#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_Start_position_hg18	i_TranscriptID	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
PLXDC2	84898	broad.mit.edu	37	10	20290768	20290768	+	Silent	SNP	C	C	T			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr10:20290768C>T	ENST00000377252.4	+	2	1018	c.177C>T	c.(175-177)caC>caT	p.H59H	PLXDC2_ENST00000377242.3_Silent_p.H59H	NM_001282736.1|NM_032812.7	NP_001269665.1|NP_116201.7	Q6UX71	PXDC2_HUMAN	plexin domain containing 2	59					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.H59H(1)|p.H59Q(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(9)|ovary(2)|skin(3)|stomach(1)	34						TTGATTCACACGCGTACAGCC	0.498																																					p.H59H												.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	c.C177T	10						.						93.0	75.0	81.0					10																	20290768		2203	4300	6503	20330774	SO:0001819	synonymous_variant	84898	exon2			AF378757	CCDS7132.1, CCDS60497.1	10p12.33	2006-04-12			ENSG00000120594	ENSG00000120594			21013	protein-coding gene	gene with protein product	"""tumor endothelial marker 7-related precursor"""	606827				11559528	Standard	NM_001282736		Approved	TEM7R, FLJ14623	uc001iqg.1	Q6UX71	OTTHUMG00000017781	ENST00000377252.4:c.177C>T	10.37:g.20290768C>T			20330774	NM_032812	Q96E59|Q96PD9|Q96SU9	Silent	SNP	ENST00000377252.4	37	CCDS7132.1																																																																																				0.498	PLXDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047101.2	NM_032812	
SFMBT2	57713	broad.mit.edu	37	10	7214560	7214560	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr10:7214560C>T	ENST00000361972.4	-	18	2138	c.2048G>A	c.(2047-2049)aGc>aAc	p.S683N	SFMBT2_ENST00000397167.1_Missense_Mutation_p.S683N	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	683					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)	p.S683N(1)		NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						GGGGTGTCCGCTGTCGGGGTT	0.547																																					p.S683N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2048A	10						.						47.0	55.0	52.0					10																	7214560		2203	4300	6503	7254566	SO:0001583	missense	57713	exon18			AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"""Sterile alpha motif (SAM) domain containing"""	20256	protein-coding gene	gene with protein product		615392	"""Scm-related gene containing four mbt domains 2"""			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.2048G>A	10.37:g.7214560C>T	ENSP00000355109:p.Ser683Asn		7254566	NM_001029880	A7MD09|Q9HCF5	Missense_Mutation	SNP	ENST00000361972.4	37	CCDS31138.1	.	.	.	.	.	.	.	.	.	.	C	7.728	0.698667	0.15106	.	.	ENSG00000198879	ENST00000361972;ENST00000397167	T;T	0.14640	2.49;2.49	5.37	0.584	0.17422	.	0.430607	0.30302	N	0.009932	T	0.09949	0.0244	L	0.44542	1.39	0.09310	N	0.999995	B	0.27559	0.181	B	0.21151	0.033	T	0.34675	-0.9819	10	0.15499	T	0.54	.	11.4222	0.49989	0.2338:0.5612:0.205:0.0	.	683	Q5VUG0	SMBT2_HUMAN	N	683	ENSP00000355109:S683N;ENSP00000380353:S683N	ENSP00000355109:S683N	S	-	2	0	SFMBT2	7254566	0.268000	0.24133	0.001000	0.08648	0.119000	0.20118	1.206000	0.32321	0.199000	0.20427	0.484000	0.47621	AGC		0.547	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880	
C10orf71	118461	broad.mit.edu	37	10	50530623	50530623	+	Silent	SNP	G	G	A	rs370127754		TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr10:50530623G>A	ENST00000374144.3	+	3	321	c.33G>A	c.(31-33)gcG>gcA	p.A11A	C10orf71_ENST00000323868.4_Silent_p.A11A			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	11								p.A11A(2)		endometrium(1)	1						GCACAGACGCGTTCAGCGACT	0.542																																					p.A11A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G33A	10						.	G	,	1,4305		0,1,2152	38.0	41.0	40.0		33,33	-3.0	0.9	10		40	0,8500		0,0,4250	no	coding-synonymous,coding-synonymous	C10orf71	NM_001135196.1,NM_199459.3	,	0,1,6402	AA,AG,GG		0.0,0.0232,0.0078	,	11/1436,11/720	50530623	1,12805	2153	4250	6403	50200629	SO:0001819	synonymous_variant	118461	exon3			AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.33G>A	10.37:g.50530623G>A			50200629	NM_001135196	A0AVL8	Silent	SNP	ENST00000374144.3	37	CCDS44387.1																																																																																				0.542	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
MTNR1B	4544	broad.mit.edu	37	11	92714701	92714701	+	Silent	SNP	C	C	T	rs139515067		TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr11:92714701C>T	ENST00000257068.2	+	2	318	c.312C>T	c.(310-312)gaC>gaT	p.D104D		NM_005959.3	NP_005950.1	P49286	MTR1B_HUMAN	melatonin receptor 1B	104					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|regulation of insulin secretion (GO:0050796)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|melatonin receptor activity (GO:0008502)	p.D104D(2)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	33		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	TCTTCTATGACGGCTGGGCCC	0.567																																					p.D104D												.	.	2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)	c.C312T	11						.	C		0,4402		0,0,2201	171.0	168.0	169.0		312	-7.9	0.0	11	dbSNP_134	169	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous	MTNR1B	NM_005959.3		0,1,6498	TT,TC,CC		0.0116,0.0,0.0077		104/363	92714701	1,12997	2201	4298	6499	92354349	SO:0001819	synonymous_variant	4544	exon2			AB033598	CCDS8290.1	11q21-q22	2012-08-08			ENSG00000134640	ENSG00000134640		"""GPCR / Class A : Melatonin receptors"""	7464	protein-coding gene	gene with protein product		600804					Standard	NM_005959		Approved		uc001pdk.1	P49286	OTTHUMG00000167364	ENST00000257068.2:c.312C>T	11.37:g.92714701C>T			92354349	NM_005959		Silent	SNP	ENST00000257068.2	37	CCDS8290.1																																																																																				0.567	MTNR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394323.1		
KRT1	3848	broad.mit.edu	37	12	53069199	53069199	+	Silent	SNP	G	G	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr12:53069199G>A	ENST00000252244.3	-	9	1771	c.1713C>T	c.(1711-1713)ggC>ggT	p.G571G		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	571	Gly/Ser-rich.|Tail.				complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)	p.G571G(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						ggccgccgccgccacctccag	0.726																																					p.G571G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1713T	12						.						4.0	5.0	5.0					12																	53069199		1802	3631	5433	51355466	SO:0001819	synonymous_variant	3848	exon9			X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6412	protein-coding gene	gene with protein product		139350	"""epidermolytic hyperkeratosis 1"""	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1713C>T	12.37:g.53069199G>A			51355466	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Silent	SNP	ENST00000252244.3	37	CCDS8836.1																																																																																				0.726	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121	
STAB2	55576	broad.mit.edu	37	12	104100754	104100754	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr12:104100754A>C	ENST00000388887.2	+	38	4385	c.4181A>C	c.(4180-4182)cAc>cCc	p.H1394P		NM_017564.9	NP_060034.9			stabilin 2									p.H1394P(1)		NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						TACGGCATCCACTGTGACCAA	0.567																																					p.H1394P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4181C	12						.						74.0	58.0	63.0					12																	104100754		2203	4300	6503	102624884	SO:0001583	missense	55576	exon38			AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.4181A>C	12.37:g.104100754A>C	ENSP00000373539:p.His1394Pro		102624884	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	A	15.32	2.799822	0.50208	.	.	ENSG00000136011	ENST00000388887;ENST00000258495	D	0.84660	-1.88	5.69	2.11	0.27256	EGF-like, laminin (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.249410	0.40640	N	0.001055	T	0.78604	0.4309	L	0.55834	1.745	0.41290	D	0.986971	P	0.51351	0.944	B	0.44044	0.439	T	0.73122	-0.4082	10	0.29301	T	0.29	.	4.7741	0.13171	0.5993:0.1625:0.2382:0.0	.	1394	Q8WWQ8	STAB2_HUMAN	P	1394;81	ENSP00000373539:H1394P	ENSP00000258495:H81P	H	+	2	0	STAB2	102624884	0.990000	0.36364	0.997000	0.53966	0.993000	0.82548	2.351000	0.44071	0.972000	0.38314	0.533000	0.62120	CAC		0.567	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
