#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
TRIM51	84767	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	55655604	55655604	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr11:55655604C>T	ENST00000449290.2	+	4	696	c.604C>T	c.(604-606)Cga>Tga	p.R202*	TRIM51_ENST00000244891.3_Nonsense_Mutation_p.R59*	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	202						intracellular (GO:0005622)	zinc ion binding (GO:0008270)										GGAAAGGCTGCGAAAGGAGGG	0.433																																																0													63.0	60.0	61.0					11																	55655604		2201	4296	6497	SO:0001587	stop_gained	84767			BC005014		11p11	2013-01-09	2012-05-18	2012-05-18	ENSG00000124900	ENSG00000124900		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19023	protein-coding gene	gene with protein product			"""SPRY domain containing 5"""	SPRYD5			Standard	NM_032681		Approved	TRIM51A	uc010rip.2	Q9BSJ1	OTTHUMG00000156437	ENST00000449290.2:c.604C>T	11.37:g.55655604C>T	ENSP00000395086:p.Arg202*		A6NMG2	Nonsense_Mutation	SNP	ENST00000449290.2	37		.	.	.	.	.	.	.	.	.	.	.	9.031	0.987390	0.18889	.	.	ENSG00000124900	ENST00000449290;ENST00000244891	.	.	.	0.757	-1.51	0.08664	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	.	2.2227	0.03976	0.326:0.3465:0.3275:0.0	.	.	.	.	X	202;59	.	ENSP00000244891:R59X	R	+	1	2	SPRYD5	55412180	0.004000	0.15560	0.000000	0.03702	0.340000	0.28889	-0.452000	0.06787	-1.096000	0.03046	0.152000	0.16155	CGA		0.433	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681		22	42	22	42
PRICKLE1	144165	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	42858963	42858963	+	Silent	SNP	A	A	G			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr12:42858963A>G	ENST00000455697.1	-	7	1158	c.873T>C	c.(871-873)tgT>tgC	p.C291C	PRICKLE1_ENST00000445766.2_Silent_p.C291C|PRICKLE1_ENST00000552240.1_Silent_p.C291C|RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000548696.1_Silent_p.C291C|PRICKLE1_ENST00000345127.3_Silent_p.C291C	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	291	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.C291C(1)		NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		GAAGGAAGGGACATCCCAACA	0.522																																																1	Substitution - coding silent(1)	large_intestine(1)											84.0	84.0	84.0					12																	42858963		2203	4300	6503	SO:0001819	synonymous_variant	144165			AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"""prickle-like 1 (Drosophila)"""			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.873T>C	12.37:g.42858963A>G			Q14C83|Q71QF8|Q96N00	Silent	SNP	ENST00000455697.1	37	CCDS8742.1																																																																																				0.522	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1			19	27	19	27
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7578394	7578394	+	Missense_Mutation	SNP	T	T	C			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr17:7578394T>C	ENST00000269305.4	-	5	725	c.536A>G	c.(535-537)cAt>cGt	p.H179R	TP53_ENST00000574684.1_5'UTR|TP53_ENST00000455263.2_Missense_Mutation_p.H179R|TP53_ENST00000359597.4_Missense_Mutation_p.H179R|TP53_ENST00000445888.2_Missense_Mutation_p.H179R|TP53_ENST00000420246.2_Missense_Mutation_p.H179R|TP53_ENST00000413465.2_Missense_Mutation_p.H179R	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	179	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		H -> D (in sporadic cancers; somatic mutation).|H -> L (in sporadic cancers; somatic mutation).|H -> N (in sporadic cancers; somatic mutation).|H -> P (in sporadic cancers; somatic mutation).|H -> Q (in sporadic cancers; somatic mutation).|H -> R (in sporadic cancers; somatic mutation).|H -> Y (in LFS; germline mutation and in sporadic cancers; somatic mutation).|HH -> QS (in a sporadic cancer; 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.H179R(108)|p.H179L(43)|p.P177_C182delPHHERC(8)|p.0?(8)|p.H47L(4)|p.H86L(4)|p.C176_R181delCPHHER(3)|p.R174fs*24(3)|p.H179P(3)|p.H178_S183delHHERCS(3)|p.R175_E180delRCPHHE(3)|p.P177fs*3(2)|p.V173fs*59(2)|p.H86R(2)|p.H47R(2)|p.R174fs*1(2)|p.H179fs*68(1)|p.C176fs*65(1)|p.P177_H179delPHH(1)|p.V173fs*23(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.H46_S51delHHERCS(1)|p.H178fs*6(1)|p.P177_E180delPHHE(1)|p.R42fs*24(1)|p.H85_S90delHHERCS(1)|p.E171fs*1(1)|p.R174fs*3(1)|p.E171fs*61(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)	GCAGCGCTCATGGTGGGGGCA	0.642		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	217	Substitution - Missense(166)|Deletion - In frame(24)|Deletion - Frameshift(18)|Whole gene deletion(8)|Complex - deletion inframe(1)	lung(35)|breast(32)|large_intestine(29)|upper_aerodigestive_tract(26)|oesophagus(21)|ovary(21)|central_nervous_system(16)|haematopoietic_and_lymphoid_tissue(8)|urinary_tract(6)|pancreas(6)|liver(5)|bone(4)|biliary_tract(3)|cervix(1)|stomach(1)|endometrium(1)|salivary_gland(1)|skin(1)											47.0	47.0	47.0					17																	7578394		2203	4300	6503	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.536A>G	17.37:g.7578394T>C	ENSP00000269305:p.His179Arg		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.694391	0.88830	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99909	-7.87;-7.87;-7.87;-7.87;-7.87;-7.87;-7.87;-7.87	5.47	5.47	0.80525	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.048592	0.85682	D	0.000000	D	0.99917	0.9961	M	0.92507	3.315	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.989;1.0;0.985;1.0;0.995;1.0;0.996	D;D;D;D;D;D;D	0.97110	0.929;0.996;0.912;1.0;0.985;0.995;0.937	D	0.95874	0.8893	10	0.87932	D	0	-15.4889	13.8032	0.63214	0.0:0.0:0.0:1.0	.	140;179;179;86;179;179;179	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	R	179;179;179;179;179;179;168;86;47;86;47	ENSP00000410739:H179R;ENSP00000352610:H179R;ENSP00000269305:H179R;ENSP00000398846:H179R;ENSP00000391127:H179R;ENSP00000391478:H179R;ENSP00000425104:H47R;ENSP00000423862:H86R	ENSP00000269305:H179R	H	-	2	0	TP53	7519119	1.000000	0.71417	0.945000	0.38365	0.856000	0.48823	6.263000	0.72521	2.208000	0.71279	0.460000	0.39030	CAT		0.642	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		45	15	45	15
