;P;P;D;P	.|0.72338	.|0.977;0.731;0.862;0.899;0.862;0.608;0.91;0.815	T|T	0.63377|0.63377	-0.6651|-0.6651	5|10	.|0.87932	.|D	.|0	-9.8039|-9.8039	19.9196|19.9196	0.97082|0.97082	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|876;850;888;905;847;658;908;847	.|Q12791-4;B7ZMF5;Q12791-2;Q12791;Q12791-5;C9JFZ9;F8WA96;Q5SVJ7	.|.;.;.;KCMA1_HUMAN;.;.;.;.	C|M	798|847;784;840;879;842;847;847;879;909;908;888;658	.|ENSP00000361517:T847M;ENSP00000361485:T784M;ENSP00000361514:T840M;ENSP00000396608:T879M;ENSP00000361520:T847M;ENSP00000286627:T847M;ENSP00000385552:T909M;ENSP00000346321:T908M;ENSP00000385806:T888M	.|ENSP00000286627:T847M	R|T	-|-	1|2	0|0	KCNMA1|KCNMA1	78374725|78374725	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	9.758000|9.758000	0.98927|0.98927	2.708000|2.708000	0.92522|0.92522	0.650000|0.650000	0.86243|0.86243	CGC|ACG		0.453	KCNMA1-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000048885.3	NM_002247	
TECTB	6975	hgsc.bcm.edu	37	10	114063040	114063040	+	Silent	SNP	C	C	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	WXS	.			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr10:114063040C>T	ENST00000369422.3	+	10	960	c.960C>T	c.(958-960)atC>atT	p.I320I		NM_058222.1	NP_478129.1	Q96PL2	TECTB_HUMAN	tectorin beta	320						anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.I320I(1)		kidney(2)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	19		Colorectal(252;0.198)		Epithelial(162;0.0143)|all cancers(201;0.0242)		ACCACCTCATCATGATGTTGG	0.493																																					p.I320I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C960T	10						.						245.0	205.0	219.0					10																	114063040		2203	4300	6503	114053030	SO:0001819	synonymous_variant	6975	exon10			AF312827	CCDS7571.1	10q25-q26	2005-06-09			ENSG00000119913	ENSG00000119913			11721	protein-coding gene	gene with protein product		602653				9079715	Standard	NM_058222		Approved		uc001kzr.1	Q96PL2	OTTHUMG00000019056	ENST00000369422.3:c.960C>T	10.37:g.114063040C>T		Somatic		Capture	SOLID	Phase_I	114053030	NM_058222	Q5VW53	Silent	SNP	ENST00000369422.3	37	CCDS7571.1																																																																																				0.493	TECTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050381.1	NM_058222	
CD180	4064	hgsc.bcm.edu	37	5	66479890	66479890	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	TCGA-AA-3524-01A-02W-0831-10	TCGA-AA-3524-10A-01W-0831-10	g.chr5:66479890C>T	ENST00000256447.4	-	3	938	c.781G>A	c.(781-783)Gaa>Aaa	p.E261K		NM_005582.2	NP_005573.2	Q99467	CD180_HUMAN	CD180 molecule	261					B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.E261K(1)		cervix(1)|endometrium(2)|kidney(7)|large_intestine(12)|liver(1)|lung(8)|ovary(1)|stomach(2)	34		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)		CTAATATCTTCGTCATCAATG	0.448																																					p.E261K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G781A	5						.						95.0	98.0	97.0					5																	66479890		2203	4300	6503	66515646	SO:0001583	missense	4064	exon3			D83597	CCDS3992.1	5q12	2008-02-05	2006-03-28	2005-06-07	ENSG00000134061	ENSG00000134061		"""CD molecules"""	6726	protein-coding gene	gene with protein product		602226	"""lymphocyte antigen 64 (mouse) homolog, radioprotective, 105kD"", ""CD180 antigen"""	LY64		9763566, 8975706	Standard	NM_005582		Approved	RP105, Ly78	uc003juy.2	Q99467	OTTHUMG00000131229	ENST00000256447.4:c.781G>A	5.37:g.66479890C>T	ENSP00000256447:p.Glu261Lys	Somatic		Capture	SOLID	Phase_I	66515646	NM_005582	B2R7Z7|Q32MM5	Missense_Mutation	SNP	ENST00000256447.4	37	CCDS3992.1	.	.	.	.	.	.	.	.	.	.	C	0.155	-1.087123	0.01873	.	.	ENSG00000134061	ENST00000256447	T	0.35789	1.29	5.25	-1.51	0.08664	.	1.209820	0.05713	N	0.596369	T	0.15176	0.0366	N	0.11064	0.09	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20571	-1.0271	10	0.05959	T	0.93	.	4.5845	0.12275	0.1247:0.4615:0.2222:0.1917	.	261	Q99467	CD180_HUMAN	K	261	ENSP00000256447:E261K	ENSP00000256447:E261K	E	-	1	0	CD180	66515646	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.300000	0.08243	-0.525000	0.06391	-0.823000	0.03104	GAA		0.448	CD180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253973.2	NM_005582	