CSNK1A1L	122011	broad.mit.edu	37	13	37679161	37679161	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr13:37679161C>T	ENST00000379800.3	-	1	642	c.233G>A	c.(232-234)tGg>tAg	p.W78*		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	78	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell morphogenesis (GO:0000902)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.W78*(1)		NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	37		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)		CTGACCATACCAGTGCATGTG	0.483																																					p.W78X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G233A	13						.						131.0	117.0	122.0					13																	37679161		2203	4300	6503	36577161	SO:0001587	stop_gained	122011	exon1			BC028723	CCDS9363.1	13q13.2	2008-02-05			ENSG00000180138	ENSG00000180138			20289	protein-coding gene	gene with protein product							Standard	NM_145203		Approved	MGC33182	uc001uwm.1	Q8N752	OTTHUMG00000016748	ENST00000379800.3:c.233G>A	13.37:g.37679161C>T	ENSP00000369126:p.Trp78*		36577161	NM_145203	Q5T2N2	Nonsense_Mutation	SNP	ENST00000379800.3	37	CCDS9363.1	.	.	.	.	.	.	.	.	.	.	C	36	5.725958	0.96847	.	.	ENSG00000180138	ENST00000379800	.	.	.	1.01	0.0914	0.14468	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.1036	0.14772	0.0:0.7645:0.0:0.2355	.	.	.	.	X	78	.	ENSP00000369126:W78X	W	-	2	0	CSNK1A1L	36577161	1.000000	0.71417	0.635000	0.29338	0.790000	0.44656	5.366000	0.66122	-0.013000	0.14199	0.561000	0.74099	TGG		0.483	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044563.1	NM_145203	
MYCBP2	23077	broad.mit.edu	37	13	77743778	77743778	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr13:77743778T>A	ENST00000544440.2	-	39	5769	c.5752A>T	c.(5752-5754)Ata>Tta	p.I1918L	MYCBP2_ENST00000357337.6_Missense_Mutation_p.I1918L|MYCBP2_ENST00000407578.2_Missense_Mutation_p.I1956L|MYCBP2_ENST00000360084.5_5'UTR					MYC binding protein 2, E3 ubiquitin protein ligase									p.I1918L(2)|p.I1956L(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		ACTGGTCCTATGTAGGCTATA	0.343																																					p.I1956L												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.A5866T	13						.						84.0	89.0	87.0					13																	77743778		2203	4300	6503	76641779	SO:0001583	missense	23077	exon39			AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"""MYC binding protein 2"""			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.5752A>T	13.37:g.77743778T>A	ENSP00000444596:p.Ile1918Leu		76641779	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	37		.	.	.	.	.	.	.	.	.	.	T	18.38	3.610733	0.66558	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.29917	1.56;1.55;1.56	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.30727	0.0774	N	0.21282	0.65	0.58432	D	0.999995	P	0.35745	0.518	P	0.44647	0.456	T	0.16247	-1.0409	10	0.52906	T	0.07	.	14.9058	0.70718	0.0:0.0:0.0:1.0	.	1918	O75592	MYCB2_HUMAN	L	1918;1956;1918	ENSP00000349892:I1918L;ENSP00000384288:I1956L;ENSP00000444596:I1918L	ENSP00000349892:I1918L	I	-	1	0	MYCBP2	76641779	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.922000	0.87538	1.979000	0.57680	0.524000	0.50904	ATA		0.343	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057	
OR4N2	390429	broad.mit.edu	37	14	20295782	20295782	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr14:20295782C>G	ENST00000315947.1	+	1	175	c.175C>G	c.(175-177)Ctc>Gtc	p.L59V	OR4N2_ENST00000568211.1_Missense_Mutation_p.L59V	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	59						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L59V(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CACAGCCCCCCTCTATTTCTT	0.463																																					p.L59V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C175G	14						.						176.0	211.0	199.0					14																	20295782		2203	4298	6501	19365622	SO:0001583	missense	390429	exon1				CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"""GPCR / Class A : Olfactory receptors"""	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.175C>G	14.37:g.20295782C>G	ENSP00000319601:p.Leu59Val		19365622	NM_001004723	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	37	CCDS32022.1	.	.	.	.	.	.	.	.	.	.	.	12.06	1.823631	0.32237	.	.	ENSG00000176294	ENST00000557677;ENST00000315947	T;T	0.03272	3.99;3.99	4.3	3.33	0.38152	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43260	D	0.000581	T	0.02193	0.0068	N	0.04787	-0.16	0.28095	N	0.931667	B	0.12013	0.005	B	0.12837	0.008	T	0.33828	-0.9853	10	0.87932	D	0	-21.2456	9.0727	0.36502	0.3242:0.6757:0.0:0.0	.	59	Q8NGD1	OR4N2_HUMAN	V	59	ENSP00000452022:L59V;ENSP00000319601:L59V	ENSP00000319601:L59V	L	+	1	0	OR4N2	19365622	0.999000	0.42202	0.943000	0.38184	0.639000	0.38242	4.395000	0.59678	2.374000	0.81015	0.591000	0.81541	CTC		0.463	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2		
SYT16	83851	broad.mit.edu	37	14	62567225	62567225	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr14:62567225C>T	ENST00000430451.2	+	6	1935	c.1738C>T	c.(1738-1740)Cag>Tag	p.Q580*	RP11-355I22.2_ENST00000554252.1_lincRNA	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	580	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)			p.Q560*(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		CTTTGTTTTCCAGGTGGCCCT	0.488																																					p.Q580X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1738T	14						.						81.0	79.0	80.0					14																	62567225		1968	4144	6112	61636978	SO:0001587	stop_gained	83851	exon6			BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"""Synaptotagmins"""	23142	protein-coding gene	gene with protein product	"""synaptotagmin XIV-related"", "" chr14 synaptotagmin"""	610950	"""synaptotagmin XIV-like"""	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.1738C>T	14.37:g.62567225C>T	ENSP00000394700:p.Gln580*		61636978	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Nonsense_Mutation	SNP	ENST00000430451.2	37	CCDS45121.1	.	.	.	.	.	.	.	.	.	.	C	38	7.095189	0.98059	.	.	ENSG00000139973	ENST00000430451	.	.	.	5.08	4.17	0.49024	.	0.193443	0.46758	D	0.000274	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-2.6889	15.4546	0.75302	0.0:0.8608:0.1392:0.0	.	.	.	.	X	580	.	ENSP00000394700:Q580X	Q	+	1	0	SYT16	61636978	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	7.294000	0.78760	1.324000	0.45282	0.655000	0.94253	CAG		0.488	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914	
FAM181A	90050	broad.mit.edu	37	14	94391700	94391700	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr14:94391700C>T	ENST00000267594.5	+	2	390	c.83C>T	c.(82-84)gCg>gTg	p.A28V	FAM181A_ENST00000557000.2_5'Flank|FAM181A_ENST00000557719.1_Intron|FAM181A_ENST00000556222.1_5'Flank|FAM181A-AS1_ENST00000554742.1_RNA	NM_001207073.1|NM_001207074.1|NM_138344.4	NP_001194002.1|NP_001194003.1|NP_612353.3	Q8N9Y4	F181A_HUMAN	family with sequence similarity 181, member A	28			A -> T (in dbSNP:rs10141024). {ECO:0000269|PubMed:14702039}.					p.A28V(1)		cervix(1)|endometrium(2)|large_intestine(8)|lung(4)|prostate(1)|skin(2)	18						GAGAAAAGGGCGAGCACAGCA	0.527																																					p.A28V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C83T	14						.						78.0	71.0	73.0					14																	94391700		2203	4300	6503	93461453	SO:0001583	missense	90050	exon2			BC009073	CCDS9914.1, CCDS55939.1	14q32.12	2011-11-30	2008-07-22	2008-07-22	ENSG00000140067	ENSG00000140067			20491	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 152"""	C14orf152			Standard	NM_138344		Approved		uc021saz.1	Q8N9Y4	OTTHUMG00000171297	ENST00000267594.5:c.83C>T	14.37:g.94391700C>T	ENSP00000267594:p.Ala28Val		93461453	NM_138344	B2RD39|Q96GY1	Missense_Mutation	SNP	ENST00000267594.5	37	CCDS9914.1	.	.	.	.	.	.	.	.	.	.	C	10.08	1.251363	0.22880	.	.	ENSG00000140067	ENST00000267594	T	0.34472	1.36	2.54	1.64	0.23874	.	.	.	.	.	T	0.17662	0.0424	N	0.08118	0	0.09310	N	0.999991	B	0.11235	0.004	B	0.04013	0.001	T	0.18461	-1.0336	9	0.62326	D	0.03	.	5.3229	0.15891	0.0:0.8364:0.0:0.1636	.	28	Q8N9Y4	F181A_HUMAN	V	28	ENSP00000267594:A28V	ENSP00000267594:A28V	A	+	2	0	FAM181A	93461453	0.001000	0.12720	0.004000	0.12327	0.072000	0.16883	0.115000	0.15540	0.633000	0.30452	0.462000	0.41574	GCG		0.527	FAM181A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412840.1	NM_138344	