PSMD12	5718	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	65341917	65341917	+	Silent	SNP	T	T	A			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr17:65341917T>A	ENST00000356126.3	-	8	959	c.852A>T	c.(850-852)tcA>tcT	p.S284S	PSMD12_ENST00000357146.4_Silent_p.S264S	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	284	PCI.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|large_intestine(4)|lung(6)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)					GAACCAAATCTGACTGTTCAT	0.358																																																0													147.0	134.0	138.0					17																	65341917		2203	4300	6503	SO:0001819	synonymous_variant	5718			AB003103	CCDS11669.1, CCDS11670.1	17q24.3	2008-05-22			ENSG00000197170	ENSG00000197170		"""Proteasome (prosome, macropain) subunits"""	9557	protein-coding gene	gene with protein product		604450				9426256	Standard	NM_002816		Approved	p55, Rpn5	uc002jfy.3	O00232	OTTHUMG00000140376	ENST00000356126.3:c.852A>T	17.37:g.65341917T>A			A6NP15|Q53HA2|Q6P053	Silent	SNP	ENST00000356126.3	37	CCDS11669.1																																																																																				0.358	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871		27	38	27	38
LAMA3	3909	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	21425086	21425086	+	Silent	SNP	T	T	G			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr18:21425086T>G	ENST00000313654.9	+	30	3958	c.3717T>G	c.(3715-3717)ctT>ctG	p.L1239L	LAMA3_ENST00000399516.3_Silent_p.L1239L	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1239	Domain IV 1 (domain IV B).				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GCTTTTACCTTGAGTGAGTAT	0.493																																																0													116.0	112.0	113.0					18																	21425086		1939	4126	6065	SO:0001819	synonymous_variant	3909			L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.3717T>G	18.37:g.21425086T>G			B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																				0.493	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		16	20	16	20
RERE	473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	8421423	8421423	+	Missense_Mutation	SNP	A	A	G			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr1:8421423A>G	ENST00000337907.3	-	19	2778	c.2144T>C	c.(2143-2145)aTc>aCc	p.I715T	RERE_ENST00000377464.1_Missense_Mutation_p.I447T|RERE_ENST00000476556.1_Missense_Mutation_p.I161T|RERE_ENST00000400908.2_Missense_Mutation_p.I715T|RERE_ENST00000400907.2_Intron	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	715					chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		GGGGCTGGGGATGCTCGGGGA	0.627																																																0													104.0	100.0	101.0					1																	8421423		2203	4300	6503	SO:0001583	missense	473			AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"""GATA zinc finger domain containing"""	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.2144T>C	1.37:g.8421423A>G	ENSP00000338629:p.Ile715Thr		O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation	SNP	ENST00000337907.3	37	CCDS95.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.702658	0.88924	.	.	ENSG00000142599	ENST00000337907;ENST00000377464;ENST00000476556;ENST00000400908	T;T;T;T	0.64991	-0.13;0.79;2.24;-0.13	5.6	5.6	0.85130	.	.	.	.	.	T	0.73869	0.3642	M	0.65975	2.015	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.67725	0.932;0.953	T	0.70215	-0.4933	9	0.13853	T	0.58	-21.0673	14.9577	0.71131	1.0:0.0:0.0:0.0	.	447;715	B1AKN3;Q9P2R6	.;RERE_HUMAN	T	715;447;161;715	ENSP00000338629:I715T;ENSP00000366684:I447T;ENSP00000422246:I161T;ENSP00000383700:I715T	ENSP00000338629:I715T	I	-	2	0	RERE	8344010	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.275000	0.95738	2.143000	0.66587	0.459000	0.35465	ATC		0.627	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			23	39	23	39
TAS1R2	80834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	19166820	19166820	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr1:19166820G>T	ENST00000375371.3	-	6	1814	c.1793C>A	c.(1792-1794)tCg>tAg	p.S598*		NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	598					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	GCCCCCAGCCGAGCGAACTAT	0.647																																																0													56.0	59.0	58.0					1																	19166820		2202	4300	6502	SO:0001587	stop_gained	80834				CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14905	protein-coding gene	gene with protein product		606226	"""G protein-coupled receptor 71"""	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.1793C>A	1.37:g.19166820G>T	ENSP00000364520:p.Ser598*		Q5TZ19	Nonsense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.569223	0.86439	.	.	ENSG00000179002	ENST00000375371	.	.	.	5.48	5.48	0.80851	.	0.000000	0.48286	D	0.000193	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	.	16.8255	0.85930	0.0:0.0:1.0:0.0	.	.	.	.	X	598	.	ENSP00000364520:S598X	S	-	2	0	TAS1R2	19039407	1.000000	0.71417	0.992000	0.48379	0.089000	0.18198	9.664000	0.98607	2.578000	0.87016	0.655000	0.94253	TCG		0.647	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			26	45	26	45
COL11A1	1301	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	103380351	103380351	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr1:103380351C>T	ENST00000370096.3	-	51	4145	c.3833G>A	c.(3832-3834)aGa>aAa	p.R1278K	COL11A1_ENST00000512756.1_Missense_Mutation_p.R1162K|COL11A1_ENST00000353414.4_Missense_Mutation_p.R1239K|COL11A1_ENST00000358392.2_Missense_Mutation_p.R1290K	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1278	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)	p.R1278T(1)|p.R1290T(1)		NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TTTCTCTCCTCTTTCTCCTTT	0.453																																																2	Substitution - Missense(2)	lung(2)											43.0	42.0	43.0					1																	103380351		2203	4300	6503	SO:0001583	missense	1301			J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.3833G>A	1.37:g.103380351C>T	ENSP00000359114:p.Arg1278Lys		B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	16.59	3.166737	0.57476	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000370090;ENST00000512756	D;D;D;D	0.94046	-3.34;-3.16;-3.23;-3.23	5.73	5.73	0.89815	.	0.054398	0.64402	D	0.000001	D	0.88819	0.6540	N	0.05441	-0.05	0.80722	D	1	P;D;P;D;P	0.61697	0.932;0.99;0.936;0.982;0.902	P;D;P;D;D	0.72982	0.867;0.979;0.802;0.952;0.91	D	0.85276	0.1059	10	0.05959	T	0.93	.	19.8928	0.96935	0.0:1.0:0.0:0.0	.	1162;1239;1290;1278;498	E9PCU0;P12107-3;P12107-2;P12107;F5H5Z5	.;.;.;COBA1_HUMAN;.	K	1278;1290;1239;498;1162	ENSP00000359114:R1278K;ENSP00000351163:R1290K;ENSP00000302551:R1239K;ENSP00000426533:R1162K	ENSP00000302551:R1239K	R	-	2	0	COL11A1	103152939	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.540000	0.60664	2.713000	0.92767	0.591000	0.81541	AGA		0.453	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		12	22	12	22