TCL1B	9623	broad.mit.edu	37	14	96157169	96157169	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr14:96157169G>A	ENST00000340722.7	+	2	310	c.259G>A	c.(259-261)Gtg>Atg	p.V87M	RP11-1070N10.6_ENST00000461160.1_RNA	NM_004918.3	NP_004909.1	O95988	TCL1B_HUMAN	T-cell leukemia/lymphoma 1B	87								p.V87M(1)		cervix(1)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(154;0.103)		COAD - Colon adenocarcinoma(157;0.205)|Epithelial(152;0.248)		GCTGCCCGCCGTGTGGCAGCT	0.587																																					p.V87M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G259A	14						.						75.0	78.0	77.0					14																	96157169		2203	4300	6503	95226922	SO:0001583	missense	9623	exon2			AB018563	CCDS32151.1	14q32.1	2008-09-05			ENSG00000213231	ENSG00000213231			11649	protein-coding gene	gene with protein product		603769				10077617	Standard	NM_004918		Approved	TML1	uc001yez.3	O95988	OTTHUMG00000028912	ENST00000340722.7:c.259G>A	14.37:g.96157169G>A	ENSP00000343223:p.Val87Met		95226922	NM_004918	A6NEK7|Q6IAR7|Q9UBQ4	Missense_Mutation	SNP	ENST00000340722.7	37	CCDS32151.1	.	.	.	.	.	.	.	.	.	.	G	3.281	-0.147000	0.06627	.	.	ENSG00000213231	ENST00000340722;ENST00000538038	T	0.27890	1.64	3.11	-2.93	0.05598	.	.	.	.	.	T	0.11024	0.0269	N	0.10733	0.035	0.09310	N	1	B	0.26635	0.155	B	0.15052	0.012	T	0.23119	-1.0197	9	0.26408	T	0.33	-1.4153	3.4045	0.07336	0.5557:0.0:0.2461:0.1981	.	87	O95988	TCL1B_HUMAN	M	87	ENSP00000343223:V87M	ENSP00000343223:V87M	V	+	1	0	TCL1B	95226922	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.327000	0.02682	-0.583000	0.05921	-1.214000	0.01621	GTG		0.587	TCL1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315123.2		
C15orf40	123207	broad.mit.edu	37	15	83674373	83674373	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr15:83674373T>A	ENST00000513601.2	-	4	445	c.438A>T	c.(436-438)ttA>ttT	p.L146F	C15orf40_ENST00000538348.2_Intron|RP11-382A20.5_ENST00000566841.1_RNA|C15orf40_ENST00000304177.5_Missense_Mutation_p.L119F|C15orf40_ENST00000451195.3_Intron|C15orf40_ENST00000565712.1_Missense_Mutation_p.L61F			Q8WUR7	CO040_HUMAN	chromosome 15 open reading frame 40	146								p.L119F(1)		large_intestine(3)|lung(2)|skin(1)	6						CTTCCTTTTTTAATTTCTCCA	0.458																																					p.L146F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A438T	15						.						129.0	140.0	136.0					15																	83674373		2203	4300	6503	81465377	SO:0001583	missense	123207	exon4			BC019820	CCDS32312.1, CCDS32312.2, CCDS53968.1, CCDS53969.1	15q25.2	2012-05-30			ENSG00000169609	ENSG00000169609			28443	protein-coding gene	gene with protein product							Standard	NM_144597		Approved	MGC29937	uc010uoo.1	Q8WUR7	OTTHUMG00000160473	ENST00000513601.2:c.438A>T	15.37:g.83674373T>A	ENSP00000424666:p.Leu146Phe		81465377	NM_144597	A6NIC9|B2R5E7|F5GX92|F8WD31|G5EA00	Missense_Mutation	SNP	ENST00000513601.2	37	CCDS32312.2	.	.	.	.	.	.	.	.	.	.	T	15.87	2.959667	0.53400	.	.	ENSG00000169609	ENST00000304177;ENST00000513601	.	.	.	5.86	-2.3	0.06785	.	0.000000	0.64402	D	0.000002	T	0.74711	0.3752	.	.	.	0.49915	D	0.999836	D	0.89917	1.0	D	0.91635	0.999	T	0.75379	-0.3338	8	0.51188	T	0.08	-2.0313	13.0377	0.58881	0.0:0.6314:0.0:0.3686	.	146	G5EA00	.	F	119;146	.	ENSP00000307071:L119F	L	-	3	2	C15orf40	81465377	1.000000	0.71417	0.935000	0.37517	0.872000	0.50106	0.834000	0.27518	-0.228000	0.09869	-0.256000	0.11100	TTA		0.458	C15orf40-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360737.2	NM_144597	
SEC14L5	9717	broad.mit.edu	37	16	5041924	5041924	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr16:5041924G>A	ENST00000251170.7	+	6	740	c.560G>A	c.(559-561)cGt>cAt	p.R187H		NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	187						integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)	p.R187H(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						GCCCCAGTCCGTGAGGAGGAT	0.667																																					p.R187H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G560A	16						.						32.0	33.0	32.0					16																	5041924		2025	4168	6193	4981925	SO:0001583	missense	9717	exon6			AB007880	CCDS45403.1	16p13.3	2008-02-05				ENSG00000103184			29032	protein-coding gene	gene with protein product						9455477	Standard	NM_014692		Approved	KIAA0420, PRELID4B	uc002cye.2	O43304		ENST00000251170.7:c.560G>A	16.37:g.5041924G>A	ENSP00000251170:p.Arg187His		4981925	NM_014692		Missense_Mutation	SNP	ENST00000251170.7	37	CCDS45403.1	.	.	.	.	.	.	.	.	.	.	G	8.553	0.876051	0.17395	.	.	ENSG00000103184	ENST00000251170	T	0.70399	-0.48	4.3	1.1	0.20463	.	0.757705	0.11517	N	0.556086	T	0.53802	0.1819	L	0.57536	1.79	0.09310	N	1	P	0.36495	0.556	B	0.20955	0.032	T	0.49934	-0.8886	10	0.46703	T	0.11	-16.18	0.9059	0.01284	0.2336:0.1774:0.4074:0.1815	.	187	O43304	S14L5_HUMAN	H	187	ENSP00000251170:R187H	ENSP00000251170:R187H	R	+	2	0	SEC14L5	4981925	0.000000	0.05858	0.072000	0.20136	0.360000	0.29518	-0.426000	0.07008	0.085000	0.17107	0.650000	0.86243	CGT		0.667	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1		
SEPT1	1731	broad.mit.edu	37	16	30387814	30387814	+	IGR	SNP	C	C	T	rs149087136		TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr16:30387814C>T	ENST00000571393.1	-	0	1589				MYLPF_ENST00000322861.7_Silent_p.T81T			Q8WYJ6	SEPT1_HUMAN	septin 1						cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)	p.T81T(2)		breast(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)|urinary_tract(1)	24			Colorectal(24;0.193)			TCAACTTCACCGTCTTCCTGA	0.597																																					p.T81T												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.C243T	16						.	C		1,4393	2.1+/-5.4	0,1,2196	127.0	124.0	125.0		243	-11.0	0.1	16	dbSNP_134	125	0,8600		0,0,4300	no	coding-synonymous	MYLPF	NM_013292.3		0,1,6496	TT,TC,CC		0.0,0.0228,0.0077		81/170	30387814	1,12993	2197	4300	6497	30295315	SO:0001628	intergenic_variant	29895	exon4			AF308288	CCDS10678.1, CCDS10678.2, CCDS10678.3	16p11.2	2013-01-21		2001-09-10	ENSG00000180096	ENSG00000180096	3.1.5.1	"""Septins"""	2879	protein-coding gene	gene with protein product		612897		DIFF6		8697812	Standard	NM_052838		Approved	PNUTL3	uc002dxy.4	Q8WYJ6	OTTHUMG00000176984		16.37:g.30387814C>T			30295315	NM_013292	B4DVE6|Q658T1|Q8NEZ1|Q96EL4|Q9H285	Silent	SNP	ENST00000571393.1	37																																																																																					0.597	SEPT1-201	KNOWN	basic	protein_coding	protein_coding		NM_052838	
CHST4	10164	broad.mit.edu	37	16	71571118	71571118	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr16:71571118C>T	ENST00000338482.5	+	3	881	c.538C>T	c.(538-540)Cgc>Tgc	p.R180C	CHST4_ENST00000572450.1_Missense_Mutation_p.R180C|RP11-510M2.5_ENST00000568523.1_RNA|CHST4_ENST00000539698.3_Missense_Mutation_p.R180C|ZNF19_ENST00000568446.1_Intron			Q8NCG5	CHST4_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 4	180					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|immune response (GO:0006955)|inflammatory response (GO:0006954)|leukocyte tethering or rolling (GO:0050901)|N-acetylglucosamine metabolic process (GO:0006044)|protein sulfation (GO:0006477)|sulfur compound metabolic process (GO:0006790)	integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)	p.R180C(1)		cervix(1)|kidney(3)|large_intestine(9)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	21						CAAGGAGGTGCGCTTCTTCAA	0.637																																					p.R180C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C538T	16						.						87.0	87.0	87.0					16																	71571118		2198	4300	6498	70128619	SO:0001583	missense	10164	exon2			AF131235	CCDS10902.1	16q22.2	2008-02-05			ENSG00000140835	ENSG00000140835		"""Sulfotransferases, membrane-bound"""	1972	protein-coding gene	gene with protein product						10330415	Standard	NM_001166395		Approved	HEC-GLCNAC-6-ST, LSST	uc002fao.3	Q8NCG5	OTTHUMG00000137592	ENST00000338482.5:c.538C>T	16.37:g.71571118C>T	ENSP00000341206:p.Arg180Cys		70128619	NM_001166395	Q8IV46|Q9Y5R3	Missense_Mutation	SNP	ENST00000338482.5	37	CCDS10902.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.410209	0.83340	.	.	ENSG00000140835	ENST00000338482;ENST00000539698	D;D	0.84730	-1.89;-1.89	5.8	5.8	0.92144	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	D	0.94725	0.8298	H	0.94503	3.545	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95673	0.8725	10	0.87932	D	0	-3.2798	17.5569	0.87894	0.0:1.0:0.0:0.0	.	180	Q8NCG5	CHST4_HUMAN	C	180	ENSP00000341206:R180C;ENSP00000441204:R180C	ENSP00000341206:R180C	R	+	1	0	CHST4	70128619	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	3.915000	0.56409	2.735000	0.93741	0.655000	0.94253	CGC		0.637	CHST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268992.4	NM_005769	
GRIN2C	2905	broad.mit.edu	37	17	72851074	72851075	+	Frame_Shift_Ins	INS	-	-	G	rs371191120		TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	-	-	-	-	-	-	Unknown	Wildtype	None	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr17:72851074_72851075insG	ENST00000293190.5	-	2	303_304	c.157_158insC	c.(157-159)cagfs	p.Q53fs	GRIN2C_ENST00000347612.4_Frame_Shift_Ins_p.Q53fs|GRIN2C_ENST00000578159.1_Intron	NM_000835.3	NP_000826.2	Q14957	NMDE3_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2C	53					directional locomotion (GO:0033058)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of protein catabolic process (GO:0042177)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	33	all_lung(278;0.172)|Lung NSC(278;0.207)				Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CAGGAAGCTCTGGGGGGTGAGG	0.683																																					p.Q53fs												.	.	0			c.158_159insC	17						.																																			70362670	SO:0001589	frameshift_variant	2905	exon2				CCDS32724.1, CCDS62330.1	17q25.1	2012-08-29			ENSG00000161509	ENSG00000161509		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4587	protein-coding gene	gene with protein product		138254		NMDAR2C		9480759	Standard	NM_001278553		Approved	GluN2C	uc002jlt.1	Q14957	OTTHUMG00000044524	ENST00000293190.5:c.158dupC	17.37:g.72851080_72851080dupG	ENSP00000293190:p.Gln53fs		70362669	NM_000835	B2RTT1	Frame_Shift_Ins	INS	ENST00000293190.5	37	CCDS32724.1																																																																																				0.683	GRIN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103824.1		
H3F3B	3021	broad.mit.edu	37	17	73775203	73775204	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr17:73775203_73775204insG	ENST00000254810.4	-	2	184_185	c.52_53insC	c.(52-54)cgcfs	p.R18fs	H3F3B_ENST00000591890.1_Frame_Shift_Ins_p.R18fs|H3F3B_ENST00000589599.1_Frame_Shift_Ins_p.R18fs|H3F3B_ENST00000592643.1_Frame_Shift_Ins_p.R18fs|H3F3B_ENST00000593254.1_Intron|H3F3B_ENST00000587560.1_Frame_Shift_Ins_p.R18fs|H3F3B_ENST00000586607.1_Frame_Shift_Ins_p.R18fs	NM_005324.3	NP_005315.1	P84243	H33_HUMAN	H3 histone, family 3B (H3.3B)	18					blood coagulation (GO:0007596)|brain development (GO:0007420)|DNA replication-independent nucleosome assembly (GO:0006336)|positive regulation of cell growth (GO:0030307)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nuclear nucleosome (GO:0000788)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	nucleosomal DNA binding (GO:0031492)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)	p.R18fs*80(2)		large_intestine(1)|lung(4)|ovary(2)|skin(1)	8	all_cancers(13;1.5e-07)		all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)			CAGCTGTTTGCGGGGGGCTTTC	0.614											OREG0024740	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R18fs												.	.	2	Insertion - Frameshift(2)	ovary(1)|large_intestine(1)	c.53_54insC	17						.																																			71286799	SO:0001589	frameshift_variant	3021	exon2			Z48950	CCDS11729.1	17q25.1	2011-06-01			ENSG00000132475	ENSG00000132475		"""Histones / Replication-independent"""	4765	protein-coding gene	gene with protein product		601058				8586426	Standard	NM_005324		Approved	H3.3B	uc002jpl.3	P84243		ENST00000254810.4:c.53dupC	17.37:g.73775209_73775209dupG	ENSP00000254810:p.Arg18fs	1147	71286798	NM_005324	P06351|P33155|Q5VV55|Q5VV56|Q66I33|Q9V3W4	Frame_Shift_Ins	INS	ENST00000254810.4	37	CCDS11729.1																																																																																				0.614	H3F3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448499.1	NM_005324	
TP53	7157	broad.mit.edu	37	17	7579582	7579583	+	Frame_Shift_Ins	INS	-	-	A	rs121912661		TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr17:7579582_7579583insA	ENST00000269305.4	-	4	293_294	c.104_105insT	c.(103-105)ttgfs	p.L35fs	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Frame_Shift_Ins_p.L35fs|TP53_ENST00000455263.2_Frame_Shift_Ins_p.L35fs|TP53_ENST00000445888.2_Frame_Shift_Ins_p.L35fs|TP53_ENST00000413465.2_Frame_Shift_Ins_p.L35fs|TP53_ENST00000359597.4_Frame_Shift_Ins_p.L35fs	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	35	Interaction with HRMT1L2.|Transcription activation (acidic).		L -> F (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.L35fs*8(4)|p.L35F(3)|p.?(1)|p.S33fs*23(1)|p.P13fs*18(1)|p.S33fs*6(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)	CTTGGGACGGCAAGGGGGACTG	0.599		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.L35fs	Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	.	.	19	Whole gene deletion(8)|Insertion - Frameshift(4)|Substitution - Missense(3)|Deletion - Frameshift(3)|Unknown(1)	large_intestine(4)|bone(4)|upper_aerodigestive_tract(2)|central_nervous_system(2)|lung(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|liver(1)|breast(1)|pancreas(1)	c.105_106insT	17						.																																			7520308	SO:0001589	frameshift_variant	7157	exon4	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.105dupT	17.37:g.7579584_7579584dupA	ENSP00000269305:p.Leu35fs		7520307	NM_001126112	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	Frame_Shift_Ins	INS	ENST00000269305.4	37	CCDS11118.1																																																																																				0.599	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
STXBP4	252983	broad.mit.edu	37	17	53150373	53150373	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr17:53150373G>A	ENST00000376352.2	+	13	1331	c.1124G>A	c.(1123-1125)cGt>cAt	p.R375H	STXBP4_ENST00000434978.2_Missense_Mutation_p.R353H	NM_178509.5	NP_848604.3	Q6ZWJ1	STXB4_HUMAN	syntaxin binding protein 4	375					cellular response to DNA damage stimulus (GO:0006974)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of keratinocyte proliferation (GO:0010838)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.R375H(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19						GAAGTGATCCGTCTGTTAGAG	0.443																																					p.R375H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1124A	17						.						133.0	122.0	125.0					17																	53150373		2203	4300	6503	50505372	SO:0001583	missense	252983	exon13			BC041485	CCDS11584.2	17q22	2008-02-05			ENSG00000166263	ENSG00000166263			19694	protein-coding gene	gene with protein product		610415				12855681	Standard	XM_005257187		Approved	Synip, MGC50337	uc002iuf.1	Q6ZWJ1	OTTHUMG00000074043	ENST00000376352.2:c.1124G>A	17.37:g.53150373G>A	ENSP00000365530:p.Arg375His		50505372	NM_178509	Q8IVZ5	Missense_Mutation	SNP	ENST00000376352.2	37	CCDS11584.2	.	.	.	.	.	.	.	.	.	.	G	12.26	1.886064	0.33348	.	.	ENSG00000166263	ENST00000376352;ENST00000434978	T;T	0.50277	0.75;0.75	5.57	3.57	0.40892	.	0.164927	0.56097	N	0.000040	T	0.27594	0.0678	N	0.12961	0.28	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.06405	0.001;0.002	T	0.06180	-1.0841	10	0.14656	T	0.56	-1.1044	11.521	0.50551	0.1473:0.0:0.8527:0.0	.	353;375	E7EPP7;Q6ZWJ1	.;STXB4_HUMAN	H	375;353	ENSP00000365530:R375H;ENSP00000391087:R353H	ENSP00000365530:R375H	R	+	2	0	STXBP4	50505372	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.372000	0.34261	1.336000	0.45506	0.650000	0.86243	CGT		0.443	STXBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157184.1	NM_178509	