PIAS3	10401	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	145585437	145585437	+	Missense_Mutation	SNP	C	C	G			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr1:145585437C>G	ENST00000393045.2	+	14	1792	c.1702C>G	c.(1702-1704)Cac>Gac	p.H568D	PIAS3_ENST00000369298.1_Missense_Mutation_p.H533D|NUDT17_ENST00000444015.2_5'Flank	NM_006099.3	NP_006090.2	Q9Y6X2	PIAS3_HUMAN	protein inhibitor of activated STAT, 3	568					positive regulation of gene expression (GO:0010628)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein sumoylation (GO:0033235)|protein sumoylation (GO:0016925)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|nucleus (GO:0005634)|synapse (GO:0045202)	enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|SUMO ligase activity (GO:0019789)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)	28	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GACCCCTTCTCACTTTCTGGG	0.637																																																0													72.0	76.0	75.0					1																	145585437		2203	4300	6503	SO:0001583	missense	10401			AB021868	CCDS72866.1	1q21	2011-10-11			ENSG00000131788	ENSG00000131788		"""Zinc fingers, MIZ-type"""	16861	protein-coding gene	gene with protein product	"""zinc finger, MIZ-type containing 5"""	605987				10319586	Standard	NM_006099		Approved	FLJ14651, ZMIZ5	uc001eoc.1	Q9Y6X2	OTTHUMG00000013750	ENST00000393045.2:c.1702C>G	1.37:g.145585437C>G	ENSP00000376765:p.His568Asp		Q9UFI3	Missense_Mutation	SNP	ENST00000393045.2	37	CCDS920.2	.	.	.	.	.	.	.	.	.	.	C	17.28	3.350653	0.61183	.	.	ENSG00000131788	ENST00000393045;ENST00000369298	T;T	0.30182	1.55;1.54	5.15	5.15	0.70609	.	0.000000	0.64402	D	0.000002	T	0.33235	0.0856	L	0.36672	1.1	0.80722	D	1	P	0.50156	0.932	P	0.58520	0.84	T	0.05716	-1.0868	10	0.72032	D	0.01	-14.7211	16.1575	0.81676	0.0:1.0:0.0:0.0	.	568	Q9Y6X2	PIAS3_HUMAN	D	568;533	ENSP00000376765:H568D;ENSP00000358304:H533D	ENSP00000358304:H533D	H	+	1	0	PIAS3	144296794	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.301000	0.51842	2.681000	0.91329	0.561000	0.74099	CAC		0.637	PIAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038533.4	NM_006099		52	55	52	55
FAM161A	84140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	62067511	62067511	+	Missense_Mutation	SNP	C	C	A			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr2:62067511C>A	ENST00000405894.3	-	3	729	c.628G>T	c.(628-630)Gat>Tat	p.D210Y	FAM161A_ENST00000404929.1_Missense_Mutation_p.D210Y	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	210					cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						CGAATATAATCCTCAACACAA	0.408																																																0													208.0	185.0	192.0					2																	62067511		1871	4101	5972	SO:0001583	missense	84140				CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"""retinitis pigmentosa 28 (autosomal recessive)"""	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.628G>T	2.37:g.62067511C>A	ENSP00000385893:p.Asp210Tyr		B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	37	CCDS42687.2	.	.	.	.	.	.	.	.	.	.	C	13.79	2.341731	0.41498	.	.	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.35048	2.16;1.33	5.55	4.66	0.58398	.	0.323633	0.32533	N	0.005979	T	0.56124	0.1964	M	0.63843	1.955	0.41340	D	0.987298	D;D	0.89917	1.0;0.958	D;P	0.74023	0.982;0.601	T	0.59637	-0.7417	10	0.87932	D	0	-6.6025	14.362	0.66779	0.0:0.9272:0.0:0.0728	.	210;210	Q3B820;Q3B820-3	F161A_HUMAN;.	Y	210	ENSP00000385158:D210Y;ENSP00000385893:D210Y	ENSP00000385158:D210Y	D	-	1	0	FAM161A	61921015	1.000000	0.71417	0.997000	0.53966	0.114000	0.19823	3.827000	0.55745	2.603000	0.88011	0.655000	0.94253	GAT		0.408	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180		68	118	68	118
BUB1	699	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	111423902	111423902	+	Missense_Mutation	SNP	T	T	C			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr2:111423902T>C	ENST00000302759.6	-	9	1013	c.895A>G	c.(895-897)Aag>Gag	p.K299E	BUB1_ENST00000535254.1_Missense_Mutation_p.K279E|BUB1_ENST00000409311.1_Missense_Mutation_p.K299E	NM_004336.3	NP_004327.1	O43683	BUB1_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase	299					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of chromosome segregation (GO:0051983)|regulation of sister chromatid cohesion (GO:0007063)|spindle assembly checkpoint (GO:0071173)|viral process (GO:0016032)	condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(8)|kidney(4)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|stomach(1)	45		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		TGATGCAACTTCTTATGAAGT	0.428																																																0													157.0	140.0	145.0					2																	111423902		2203	4300	6503	SO:0001583	missense	699			AF046078	CCDS33273.1, CCDS62984.1, CCDS62985.1	2q13	2013-01-17	2013-01-17		ENSG00000169679	ENSG00000169679			1148	protein-coding gene	gene with protein product		602452	"""budding uninhibited by benzimidazoles 1 (yeast homolog)"", ""budding uninhibited by benzimidazoles 1 homolog (yeast)"""	BUB1L			Standard	NM_004336		Approved	hBUB1, BUB1A	uc002tgc.3	O43683	OTTHUMG00000153638	ENST00000302759.6:c.895A>G	2.37:g.111423902T>C	ENSP00000302530:p.Lys299Glu		E9PC26|F5GXI5|O43430|O43643|O60626|Q53QE4	Missense_Mutation	SNP	ENST00000302759.6	37	CCDS33273.1	.	.	.	.	.	.	.	.	.	.	T	14.34	2.504987	0.44558	.	.	ENSG00000169679	ENST00000535254;ENST00000409311;ENST00000302759;ENST00000541432	T;T;T	0.32023	2.2;1.47;2.47	5.82	2.17	0.27698	.	0.574187	0.18157	N	0.149920	T	0.22589	0.0545	L	0.50333	1.59	0.26897	N	0.967196	B;B;B	0.29988	0.264;0.179;0.146	B;B;B	0.28011	0.085;0.039;0.039	T	0.27262	-1.0079	10	0.05351	T	0.99	-11.5893	11.5841	0.50908	0.0:0.0:0.5644:0.4356	.	279;299;299	F5GXI5;E9PC26;O43683	.;.;BUB1_HUMAN	E	279;299;299;299	ENSP00000441013:K279E;ENSP00000386701:K299E;ENSP00000302530:K299E	ENSP00000302530:K299E	K	-	1	0	BUB1	111140373	0.996000	0.38824	0.949000	0.38748	0.974000	0.67602	1.407000	0.34657	0.444000	0.26612	0.533000	0.62120	AAG		0.428	BUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331925.1	NM_004336		12	25	12	25