CETN1	1068	broad.mit.edu	37	18	580532	580532	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr18:580532G>A	ENST00000327228.3	+	1	166	c.124G>A	c.(124-126)Gtg>Atg	p.V42M		NM_004066.1	NP_004057.1	Q12798	CETN1_HUMAN	centrin, EF-hand protein, 1	42	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cellular response to heat (GO:0034605)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|photoreceptor connecting cilium (GO:0032391)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|calcium ion binding (GO:0005509)|nucleic acid binding (GO:0003676)	p.V42M(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(2)	25						CCTCTTCGACGTGGACGGAAG	0.562																																					p.V42M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G124A	18						.						75.0	57.0	63.0					18																	580532		2203	4300	6503	570532	SO:0001583	missense	1068	exon1			U03270	CCDS11820.1	18p11.32	2013-01-10			ENSG00000177143	ENSG00000177143		"""EF-hand domain containing"""	1866	protein-coding gene	gene with protein product		603187		CETN		8175926	Standard	NM_004066		Approved	CEN1	uc002kko.1	Q12798	OTTHUMG00000131471	ENST00000327228.3:c.124G>A	18.37:g.580532G>A	ENSP00000319052:p.Val42Met		570532	NM_004066	B2R536	Missense_Mutation	SNP	ENST00000327228.3	37	CCDS11820.1	.	.	.	.	.	.	.	.	.	.	G	7.845	0.722774	0.15439	.	.	ENSG00000177143	ENST00000327228	T	0.72051	-0.62	5.2	2.35	0.29111	EF-hand-like domain (1);	0.354615	0.28989	N	0.013484	T	0.51584	0.1683	N	0.25380	0.74	0.20074	N	0.999938	B	0.12630	0.006	B	0.14578	0.011	T	0.45234	-0.9275	10	0.62326	D	0.03	.	4.0542	0.09810	0.1502:0.0:0.4581:0.3917	.	42	Q12798	CETN1_HUMAN	M	42	ENSP00000319052:V42M	ENSP00000319052:V42M	V	+	1	0	CETN1	570532	0.602000	0.26916	0.569000	0.28460	0.001000	0.01503	2.054000	0.41335	0.838000	0.34948	-0.169000	0.13324	GTG		0.562	CETN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254314.2	NM_004066	
CELF4	56853	broad.mit.edu	37	18	34854360	34854360	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr18:34854360G>A	ENST00000591282.1	-	6	714	c.715C>T	c.(715-717)Cgg>Tgg	p.R239W	CELF4_ENST00000334919.5_Missense_Mutation_p.R229W|CELF4_ENST00000601019.1_Missense_Mutation_p.R238W|CELF4_ENST00000588597.1_Missense_Mutation_p.R228W|CELF4_ENST00000361795.5_Missense_Mutation_p.R238W|RP11-797E24.3_ENST00000588766.1_RNA|CELF4_ENST00000412753.1_Missense_Mutation_p.R239W|CELF4_ENST00000591287.1_Missense_Mutation_p.R238W|CELF4_ENST00000420428.2_Missense_Mutation_p.R239W|CELF4_ENST00000603232.1_Missense_Mutation_p.R239W|RP11-797E24.3_ENST00000586610.1_RNA			Q9BZC1	CELF4_HUMAN	CUGBP, Elav-like family member 4	239	Necessary for TNNT2 exon 5 inclusion.|Sufficient for RNA-binding and MSE- dependent splicing activity.				alternative mRNA splicing, via spliceosome (GO:0000380)|embryo development (GO:0009790)|germ cell development (GO:0007281)|mRNA splice site selection (GO:0006376)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of translation (GO:0017148)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	BRE binding (GO:0042835)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|translation repressor activity, nucleic acid binding (GO:0000900)	p.R239W(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	44						TGCATTCGCCGCATCGTGCGC	0.667																																					p.R229W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C685T	18						.						103.0	85.0	91.0					18																	34854360		2203	4300	6503	33108358	SO:0001583	missense	56853	exon6			AF248651	CCDS32818.1, CCDS45857.1, CCDS45858.1	18q12	2013-02-12	2010-02-19	2010-02-19				"""RNA binding motif (RRM) containing"""	14015	protein-coding gene	gene with protein product		612679	"""Bruno (Drosophila) -like 4, RNA binding protein"", ""bruno-like 4, RNA binding protein (Drosophila)"""	BRUNOL4		10893231	Standard	NM_020180		Approved		uc002lae.2	Q9BZC1		ENST00000591282.1:c.715C>T	18.37:g.34854360G>A	ENSP00000464794:p.Arg239Trp		33108358	NM_001025089	Q59EN7|Q86XB9|Q8N2M6|Q9BQ96|Q9NR84|Q9NR85	Missense_Mutation	SNP	ENST00000591282.1	37	CCDS32818.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.159388	0.78226	.	.	ENSG00000101489	ENST00000361795;ENST00000412753;ENST00000420428;ENST00000334919;ENST00000361683	T;T;T	0.06449	3.3;3.31;3.31	4.55	3.59	0.41128	.	0.000000	0.85682	D	0.000000	T	0.29882	0.0747	M	0.91510	3.215	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.993;1.0;0.999;0.996	T	0.19614	-1.0300	10	0.87932	D	0	-12.5849	12.0837	0.53686	0.0:0.0:0.7247:0.2753	.	238;228;229;238;239	Q9BZC1-3;B4DHA8;Q9BZC1-5;Q9BZC1-2;Q9BZC1	.;.;.;.;CELF4_HUMAN	W	239;239;238;229;122	ENSP00000355089:R239W;ENSP00000406823:R239W;ENSP00000335631:R229W	ENSP00000335631:R229W	R	-	1	2	CELF4	33108358	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.280000	0.43443	2.373000	0.80994	0.561000	0.74099	CGG		0.667	CELF4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440892.1	NM_020180	
TLE2	7089	broad.mit.edu	37	19	3005507	3005508	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr19:3005507_3005508insC	ENST00000262953.6	-	17	2085_2086	c.1823_1824insG	c.(1822-1824)ggcfs	p.G608fs	TLE2_ENST00000591529.1_Frame_Shift_Ins_p.G622fs|TLE2_ENST00000443826.3_Frame_Shift_Ins_p.G486fs|TLE2_ENST00000426948.2_Frame_Shift_Ins_p.G622fs|TLE2_ENST00000447365.2_Frame_Shift_Ins_p.G275fs|TLE2_ENST00000455444.2_Frame_Shift_Ins_p.G486fs|TLE2_ENST00000586422.1_Intron|TLE2_ENST00000590536.1_Frame_Shift_Ins_p.G609fs	NM_003260.4	NP_003251.2	Q04725	TLE2_HUMAN	transducin-like enhancer of split 2	608					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)	p.L609fs*20(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	13				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGTTGTCCAGGCCCCCTGTCCA	0.663																																					p.G608fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1824_1825insG	19						.		,,	0,3966		0,0,1983					,,	2.0	1.0			52	4,8084		0,4,4040	no	frameshift,frameshift,frameshift	TLE2	NM_003260.4,NM_001144762.1,NM_001144761.1	,,	0,4,6023	A1A1,A1R,RR		0.0495,0.0,0.0332	,,	,,		4,12050				2956508	SO:0001589	frameshift_variant	7089	exon17			M99436	CCDS45911.1, CCDS45912.1, CCDS45913.1, CCDS74255.1	19p13.3	2014-03-07	2014-03-07					"""WD repeat domain containing"""	11838	protein-coding gene	gene with protein product	"""enhancer of split groucho 2"""	601041	"""transducin-like enhancer of split 2, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 2 (E(sp1) homolog, Drosophila)"""			8808280	Standard	NM_003260		Approved	ESG2, GRG2, ESG, FLJ41188	uc002lww.3	Q04725		ENST00000262953.6:c.1824dupG	19.37:g.3005512_3005512dupC	ENSP00000262953:p.Gly608fs		2956507	NM_003260	B4DE03|E9PEV7|F8WCH2|Q8WVY0|Q9Y6S0	Frame_Shift_Ins	INS	ENST00000262953.6	37	CCDS45911.1																																																																																				0.663	TLE2-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452194.2	NM_003260	
ZNF536	9745	broad.mit.edu	37	19	30935968	30935968	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr19:30935968C>A	ENST00000355537.3	+	2	1646	c.1499C>A	c.(1498-1500)tCc>tAc	p.S500Y		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	500					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)	p.S500Y(1)		NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					CCGCTGAAATCCAGCTGCATC	0.662																																					p.S500Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1499A	19						.						35.0	40.0	38.0					19																	30935968		2198	4293	6491	35627808	SO:0001583	missense	9745	exon2				CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"""Zinc fingers, C2H2-type"""	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.1499C>A	19.37:g.30935968C>A	ENSP00000347730:p.Ser500Tyr		35627808	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	37	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	C	16.29	3.081526	0.55753	.	.	ENSG00000198597	ENST00000355537	T	0.09911	2.93	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.29783	0.0744	L	0.47716	1.5	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.00666	-1.1619	10	0.72032	D	0.01	-32.9743	19.4573	0.94900	0.0:1.0:0.0:0.0	.	500;500	A7E228;O15090	.;ZN536_HUMAN	Y	500	ENSP00000347730:S500Y	ENSP00000347730:S500Y	S	+	2	0	ZNF536	35627808	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.788000	0.85771	2.582000	0.87167	0.655000	0.94253	TCC		0.662	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
DHDH	27294	broad.mit.edu	37	19	49442819	49442819	+	Silent	SNP	C	C	T	rs148646797		TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr19:49442819C>T	ENST00000221403.2	+	4	520	c.480C>T	c.(478-480)caC>caT	p.H160H	DHDH_ENST00000523250.1_Intron|DHDH_ENST00000522614.1_Silent_p.H160H	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	160					carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)	p.H160H(1)		central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		ATCTCATCCACGTTCCCCGGG	0.617													T|||	1	0.000199681	0.0008	0.0	5008	,	,		16754	0.0		0.0	False		,,,				2504	0.0				p.H160H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C480T	19						.	T		4,4402	825.7+/-416.5	0,4,2199	49.0	51.0	51.0		480	-1.8	0.0	19	dbSNP_134	51	0,8600		0,0,4300	no	coding-synonymous	DHDH	NM_014475.3		0,4,6499	TT,TC,CC		0.0,0.0908,0.0308		160/335	49442819	4,13002	2203	4300	6503	54134631	SO:0001819	synonymous_variant	27294	exon4			AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.480C>T	19.37:g.49442819C>T			54134631	NM_014475		Silent	SNP	ENST00000221403.2	37	CCDS12741.1																																																																																				0.617	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475	
PTH2	113091	broad.mit.edu	37	19	49926509	49926509	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr19:49926509T>G	ENST00000270631.1	-	1	189	c.88A>C	c.(88-90)Act>Cct	p.T30P	CTD-3148I10.1_ENST00000576655.1_5'Flank	NM_178449.3	NP_848544.1	Q96A98	TIP39_HUMAN	parathyroid hormone 2	30					neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)		p.T30P(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(262;0.0015)|GBM - Glioblastoma multiforme(486;0.044)|Lung(386;0.0785)|LUSC - Lung squamous cell carcinoma(496;0.0836)		CCCGAGGCAGTGCGGACGCCC	0.672																																					p.T30P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A88C	19						.						19.0	25.0	23.0					19																	49926509		2203	4300	6503	54618321	SO:0001583	missense	113091	exon1			AY037555	CCDS12763.1	19q13.33	2013-02-28				ENSG00000142538		"""Endogenous ligands"""	30828	protein-coding gene	gene with protein product	"""tuberoinfundibular 39 residues"""	608386				11861531	Standard	NM_178449		Approved	TIP39	uc002pnn.1	Q96A98		ENST00000270631.1:c.88A>C	19.37:g.49926509T>G	ENSP00000270631:p.Thr30Pro		54618321	NM_178449	Q96DJ4	Missense_Mutation	SNP	ENST00000270631.1	37	CCDS12763.1	.	.	.	.	.	.	.	.	.	.	t	12.20	1.866113	0.32977	.	.	ENSG00000142538	ENST00000270631	.	.	.	4.3	-5.52	0.02560	.	0.913256	0.09114	N	0.846675	T	0.15046	0.0363	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.22695	-1.0209	9	0.33141	T	0.24	0.7367	7.2766	0.26288	0.1072:0.0828:0.6378:0.1722	.	30	Q96A98	TIP39_HUMAN	P	30	.	ENSP00000270631:T30P	T	-	1	0	PTH2	54618321	0.000000	0.05858	0.000000	0.03702	0.329000	0.28539	-1.633000	0.02022	-1.117000	0.02965	0.375000	0.23000	ACT		0.672	PTH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465366.1	NM_178449	
SIGLEC10	89790	broad.mit.edu	37	19	51916978	51916978	+	Silent	SNP	C	C	T	rs144827503	byFrequency	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr19:51916978C>T	ENST00000339313.5	-	10	1925	c.1809G>A	c.(1807-1809)acG>acA	p.T603T	SIGLEC10_ENST00000353836.5_Silent_p.T508T|SIGLEC10_ENST00000436984.2_Silent_p.T460T|SIGLEC10_ENST00000525998.1_Silent_p.T418T|CTD-2616J11.3_ENST00000532473.1_RNA|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000356298.5_Silent_p.T603T|SIGLEC10_ENST00000442846.3_Silent_p.T360T|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000441969.3_Silent_p.T450T|SIGLEC10_ENST00000432469.2_Silent_p.T425T|SIGLEC10_ENST00000439889.2_Silent_p.T545T			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	603					cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.T545T(1)|p.T603T(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		GGGGGCCAGCCGTCGGGACCA	0.542													c|||	12	0.00239617	0.0091	0.0	5008	,	,		17783	0.0		0.0	False		,,,				2504	0.0				p.T508T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1524A	19						.	C	,,,,,,	18,4388		0,18,2185	90.0	93.0	92.0		1635,1524,1380,1350,1275,1080,1809	-9.8	0.0	19	dbSNP_134	92	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SIGLEC10	NM_001171156.1,NM_001171157.1,NM_001171158.1,NM_001171159.1,NM_001171160.1,NM_001171161.1,NM_033130.4	,,,,,,	0,18,6485	TT,TC,CC		0.0,0.4085,0.1384	,,,,,,	545/640,508/603,460/555,450/545,425/520,360/455,603/698	51916978	18,12988	2203	4300	6503	56608790	SO:0001819	synonymous_variant	89790	exon9			AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.1809G>A	19.37:g.51916978C>T			56608790	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																				0.542	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
CC2D1B	200014	broad.mit.edu	37	1	52820565	52820566	+	Frame_Shift_Ins	INS	-	-	CC			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	-	-	-	CC	-	-	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr1:52820565_52820566insCC	ENST00000371586.2	-	22	2441_2442	c.2303_2304insGG	c.(2302-2304)ggcfs	p.G768fs	RP11-155O18.6_ENST00000606527.1_RNA|CC2D1B_ENST00000438831.1_Frame_Shift_Ins_p.G143fs|CC2D1B_ENST00000460261.1_5'UTR|CC2D1B_ENST00000284376.3_Frame_Shift_Ins_p.G762fs	NM_032449.2	NP_115825.1	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	768	C2.					nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.F769fs*5(1)		breast(1)|large_intestine(6)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	27						CCCTCTTGAAGCCCCGGTGGTT	0.53																																					p.G768fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.2304_2305insGG	1						.																																			52593154	SO:0001589	frameshift_variant	200014	exon22			AB058739	CCDS30714.1	1p32.3	2008-02-05			ENSG00000154222	ENSG00000154222			29386	protein-coding gene	gene with protein product						11347906	Standard	NM_032449		Approved	KIAA1836	uc001ctq.2	Q5T0F9	OTTHUMG00000008102	ENST00000371586.2:c.2302_2303dupGG	1.37:g.52820568_52820569dupCC	ENSP00000360642:p.Gly768fs		52593153	NM_032449	Q49AE8|Q5T0F8|Q5T0G0|Q6ZNQ1|Q96AP3|Q96I04|Q96JJ1	Frame_Shift_Ins	INS	ENST00000371586.2	37	CCDS30714.1																																																																																				0.530	CC2D1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022189.1	NM_032449	
VPS13D	55187	broad.mit.edu	37	1	12403045	12403045	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr1:12403045G>A	ENST00000358136.3	+	42	8952	c.8822G>A	c.(8821-8823)cGa>cAa	p.R2941Q	VPS13D_ENST00000356315.4_Missense_Mutation_p.R2916Q	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)									p.R2941Q(1)		NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		AGTGAATGGCGAGAAGTCCTT	0.408																																					p.R2916Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G8747A	1						.						123.0	108.0	113.0					1																	12403045		2203	4300	6503	12325632	SO:0001583	missense	55187	exon41			AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"""vacuolar protein sorting 13D (yeast)"""				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.8822G>A	1.37:g.12403045G>A	ENSP00000350854:p.Arg2941Gln		12325632	NM_018156		Missense_Mutation	SNP	ENST00000358136.3	37	CCDS30588.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.77|16.77	3.215765|3.215765	0.58452|0.58452	.|.	.|.	ENSG00000048707|ENSG00000048707	ENST00000011700|ENST00000356315;ENST00000358136	.|T;T	.|0.47177	.|0.85;0.85	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	.|0.050705	.|0.85682	.|D	.|0.000000	T|T	0.36026|0.36026	0.0952|0.0952	L|L	0.38175|0.38175	1.15|1.15	0.80722|0.80722	D|D	1|1	.|B;B	.|0.31730	.|0.324;0.337	.|B;B	.|0.26969	.|0.075;0.034	T|T	0.13361|0.13361	-1.0512|-1.0512	5|10	.|0.27785	.|T	.|0.31	.|.	13.1853|13.1853	0.59677|0.59677	0.0826:0.0:0.9174:0.0|0.0826:0.0:0.9174:0.0	.|.	.|2916;2940	.|Q5THJ4-2;Q5THJ4	.|.;VP13D_HUMAN	K|Q	1763|2916;2941	.|ENSP00000348666:R2916Q;ENSP00000350854:R2941Q	.|ENSP00000348666:R2916Q	E|R	+|+	1|2	0|0	VPS13D|VPS13D	12325632|12325632	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	5.338000|5.338000	0.65947|0.65947	2.619000|2.619000	0.88677|0.88677	0.650000|0.650000	0.86243|0.86243	GAG|CGA		0.408	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