WDR33	55339	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	128522748	128522748	+	Splice_Site	SNP	C	C	G			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr2:128522748C>G	ENST00000322313.4	-	5	632	c.474G>C	c.(472-474)caG>caC	p.Q158H	WDR33_ENST00000409658.3_Splice_Site_p.Q158H|WDR33_ENST00000393006.1_Splice_Site_p.Q158H	NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	158					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		TTATCATTACCTGTAATATTG	0.398																																																0													54.0	50.0	51.0					2																	128522748		2203	4300	6503	SO:0001630	splice_region_variant	55339				CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"""WD repeat domain containing"""	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.474+1G>C	2.37:g.128522748C>G			Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Splice_Site	SNP	ENST00000322313.4	37	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.535560	0.85812	.	.	ENSG00000136709	ENST00000322313;ENST00000436787;ENST00000393006;ENST00000409658	T;T;T;T	0.60424	0.19;0.19;0.19;0.19	5.39	5.39	0.77823	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83022	0.5164	M	0.93241	3.395	0.80722	D	1	D;D;D	0.89917	0.994;1.0;0.996	P;D;D	0.85130	0.906;0.997;0.995	D	0.87341	0.2331	9	.	.	.	-7.9998	19.1415	0.93448	0.0:1.0:0.0:0.0	.	158;158;158	Q9C0J8-2;Q6NUQ0;Q9C0J8	.;.;WDR33_HUMAN	H	158;80;158;158	ENSP00000325377:Q158H;ENSP00000397547:Q80H;ENSP00000376730:Q158H;ENSP00000387186:Q158H	.	Q	-	3	2	WDR33	128239218	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	3.382000	0.52463	2.524000	0.85096	0.655000	0.94253	CAG		0.398	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383	Missense_Mutation	13	13	13	13
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			32	47	32	47
SPP2	6694	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	234969077	234969077	+	Missense_Mutation	SNP	G	G	A	rs376262894		TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr2:234969077G>A	ENST00000168148.3	+	4	486	c.398G>A	c.(397-399)cGc>cAc	p.R133H	SPP2_ENST00000373368.1_Missense_Mutation_p.R133H	NM_006944.2	NP_008875.1	Q13103	SPP24_HUMAN	secreted phosphoprotein 2, 24kDa	133					bone remodeling (GO:0046849)|negative regulation of endopeptidase activity (GO:0010951)|protein complex assembly (GO:0006461)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	endopeptidase inhibitor activity (GO:0004866)			breast(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	12		Breast(86;0.0109)|Renal(207;0.019)|all_lung(227;0.13)|all_hematologic(139;0.182)		Epithelial(121;5.73e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000166)|Lung(119;0.00539)|LUSC - Lung squamous cell carcinoma(224;0.00846)		GTGCATGCTCGCTGCAGCTGG	0.577																																																0													86.0	74.0	78.0					2																	234969077		2203	4300	6503	SO:0001583	missense	6694				CCDS2511.1	2q37.1	2012-08-14	2002-08-29		ENSG00000072080	ENSG00000072080			11256	protein-coding gene	gene with protein product		602637	"""secreted phosphoprotein 2, 24kD"""			9533032	Standard	XM_005246102		Approved	SPP24	uc002vvk.1	Q13103	OTTHUMG00000059208	ENST00000168148.3:c.398G>A	2.37:g.234969077G>A	ENSP00000168148:p.Arg133His		A4QMV3|Q3B892|Q546M5	Missense_Mutation	SNP	ENST00000168148.3	37	CCDS2511.1	.	.	.	.	.	.	.	.	.	.	G	4.268	0.048774	0.08243	.	.	ENSG00000072080	ENST00000373368;ENST00000168148;ENST00000425558	T;T	0.51325	0.71;0.71	5.28	-2.21	0.06973	.	0.574976	0.16956	N	0.192682	T	0.27454	0.0674	L	0.31578	0.945	0.26905	N	0.967034	B	0.11235	0.004	B	0.04013	0.001	T	0.09552	-1.0669	10	0.31617	T	0.26	-7.334	5.3011	0.15778	0.5799:0.0:0.2651:0.155	.	133	Q13103	SPP24_HUMAN	H	133;133;53	ENSP00000362466:R133H;ENSP00000168148:R133H	ENSP00000168148:R133H	R	+	2	0	SPP2	234633816	0.002000	0.14202	0.544000	0.28141	0.271000	0.26615	-0.605000	0.05661	-0.542000	0.06249	-0.122000	0.15005	CGC		0.577	SPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131313.3	NM_006944		23	40	23	40
HDAC4	9759	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	239976491	239976491	+	Silent	SNP	G	G	A			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr2:239976491G>A	ENST00000345617.3	-	25	3818	c.3027C>T	c.(3025-3027)ccC>ccT	p.P1009P	HDAC4_ENST00000543185.1_Silent_p.P593P	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	1009	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|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 cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		CGTTTGCATTGGGTCTTTGCT	0.507																																																0													140.0	130.0	133.0					2																	239976491		2203	4300	6503	SO:0001819	synonymous_variant	9759			AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"""brachydactyly-mental retardation syndrome"""	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.3027C>T	2.37:g.239976491G>A			Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1	.	.	.	.	.	.	.	.	.	.	G	3.175	-0.169245	0.06461	.	.	ENSG00000068024	ENST00000430200	T	0.49139	0.79	4.34	2.31	0.28768	.	0.169985	0.52532	D	0.000077	T	0.52484	0.1737	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54549	-0.8277	7	0.87932	D	0	.	6.9347	0.24461	0.0:0.1461:0.4236:0.4303	.	.	.	.	L	100	ENSP00000410551:P100L	ENSP00000410551:P100L	P	-	2	0	HDAC4	239641428	1.000000	0.71417	0.998000	0.56505	0.319000	0.28217	0.601000	0.24119	1.098000	0.41479	0.655000	0.94253	CCA		0.507	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037		37	70	37	70