FLG	2312	broad.mit.edu	37	1	152283518	152283518	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr1:152283518C>T	ENST00000368799.1	-	3	3879	c.3844G>A	c.(3844-3846)Gac>Aac	p.D1282N	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1282	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.D1282N(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCTCGGAGTCGTCTGAGTGT	0.547									Ichthyosis																												p.D1282N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3844A	1						.						215.0	208.0	211.0					1																	152283518		2203	4300	6503	150550142	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.3844G>A	1.37:g.152283518C>T	ENSP00000357789:p.Asp1282Asn		150550142	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	5.649	0.304481	0.10678	.	.	ENSG00000143631	ENST00000368799	T	0.01998	4.51	2.32	-1.75	0.08031	.	.	.	.	.	T	0.00815	0.0027	M	0.76574	2.34	0.09310	N	1	B	0.14805	0.011	B	0.08055	0.003	T	0.46884	-0.9159	9	0.25106	T	0.35	.	0.7644	0.01012	0.3006:0.3472:0.1955:0.1567	.	1282	P20930	FILA_HUMAN	N	1282	ENSP00000357789:D1282N	ENSP00000357789:D1282N	D	-	1	0	FLG	150550142	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.120000	0.03273	-0.363000	0.08101	-0.723000	0.03601	GAC		0.547	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
TNR	7143	broad.mit.edu	37	1	175360456	175360456	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr1:175360456C>T	ENST00000367674.2	-	7	2183	c.1475G>A	c.(1474-1476)cGc>cAc	p.R492H	TNR_ENST00000263525.2_Missense_Mutation_p.R492H			Q92752	TENR_HUMAN	tenascin R	492	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)		p.R492H(1)		NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					AGGGGGGCTGCGGGCCTGTTC	0.547																																					p.R492H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1475A	1						.						70.0	72.0	71.0					1																	175360456		2203	4300	6503	173627079	SO:0001583	missense	7143	exon7			X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11953	protein-coding gene	gene with protein product	"""restrictin"", ""janusin"""	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.1475G>A	1.37:g.175360456C>T	ENSP00000356646:p.Arg492His		173627079	NM_003285	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	37	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	C	33	5.234399	0.95207	.	.	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	T;T	0.53857	0.6;0.6	5.23	5.23	0.72850	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.72835	0.3510	M	0.73217	2.22	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75363	-0.3344	10	0.62326	D	0.03	.	18.3986	0.90507	0.0:1.0:0.0:0.0	.	492	Q92752	TENR_HUMAN	H	492	ENSP00000356646:R492H;ENSP00000263525:R492H	ENSP00000263525:R492H	R	-	2	0	TNR	173627079	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.376000	0.79658	2.429000	0.82318	0.655000	0.94253	CGC		0.547	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285	
USP48	84196	broad.mit.edu	37	1	22030058	22030058	+	Missense_Mutation	SNP	G	G	A	rs569663486		TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr1:22030058G>A	ENST00000308271.9	-	21	3217	c.2569C>T	c.(2569-2571)Cgt>Tgt	p.R857C	USP48_ENST00000529637.1_Missense_Mutation_p.R869C|USP48_ENST00000374732.3_Missense_Mutation_p.R395C|USP48_ENST00000400301.1_Missense_Mutation_p.R857C	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	857					ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.R857C(1)		NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		GTGTATTCACGCAGGTCCCTC	0.443													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17994	0.0		0.0	False		,,,				2504	0.0				p.R857C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2569T	1						.						182.0	176.0	178.0					1																	22030058		2203	4300	6503	21902645	SO:0001583	missense	84196	exon21			AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"""Ubiquitin-specific peptidases"""	18533	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"", ""ubiquitin specific protease 48"""	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.2569C>T	1.37:g.22030058G>A	ENSP00000309262:p.Arg857Cys		21902645	NM_032236	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000308271.9	37	CCDS30623.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.633894	0.47049	.	.	ENSG00000090686	ENST00000400301;ENST00000308271;ENST00000374732;ENST00000529637	T;T;T	0.05513	3.46;3.44;3.43	5.55	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.23572	0.0570	M	0.73598	2.24	0.80722	D	1	D;D;B;B;D	0.89917	1.0;0.997;0.417;0.293;1.0	P;P;B;B;D	0.72625	0.88;0.663;0.033;0.014;0.978	T	0.00832	-1.1548	10	0.52906	T	0.07	.	13.6799	0.62476	0.0744:0.0:0.9256:0.0	.	869;857;857;857;395	B7ZKS7;B7ZKS3;Q86UV5-2;Q86UV5;Q86UV5-5	.;.;.;UBP48_HUMAN;.	C	857;857;395;869	ENSP00000383157:R857C;ENSP00000309262:R857C;ENSP00000431949:R869C	ENSP00000309262:R857C	R	-	1	0	USP48	21902645	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	3.577000	0.53885	1.472000	0.48140	0.655000	0.94253	CGT		0.443	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236	
HMCN1	83872	broad.mit.edu	37	1	186084051	186084051	+	Missense_Mutation	SNP	C	C	G	rs147547755		TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr1:186084051C>G	ENST00000271588.4	+	74	11606	c.11377C>G	c.(11377-11379)Cgc>Ggc	p.R3793G	HMCN1_ENST00000367492.2_Missense_Mutation_p.R3793G	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3793	Ig-like C2-type 36.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.R3793G(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TGGAACAGATCGCAGGCGAAT	0.423																																					p.R3793G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C11377G	1						.						175.0	169.0	171.0					1																	186084051		2203	4300	6503	184350674	SO:0001583	missense	83872	exon74			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.11377C>G	1.37:g.186084051C>G	ENSP00000271588:p.Arg3793Gly		184350674	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.844314	0.91197	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.67171	-0.25;-0.25	5.03	5.03	0.67393	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.049833	0.85682	D	0.000000	T	0.78786	0.4338	L	0.60957	1.885	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	T	0.77900	-0.2415	10	0.41790	T	0.15	.	16.8988	0.86108	0.0:1.0:0.0:0.0	.	3793	Q96RW7	HMCN1_HUMAN	G	3793	ENSP00000271588:R3793G;ENSP00000356462:R3793G	ENSP00000271588:R3793G	R	+	1	0	HMCN1	184350674	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.536000	0.67180	2.480000	0.83734	0.563000	0.77884	CGC		0.423	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
UBXN11	91544	broad.mit.edu	37	1	26612398	26612398	+	Silent	SNP	G	G	A	rs369607205		TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr1:26612398G>A	ENST00000374222.1	-	10	1154	c.690C>T	c.(688-690)ctC>ctT	p.L230L	UBXN11_ENST00000374221.3_Silent_p.L230L|UBXN11_ENST00000357089.4_Silent_p.L197L|UBXN11_ENST00000314675.7_Silent_p.L110L|UBXN11_ENST00000535108.1_Silent_p.L72L|UBXN11_ENST00000374217.2_Silent_p.L197L|UBXN11_ENST00000374223.1_5'UTR|UBXN11_ENST00000436301.2_Silent_p.L155L			Q5T124	UBX11_HUMAN	UBX domain protein 11	230	SEP. {ECO:0000255|PROSITE- ProRule:PRU00732}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.L230L(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						GGATGGGCTCGAGGGTACGCA	0.622											OREG0013265	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L110L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C330T	1						.	G	,,	2,4086		0,2,2042	51.0	58.0	56.0		330,591,690	-10.1	0.4	1		56	0,8386		0,0,4193	no	coding-synonymous,coding-synonymous,coding-synonymous	UBXN11	NM_001077262.1,NM_145345.2,NM_183008.2	,,	0,2,6235	AA,AG,GG		0.0,0.0489,0.016	,,	110/401,197/488,230/521	26612398	2,12472	2044	4193	6237	26484985	SO:0001819	synonymous_variant	91544	exon5			AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.690C>T	1.37:g.26612398G>A		788	26484985	NM_001077262	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Silent	SNP	ENST00000374222.1	37	CCDS41288.1																																																																																				0.622	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