PROS1	5627	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	93624931	93624931	+	Missense_Mutation	SNP	T	T	C			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr3:93624931T>C	ENST00000394236.3	-	5	719	c.403A>G	c.(403-405)Aaa>Gaa	p.K135E	PROS1_ENST00000407433.1_Missense_Mutation_p.K4E	NM_000313.3	NP_000304.2	P07225	PROS_HUMAN	protein S (alpha)	135	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|negative regulation of endopeptidase activity (GO:0010951)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|endopeptidase inhibitor activity (GO:0004866)			endometrium(3)|kidney(5)|large_intestine(8)|lung(26)|ovary(1)|skin(2)|urinary_tract(1)	46					Drotrecogin alfa(DB00055)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	TTTCCATCTTTGCAGCTCATA	0.408																																																0													115.0	121.0	119.0					3																	93624931		2203	4300	6503	SO:0001583	missense	5627				CCDS2923.1	3q11.1	2013-06-03			ENSG00000184500	ENSG00000184500			9456	protein-coding gene	gene with protein product		176880		PROS		214811, 1833851	Standard	NM_000313		Approved		uc003drb.4	P07225	OTTHUMG00000150354	ENST00000394236.3:c.403A>G	3.37:g.93624931T>C	ENSP00000377783:p.Lys135Glu		A8KAC9|D3DN28|Q15518|Q7Z715|Q9UCZ8	Missense_Mutation	SNP	ENST00000394236.3	37	CCDS2923.1	.	.	.	.	.	.	.	.	.	.	T	7.187	0.590746	0.13812	.	.	ENSG00000184500	ENST00000394236;ENST00000407433;ENST00000348974;ENST00000472684	D;D;D;D	0.92299	-3.01;-2.22;-3.01;-2.05	4.44	1.98	0.26296	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.669254	0.15290	N	0.270203	D	0.84005	0.5377	N	0.17312	0.475	0.20489	N	0.999894	B	0.22604	0.072	B	0.29077	0.098	T	0.73238	-0.4046	10	0.44086	T	0.13	.	7.1161	0.25416	0.0:0.0787:0.1475:0.7737	.	135	P07225	PROS_HUMAN	E	135;4;167;4	ENSP00000377783:K135E;ENSP00000385794:K4E;ENSP00000330021:K167E;ENSP00000419616:K4E	ENSP00000330021:K167E	K	-	1	0	PROS1	95107621	1.000000	0.71417	0.968000	0.41197	0.920000	0.55202	1.235000	0.32671	0.231000	0.21079	0.397000	0.26171	AAA		0.408	PROS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317762.1	NM_000313		69	107	69	107
PLCH1	23007	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	155200741	155200741	+	Missense_Mutation	SNP	A	A	G			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr3:155200741A>G	ENST00000340059.7	-	23	3097	c.3098T>C	c.(3097-3099)cTc>cCc	p.L1033P	PLCH1-AS2_ENST00000472913.1_RNA|PLCH1_ENST00000334686.6_Missense_Mutation_p.L995P|PLCH1_ENST00000460012.1_Missense_Mutation_p.L995P|PLCH1_ENST00000494598.1_Intron|PLCH1_ENST00000414191.1_Missense_Mutation_p.L995P|PLCH1_ENST00000447496.2_3'UTR	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	1033					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			ATCTTTGTGGAGCAGAGCACT	0.453																																																0													146.0	147.0	146.0					3																	155200741		2203	4300	6503	SO:0001583	missense	23007			AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"""EF-hand domain containing"""	29185	protein-coding gene	gene with protein product		612835	"""phospholipase C-like 3"""	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.3098T>C	3.37:g.155200741A>G	ENSP00000345988:p.Leu1033Pro		Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Missense_Mutation	SNP	ENST00000340059.7	37	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	A	9.663	1.144540	0.21288	.	.	ENSG00000114805	ENST00000460012;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T	0.25414	1.8;1.8;1.8;1.8	4.84	2.33	0.28932	.	1.138310	0.06333	N	0.706624	T	0.24509	0.0594	L	0.29908	0.895	0.26903	N	0.967066	P;B	0.40875	0.731;0.0	P;B	0.47528	0.549;0.001	T	0.22034	-1.0228	10	0.31617	T	0.26	.	3.6467	0.08187	0.6577:0.1365:0.0747:0.1311	.	995;1033	Q4KWH8-2;Q4KWH8	.;PLCH1_HUMAN	P	995;1033;995;995	ENSP00000417502:L995P;ENSP00000345988:L1033P;ENSP00000335469:L995P;ENSP00000412977:L995P	ENSP00000335469:L995P	L	-	2	0	PLCH1	156683435	0.038000	0.19896	0.327000	0.25402	0.013000	0.08279	0.260000	0.18424	0.358000	0.24211	0.482000	0.46254	CTC		0.453	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996		28	53	28	53
SPATA16	83893	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	172631478	172631478	+	Silent	SNP	A	A	G			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr3:172631478A>G	ENST00000351008.3	-	10	1743	c.1560T>C	c.(1558-1560)aaT>aaC	p.N520N		NM_031955.5	NP_114161.3	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16	520					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)				breast(2)|cervix(1)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	43	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)			ACACACGTTCATTATTGTTTC	0.373																																																0													122.0	112.0	116.0					3																	172631478		2203	4300	6503	SO:0001819	synonymous_variant	83893			AF345909	CCDS3221.1	3q26.31	2009-01-05			ENSG00000144962	ENSG00000144962			29935	protein-coding gene	gene with protein product		609856				12529416, 17847006	Standard	NM_031955		Approved	NYD-SP12	uc003fin.4	Q9BXB7	OTTHUMG00000156865	ENST00000351008.3:c.1560T>C	3.37:g.172631478A>G			Q0R0N4|Q0R0S0|Q0R0W2|Q0R129|Q0R131|Q0R140|Q0R1B8|Q0R1G5|Q0R1I2|Q0R1J6|Q0R1S4|Q0R202|Q0R280|Q0R2F8|Q0R2N6|Q0R2N7|Q0R2R0|Q0R2R1|Q0R2S3|Q0R2S4|Q0R2S5|Q0R2T4|Q0R2T7|Q0R2U2|Q0R2U8|Q0R2U9|Q0R2V5|Q0R2V7|Q8NE67	Silent	SNP	ENST00000351008.3	37	CCDS3221.1																																																																																				0.373	SPATA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346322.1	NM_031955		26	40	26	40
TRRAP	8295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	98545941	98545941	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr7:98545941C>T	ENST00000359863.4	+	33	4834	c.4625C>T	c.(4624-4626)aCg>aTg	p.T1542M	TRRAP_ENST00000446306.3_Missense_Mutation_p.T1523M|TRRAP_ENST00000355540.3_Missense_Mutation_p.T1524M	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	1542					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GTCATGAAAACGGAGCGGGCG	0.498																																																0													85.0	78.0	81.0					7																	98545941		2203	4300	6503	SO:0001583	missense	8295			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.4625C>T	7.37:g.98545941C>T	ENSP00000352925:p.Thr1542Met		A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	37	CCDS59066.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.33|19.33	3.806707|3.806707	0.70682|0.70682	.|.	.|.	ENSG00000196367|ENSG00000196367	ENST00000456197|ENST00000359863;ENST00000355540;ENST00000446306	.|T;T	.|0.66099	.|-0.19;-0.19	5.74|5.74	5.74|5.74	0.90152|0.90152	.|Armadillo-like helical (1);Armadillo-type fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.77096|0.77096	0.4080|0.4080	L|L	0.58810|0.58810	1.83|1.83	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.76071	.|0.987;0.932;0.932	T|T	0.71879|0.71879	-0.4459|-0.4459	5|10	.|0.33141	.|T	.|0.24	.|.	20.2825|20.2825	0.98528|0.98528	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1524;1263;1542	.|Q9Y4A5-2;Q59FH1;Q9Y4A5	.|.;.;TRRAP_HUMAN	W|M	1264|1542;1524;1522	.|ENSP00000352925:T1542M;ENSP00000347733:T1524M	.|ENSP00000347733:T1524M	R|T	+|+	1|2	2|0	TRRAP|TRRAP	98383877|98383877	1.000000|1.000000	0.71417|0.71417	0.986000|0.986000	0.45419|0.45419	0.298000|0.298000	0.27526|0.27526	7.445000|7.445000	0.80570|0.80570	2.873000|2.873000	0.98535|0.98535	0.561000|0.561000	0.74099|0.74099	CGG|ACG		0.498	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		34	84	34	84
CRYGN	155051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	151135095	151135095	+	Missense_Mutation	SNP	C	C	T	rs148445096		TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr7:151135095C>T	ENST00000337323.2	-	2	383	c.257G>A	c.(256-258)cGg>cAg	p.R86Q	RP4-555L14.4_ENST00000465549.1_RNA|CRYGN_ENST00000491928.1_Missense_Mutation_p.R86Q|CRYGN_ENST00000476631.1_5'UTR	NM_144727.1	NP_653328.1	Q8WXF5	CRGN_HUMAN	crystallin, gamma N	86	Beta/gamma crystallin 'Greek key' 2. {ECO:0000255|PROSITE-ProRule:PRU00028}.									central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(1)|lung(4)	8			OV - Ovarian serous cystadenocarcinoma(82;0.00358)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCCTACAGGCCGACAGGAGCC	0.627																																																0								C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	47.0	51.0	50.0		257	4.2	1.0	7	dbSNP_134	50	0,8600		0,0,4300	no	missense	CRYGN	NM_144727.1	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	86/183	151135095	1,13005	2203	4300	6503	SO:0001583	missense	155051			AF445455	CCDS5926.1	7q36.1	2003-02-25			ENSG00000127377	ENSG00000127377			20458	protein-coding gene	gene with protein product		609603					Standard	NM_144727		Approved		uc003wke.3	Q8WXF5	OTTHUMG00000157353	ENST00000337323.2:c.257G>A	7.37:g.151135095C>T	ENSP00000338613:p.Arg86Gln		Q496G6	Missense_Mutation	SNP	ENST00000337323.2	37	CCDS5926.1	.	.	.	.	.	.	.	.	.	.	C	17.07	3.295917	0.60086	2.27E-4	0.0	ENSG00000127377	ENST00000337323	D	0.82344	-1.6	5.05	4.17	0.49024	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.158360	0.53938	D	0.000049	T	0.75332	0.3835	M	0.70842	2.15	0.43351	D	0.995414	P;B	0.45044	0.849;0.273	B;B	0.26864	0.074;0.073	T	0.76809	-0.2822	10	0.72032	D	0.01	.	9.1981	0.37240	0.0:0.8341:0.0:0.1659	.	86;86	Q8WXF5-2;Q8WXF5	.;CRGN_HUMAN	Q	86	ENSP00000338613:R86Q	ENSP00000338613:R86Q	R	-	2	0	CRYGN	150766028	0.998000	0.40836	0.998000	0.56505	0.963000	0.63663	1.109000	0.31135	1.120000	0.41904	-0.448000	0.05591	CGG		0.627	CRYGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348553.1			27	34	27	34
CA9	768	hgsc.bcm.edu;ucsc.edu	37	9	35674208	35674208	+	Silent	SNP	T	T	C	rs137897809|rs201260414	byFrequency	TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr9:35674208T>C	ENST00000378357.4	+	1	356	c.252T>C	c.(250-252)ccT>ccC	p.P84P	RN7SL22P_ENST00000471800.2_RNA	NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	84	Proteoglycan-like (PG).				bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)	p.P84P(1)|p.G79_P84delGEEDLP(1)		kidney(1)|large_intestine(3)|lung(5)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	17	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	AGGATCTACCTGGAGAGGAGG	0.542																																																2	Substitution - coding silent(1)|Deletion - In frame(1)	urinary_tract(1)|skin(1)											57.0	55.0	55.0					9																	35674208		2203	4300	6503	SO:0001819	synonymous_variant	768			X66839	CCDS6585.1	9p13.3	2012-08-21			ENSG00000107159	ENSG00000107159		"""Carbonic anhydrases"""	1383	protein-coding gene	gene with protein product	"""carbonic dehydratase"", ""RCC-associated protein G250"""	603179				8661007, 9787087	Standard	NM_001216		Approved	MN, CAIX	uc003zxo.4	Q16790	OTTHUMG00000021029	ENST00000378357.4:c.252T>C	9.37:g.35674208T>C			Q5T4R1	Silent	SNP	ENST00000378357.4	37	CCDS6585.1																																																																																				0.542	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216		7	15	7	15
RORB	6096	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	77257427	77257427	+	Missense_Mutation	SNP	G	G	C			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr9:77257427G>C	ENST00000396204.2	+	4	366	c.366G>C	c.(364-366)caG>caC	p.Q122H	RORB_ENST00000376896.3_Missense_Mutation_p.Q111H			Q92753	RORB_HUMAN	RAR-related orphan receptor B	122	Hinge. {ECO:0000255}.				amacrine cell differentiation (GO:0035881)|cellular response to retinoic acid (GO:0071300)|eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(2)|large_intestine(4)|lung(1)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	12					Melatonin(DB01065)	ggcagcagcagAGTGGGGAGG	0.592																																																0													72.0	63.0	66.0					9																	77257427		2203	4300	6503	SO:0001583	missense	6096			Y08639	CCDS6646.1	9q22	2013-01-16			ENSG00000198963	ENSG00000198963		"""Nuclear hormone receptors"""	10259	protein-coding gene	gene with protein product		601972				7926749	Standard	NM_006914		Approved	RZRB, NR1F2, ROR-BETA	uc004ajh.3	Q92753	OTTHUMG00000020026	ENST00000396204.2:c.366G>C	9.37:g.77257427G>C	ENSP00000379507:p.Gln122His		Q8WX73	Missense_Mutation	SNP	ENST00000396204.2	37		.	.	.	.	.	.	.	.	.	.	G	18.19	3.569287	0.65765	.	.	ENSG00000198963	ENST00000376896;ENST00000396204	D;D	0.94184	-3.37;-3.37	5.63	4.74	0.60224	.	0.185895	0.50627	D	0.000111	D	0.93569	0.7947	M	0.62723	1.935	0.58432	D	0.999997	D;B	0.57571	0.98;0.004	P;B	0.53146	0.719;0.014	D	0.92559	0.6056	10	0.45353	T	0.12	.	10.2962	0.43625	0.1501:0.0:0.8499:0.0	.	122;111	Q92753;Q58EY0	RORB_HUMAN;.	H	111;122	ENSP00000366093:Q111H;ENSP00000379507:Q122H	ENSP00000366093:Q111H	Q	+	3	2	RORB	76447247	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.114000	0.50383	1.387000	0.46486	0.655000	0.94253	CAG		0.592	RORB-201	KNOWN	basic	protein_coding	protein_coding				11	38	11	38
SETX	23064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	135205145	135205145	+	Missense_Mutation	SNP	T	T	C			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr9:135205145T>C	ENST00000224140.5	-	10	2022	c.1840A>G	c.(1840-1842)Atc>Gtc	p.I614V	SETX_ENST00000372169.2_Missense_Mutation_p.I614V|SETX_ENST00000393220.1_Missense_Mutation_p.I614V	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	614					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		GCAGGAGAGATTTTACATGCA	0.353																																																0													76.0	69.0	71.0					9																	135205145		2203	4299	6502	SO:0001583	missense	23064			AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"""amyotrophic lateral sclerosis 4"", ""spinocerebellar ataxia, recessive, non-Friedreich type 1"""	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.1840A>G	9.37:g.135205145T>C	ENSP00000224140:p.Ile614Val		A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	T	3.941	-0.014240	0.07681	.	.	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	D;D;D	0.86097	-1.98;-2.07;-1.69	5.68	3.38	0.38709	.	0.970350	0.08494	N	0.937495	T	0.71626	0.3362	N	0.08118	0	0.09310	N	1	B;B;B	0.15930	0.004;0.001;0.015	B;B;B	0.12837	0.008;0.002;0.008	T	0.61402	-0.7070	10	0.59425	D	0.04	.	7.5911	0.28021	0.0:0.2266:0.0:0.7734	.	614;614;614	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	V	614	ENSP00000224140:I614V;ENSP00000361242:I614V;ENSP00000376913:I614V	ENSP00000224140:I614V	I	-	1	0	SETX	134194966	0.194000	0.23325	0.006000	0.13384	0.162000	0.22319	0.650000	0.24858	0.995000	0.38917	-0.256000	0.11100	ATC		0.353	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		28	38	28	38
CCDC160	347475	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	133379653	133379653	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chrX:133379653C>T	ENST00000517294.1	+	3	1206	c.823C>T	c.(823-825)Cgc>Tgc	p.R275C	CCDC160_ENST00000370809.4_Missense_Mutation_p.R275C			A6NGH7	CC160_HUMAN	coiled-coil domain containing 160	275										endometrium(1)|kidney(2)|large_intestine(10)|lung(2)|prostate(1)|skin(1)	17						GGCAAAGATCCGCGGAGAGCT	0.383																																																0													38.0	35.0	36.0					X																	133379653		1829	4071	5900	SO:0001583	missense	347475			BC017958	CCDS48171.1	Xq26.2	2010-02-17			ENSG00000203952	ENSG00000203952			37286	protein-coding gene	gene with protein product							Standard	NM_001101357		Approved		uc011mvj.2	A6NGH7	OTTHUMG00000164183	ENST00000517294.1:c.823C>T	X.37:g.133379653C>T	ENSP00000427951:p.Arg275Cys			Missense_Mutation	SNP	ENST00000517294.1	37	CCDS48171.1	.	.	.	.	.	.	.	.	.	.	C	11.62	1.692171	0.30052	.	.	ENSG00000203952	ENST00000517294;ENST00000370809	D;D	0.91180	-2.8;-2.8	5.29	3.39	0.38822	.	0.699419	0.12699	N	0.446514	D	0.89206	0.6649	L	0.29908	0.895	0.09310	N	1	D	0.71674	0.998	P	0.56916	0.809	T	0.79888	-0.1613	10	0.72032	D	0.01	-15.5181	7.4951	0.27483	0.0:0.7371:0.1658:0.0971	.	275	A6NGH7	CC160_HUMAN	C	275	ENSP00000427951:R275C;ENSP00000359845:R275C	ENSP00000359845:R275C	R	+	1	0	CCDC160	133207319	0.000000	0.05858	0.009000	0.14445	0.017000	0.09413	0.817000	0.27281	1.117000	0.41842	0.513000	0.50165	CGC		0.383	CCDC160-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377679.1	NM_001101357		9	13	9	13
PLXNA3	55558	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	153688767	153688767	+	Missense_Mutation	SNP	A	A	G	rs142949704		TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chrX:153688767A>G	ENST00000369682.3	+	2	419	c.244A>G	c.(244-246)Agc>Ggc	p.S82G		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	82	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CCCGCCCCCCAGCATGCGCGT	0.672																																																0								A	GLY/SER	1,3825		0,1,1629,566	25.0	25.0	25.0		244	3.7	1.0	X	dbSNP_134	25	0,6724		0,0,2427,1870	no	missense	PLXNA3	NM_017514.3	56	0,1,4056,2436	GG,GA,AA,A		0.0,0.0261,0.0095	probably-damaging	82/1872	153688767	1,10549	2196	4297	6493	SO:0001583	missense	55558			X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"""Plexins"""	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.244A>G	X.37:g.153688767A>G	ENSP00000358696:p.Ser82Gly		Q5HY36	Missense_Mutation	SNP	ENST00000369682.3	37	CCDS14752.1	.	.	.	.	.	.	.	.	.	.	A	10.73	1.431639	0.25813	2.61E-4	0.0	ENSG00000130827	ENST00000369682	T	0.11169	2.8	4.86	3.69	0.42338	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.12603	0.0306	M	0.73753	2.245	0.51233	D	0.999912	B	0.14438	0.01	B	0.23150	0.044	T	0.06716	-1.0811	10	0.16896	T	0.51	.	7.0627	0.25135	0.8094:0.0:0.1906:0.0	.	82	P51805	PLXA3_HUMAN	G	82	ENSP00000358696:S82G	ENSP00000358696:S82G	S	+	1	0	PLXNA3	153341961	0.998000	0.40836	0.994000	0.49952	0.694000	0.40290	4.357000	0.59436	0.781000	0.33589	0.345000	0.21793	AGC		0.672	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514		10	15	10	15
ZNF451	26036	broad.mit.edu;ucsc.edu	37	6	57012701	57012701	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr6:57012701G>A	ENST00000370706.4	+	10	2062	c.1818G>A	c.(1816-1818)tgG>tgA	p.W606*	RP11-203B9.4_ENST00000589549.1_RNA|RP11-203B9.4_ENST00000591553.1_RNA|RP11-203B9.4_ENST00000585792.1_RNA|RP11-203B9.4_ENST00000592038.1_RNA|ZNF451_ENST00000491832.2_Nonsense_Mutation_p.W606*|RP11-203B9.4_ENST00000589263.1_RNA|RP11-203B9.4_ENST00000586668.1_RNA|RP11-203B9.4_ENST00000586053.1_RNA|RP11-203B9.4_ENST00000587815.1_RNA|RP11-203B9.4_ENST00000592500.1_RNA|RP11-203B9.4_ENST00000586466.1_RNA|RP11-203B9.4_ENST00000416069.2_RNA|RP11-203B9.4_ENST00000586432.1_RNA|ZNF451_ENST00000357489.3_Nonsense_Mutation_p.W606*|RP11-203B9.4_ENST00000588811.1_RNA	NM_001031623.2	NP_001026794.1	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451	606					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			GGGGTAAATGGCAATGCCGGA	0.418																																																0													101.0	100.0	100.0					6																	57012701		2203	4300	6503	SO:0001587	stop_gained	26036			AB011148	CCDS4960.1, CCDS43477.1, CCDS59026.1	6p12.1	2012-08-08			ENSG00000112200	ENSG00000112200		"""Zinc fingers, C2H2-type"""	21091	protein-coding gene	gene with protein product		615708				9628581	Standard	NM_001031623		Approved	KIAA0576, COASTER, dJ417I1.1, KIAA1702	uc003pdm.2	Q9Y4E5	OTTHUMG00000014916	ENST00000370706.4:c.1818G>A	6.37:g.57012701G>A	ENSP00000359740:p.Trp606*		Q5VVE9|Q5VVF1|Q86YE4|Q8N380|Q8TD15|Q9C0G1|Q9NQM1	Nonsense_Mutation	SNP	ENST00000370706.4	37	CCDS43477.1	.	.	.	.	.	.	.	.	.	.	G	39	7.528197	0.98339	.	.	ENSG00000112200	ENST00000370706;ENST00000357489;ENST00000491832	.	.	.	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.4058	19.216	0.93778	0.0:0.0:1.0:0.0	.	.	.	.	X	606	.	ENSP00000350083:W606X	W	+	3	0	ZNF451	57120660	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.035000	0.93752	2.529000	0.85273	0.650000	0.86243	TGG		0.418	ZNF451-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041035.2	NM_015555		40	58	40	58
CPO	130749	broad.mit.edu;ucsc.edu	37	2	207814342	207814342	+	Splice_Site	SNP	T	T	C			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr2:207814342T>C	ENST00000272852.3	+	2	116	c.70T>C	c.(70-72)Tcc>Ccc	p.S24P		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	24						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14				LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142)		CCTTTGCAGATCCTTAGCCCA	0.473																																																0													117.0	103.0	108.0					2																	207814342		2203	4300	6503	SO:0001630	splice_region_variant	130749				CCDS2372.1	2q34	2012-02-10			ENSG00000144410	ENSG00000144410			21011	protein-coding gene	gene with protein product	"""metallocarboxypeptidase O"", ""metallocarboxypeptidase C"""	609563				11836249	Standard	NM_173077		Approved		uc002vby.2	Q8IVL8	OTTHUMG00000088987	ENST00000272852.3:c.69-1T>C	2.37:g.207814342T>C			Q2M277|Q7RTW7	Splice_Site	SNP	ENST00000272852.3	37	CCDS2372.1	.	.	.	.	.	.	.	.	.	.	T	14.28	2.488336	0.44249	.	.	ENSG00000144410	ENST00000272852	T	0.14766	2.48	4.32	3.06	0.35304	.	0.596423	0.14969	N	0.287946	T	0.08891	0.0220	N	0.19112	0.55	0.09310	N	1	B	0.26258	0.145	B	0.31191	0.125	T	0.18777	-1.0326	10	0.72032	D	0.01	.	4.7137	0.12884	0.1869:0.0:0.1944:0.6187	.	24	Q8IVL8	CBPO_HUMAN	P	24	ENSP00000272852:S24P	ENSP00000272852:S24P	S	+	1	0	CPO	207522587	0.228000	0.23718	0.068000	0.19968	0.678000	0.39670	0.580000	0.23803	1.946000	0.56461	0.374000	0.22700	TCC		0.473	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077	Missense_Mutation	25	41	25	41
AKAP4	8852	broad.mit.edu;ucsc.edu	37	X	49957597	49957597	+	Silent	SNP	A	A	G			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chrX:49957597A>G	ENST00000376056.2	-	5	1890	c.1740T>C	c.(1738-1740)ggT>ggC	p.G580G	AKAP4_ENST00000376064.3_Silent_p.G580G|AKAP4_ENST00000481402.1_5'UTR|AKAP4_ENST00000376058.2_Silent_p.G206G|AKAP4_ENST00000358526.2_Silent_p.G589G					A kinase (PRKA) anchor protein 4											NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(6)|lung(14)|ovary(1)|skin(4)	41	Ovarian(276;0.236)					CACTTTGGCCACCTCCACACT	0.488																																																0													109.0	86.0	94.0					X																	49957597		2203	4300	6503	SO:0001819	synonymous_variant	8852			AF072756	CCDS14329.1, CCDS14330.1	Xp11.2	2009-03-12			ENSG00000147081	ENSG00000147081		"""A-kinase anchor proteins"""	374	protein-coding gene	gene with protein product	"""A-kinase anchor protein 82 kDa"", ""testis-specific gene HI"", ""protein kinase A anchoring protein 4"", ""cancer/testis antigen 99"""	300185				9822690, 9514854	Standard	NM_003886		Approved	p82, hAKAP82, AKAP82, Fsc1, HI, CT99	uc004dow.1	Q5JQC9	OTTHUMG00000021517	ENST00000376056.2:c.1740T>C	X.37:g.49957597A>G				Silent	SNP	ENST00000376056.2	37	CCDS14330.1																																																																																				0.488	AKAP4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056552.1	NM_003886		31	66	31	66
ATRX	546	broad.mit.edu;ucsc.edu	37	X	76813106	76813106	+	Missense_Mutation	SNP	T	T	G			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chrX:76813106T>G	ENST00000373344.5	-	30	6729	c.6515A>C	c.(6514-6516)gAa>gCa	p.E2172A	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Missense_Mutation_p.E2134A	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	2172	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|Interaction with MECP2.				ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						AATCTTATCTTCCATGGTTCC	0.338			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																																Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	1	Unknown(1)	bone(1)											114.0	102.0	106.0					X																	76813106		2203	4296	6499	SO:0001583	missense	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.6515A>C	X.37:g.76813106T>G	ENSP00000362441:p.Glu2172Ala		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	T	16.90	3.249516	0.59212	.	.	ENSG00000085224	ENST00000373344;ENST00000395603	D;D	0.95821	-3.82;-3.82	5.57	5.57	0.84162	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98701	0.9564	H	0.98559	4.265	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.85130	0.997;0.992	D	0.99486	1.0949	10	0.87932	D	0	-15.3171	14.7231	0.69323	0.0:0.0:0.0:1.0	.	2134;2172	P46100-4;P46100	.;ATRX_HUMAN	A	2172;2134	ENSP00000362441:E2172A;ENSP00000378967:E2134A	ENSP00000362441:E2172A	E	-	2	0	ATRX	76699762	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.694000	0.84235	1.858000	0.53909	0.486000	0.48141	GAA		0.338	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		35	65	35	65
COL1A2	1278	broad.mit.edu;ucsc.edu	37	7	94057712	94057712	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-5872-01A-11D-1705-08	TCGA-DU-5872-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	d597128b-776d-4925-908d-e5e1e4b18f8b	ded34f93-720b-42b6-8a5c-680d6beab0e7	g.chr7:94057712C>T	ENST00000297268.6	+	50	4105	c.3634C>T	c.(3634-3636)Cca>Tca	p.P1212S		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	1212	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				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)		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)	TGAAAACATCCCAGCCAAGAA	0.488										HNSCC(75;0.22)																																						0													106.0	104.0	104.0					7																	94057712		2203	4300	6503	SO:0001583	missense	1278			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.3634C>T	7.37:g.94057712C>T	ENSP00000297268:p.Pro1212Ser		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	12.45	1.941945	0.34283	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	T	0.72394	-0.65	5.3	-2.4	0.06583	Fibrillar collagen, C-terminal (3);	0.578060	0.18585	N	0.136905	T	0.56775	0.2008	L	0.58583	1.82	0.32984	D	0.52403	B	0.02656	0.0	B	0.08055	0.003	T	0.43972	-0.9358	10	0.52906	T	0.07	.	2.7388	0.05247	0.1092:0.4737:0.106:0.311	.	1212	P08123	CO1A2_HUMAN	S	1212;1213	ENSP00000297268:P1212S	ENSP00000297268:P1212S	P	+	1	0	COL1A2	93895648	1.000000	0.71417	0.000000	0.03702	0.651000	0.38670	1.746000	0.38288	-0.596000	0.05821	-0.136000	0.14681	CCA		0.488	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		34	100	34	100