PRKAA2	5563	broad.mit.edu	37	1	57169961	57169961	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr1:57169961G>T	ENST00000371244.4	+	7	1172	c.1106G>T	c.(1105-1107)aGg>aTg	p.R369M		NM_006252.3	NP_006243.2	P54646	AAPK2_HUMAN	protein kinase, AMP-activated, alpha 2 catalytic subunit	369	AIS. {ECO:0000250}.				autophagy (GO:0006914)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|cellular response to glucose starvation (GO:0042149)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of glycolytic process (GO:0045821)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.R369S(1)|p.R369M(1)		breast(6)|endometrium(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|stomach(1)	23					Acetylsalicylic acid(DB00945)	CATCCAGAAAGGATGCCACCT	0.478																																					p.R369M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1106T	1						.						80.0	77.0	78.0					1																	57169961		2203	4300	6503	56942549	SO:0001583	missense	5563	exon7			BC069823	CCDS605.1	1p31	2011-08-25			ENSG00000162409	ENSG00000162409			9377	protein-coding gene	gene with protein product		600497		PRKAA		7959015	Standard	NM_006252		Approved	AMPK, AMPKa2	uc001cyk.4	P54646	OTTHUMG00000008282	ENST00000371244.4:c.1106G>T	1.37:g.57169961G>T	ENSP00000360290:p.Arg369Met		56942549	NM_006252	Q9H1E8|Q9UD43	Missense_Mutation	SNP	ENST00000371244.4	37	CCDS605.1	.	.	.	.	.	.	.	.	.	.	G	18.01	3.527005	0.64860	.	.	ENSG00000162409	ENST00000371244	T	0.73789	-0.78	5.92	5.0	0.66597	.	0.043131	0.85682	N	0.000000	D	0.87676	0.6237	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.89970	0.4093	10	0.87932	D	0	-9.1969	17.083	0.86603	0.0:0.1269:0.8731:0.0	.	369	P54646	AAPK2_HUMAN	M	369	ENSP00000360290:R369M	ENSP00000360290:R369M	R	+	2	0	PRKAA2	56942549	1.000000	0.71417	0.999000	0.59377	0.465000	0.32709	9.476000	0.97823	1.483000	0.48342	0.655000	0.94253	AGG		0.478	PRKAA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022753.2	NM_006252	
F3	2152	broad.mit.edu	37	1	94998716	94998716	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr1:94998716C>T	ENST00000334047.7	-	4	684	c.521G>A	c.(520-522)aGc>aAc	p.S174N	F3_ENST00000370207.4_Missense_Mutation_p.S174N|F3_ENST00000480356.1_5'UTR	NM_001993.4	NP_001984.1	P13726	TF_HUMAN	coagulation factor III (thromboplastin, tissue factor)	174					activation of blood coagulation via clotting cascade (GO:0002543)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of plasma proteins involved in acute inflammatory response (GO:0002541)|blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of platelet-derived growth factor receptor signaling pathway (GO:0010641)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein kinase B signaling (GO:0051897)	cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)|protease binding (GO:0002020)	p.S174N(1)		NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(7)	14		all_lung(203;0.00106)|Lung NSC(277;0.00475)		all cancers(265;0.0232)|Epithelial(280;0.121)	Coagulation factor VIIa(DB00036)	ATCCCGGAGGCTTAGGAAAGT	0.378																																					p.S174N	Melanoma(40;358 1339 15970 39161)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G521A	1						.						107.0	98.0	101.0					1																	94998716		2203	4300	6503	94771304	SO:0001583	missense	2152	exon4			BC011029	CCDS750.1, CCDS53345.1	1p22-p21	2012-10-02			ENSG00000117525	ENSG00000117525		"""CD molecules"""	3541	protein-coding gene	gene with protein product		134390					Standard	NM_001993		Approved	CD142	uc001dqr.3	P13726	OTTHUMG00000010716	ENST00000334047.7:c.521G>A	1.37:g.94998716C>T	ENSP00000334145:p.Ser174Asn		94771304	NM_001993	D3DT47|Q6FHG2|Q86WH4	Missense_Mutation	SNP	ENST00000334047.7	37	CCDS750.1	.	.	.	.	.	.	.	.	.	.	C	14.80	2.644349	0.47258	.	.	ENSG00000117525	ENST00000334047;ENST00000370207	T;T	0.35048	1.33;1.33	5.53	2.48	0.30137	Fibronectin, type III (1);Interferon alpha/beta receptor, beta chain (1);Immunoglobulin-like fold (1);	0.375514	0.35555	N	0.003123	T	0.26882	0.0658	L	0.52126	1.63	0.26022	N	0.981851	P;D	0.55605	0.837;0.972	B;P	0.57204	0.356;0.815	T	0.03981	-1.0987	10	0.46703	T	0.11	.	7.3597	0.26739	0.0:0.469:0.432:0.099	.	174;174	P13726-2;P13726	.;TF_HUMAN	N	174	ENSP00000334145:S174N;ENSP00000359226:S174N	ENSP00000334145:S174N	S	-	2	0	F3	94771304	0.828000	0.29307	0.942000	0.38095	0.857000	0.48899	0.478000	0.22212	0.695000	0.31675	0.650000	0.86243	AGC		0.378	F3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029593.1	NM_001993	
URB2	9816	broad.mit.edu	37	1	229771507	229771507	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr1:229771507G>A	ENST00000258243.2	+	4	1283	c.1147G>A	c.(1147-1149)Gaa>Aaa	p.E383K		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	383						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.E383K(1)		breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						AATTCGGCACGAAGAGGCTCA	0.507																																					p.E383K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1147A	1						.						59.0	60.0	59.0					1																	229771507		2203	4300	6503	227838130	SO:0001583	missense	9816	exon4			D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"""nucleolar preribosomal-associated protein 1"""		"""KIAA0133"""	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.1147G>A	1.37:g.229771507G>A	ENSP00000258243:p.Glu383Lys		227838130	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	.	.	.	.	.	.	.	.	.	.	G	0.008	-1.897101	0.00517	.	.	ENSG00000135763	ENST00000258243	T	0.28666	1.6	5.2	2.08	0.27032	.	0.609878	0.18291	N	0.145710	T	0.12860	0.0312	N	0.14661	0.345	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.12682	-1.0538	9	.	.	.	-7.5752	1.9779	0.03420	0.1298:0.3741:0.3035:0.1927	.	383	Q14146	URB2_HUMAN	K	383	ENSP00000258243:E383K	.	E	+	1	0	URB2	227838130	0.037000	0.19845	0.004000	0.12327	0.040000	0.13550	2.448000	0.44926	1.316000	0.45131	0.650000	0.86243	GAA		0.507	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
APMAP	57136	broad.mit.edu	37	20	24949644	24949644	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr20:24949644G>A	ENST00000217456.2	-	8	1215	c.925C>T	c.(925-927)Cgg>Tgg	p.R309W	APMAP_ENST00000447138.1_Intron	NM_020531.2	NP_065392.1	Q9HDC9	APMAP_HUMAN	adipocyte plasma membrane associated protein	309					biosynthetic process (GO:0009058)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	arylesterase activity (GO:0004064)|strictosidine synthase activity (GO:0016844)	p.R309W(1)									CTGCTGGGCCGGATGTTGTCT	0.532																																					p.R309W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C925T	20						.						72.0	70.0	70.0					20																	24949644		2203	4300	6503	24897644	SO:0001583	missense	57136	exon8			AB033767	CCDS13166.1	20p11.2	2012-07-20	2012-07-20	2012-07-20	ENSG00000101474	ENSG00000101474			13238	protein-coding gene	gene with protein product		615884	"""chromosome 20 open reading frame 3"""	C20orf3		10945474, 11583587, 20552250	Standard	NM_020531		Approved	BSCv	uc002wty.3	Q9HDC9	OTTHUMG00000032107	ENST00000217456.2:c.925C>T	20.37:g.24949644G>A	ENSP00000217456:p.Arg309Trp		24897644	NM_020531	A8K514|B4DXG1|Q6UVZ8|Q9GZS8|Q9NUB2	Missense_Mutation	SNP	ENST00000217456.2	37	CCDS13166.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.374766	0.82573	.	.	ENSG00000101474	ENST00000217456	T	0.32023	1.47	5.54	2.45	0.29901	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.59555	0.2202	M	0.93106	3.38	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.61520	-0.7046	10	0.87932	D	0	-12.6317	8.1287	0.31014	0.0755:0.0:0.6443:0.2802	.	293;309	A2A2F9;Q9HDC9	.;APMAP_HUMAN	W	309	ENSP00000217456:R309W	ENSP00000217456:R309W	R	-	1	2	C20orf3	24897644	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	3.889000	0.56212	0.353000	0.24079	0.561000	0.74099	CGG		0.532	APMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078380.2	NM_020531	
CTSA	5476	broad.mit.edu	37	20	44520260	44520261	+	Frame_Shift_Del	DEL	TG	TG	-	rs544157818|rs530287837|rs181943893|rs562182818	byFrequency	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	TG	TG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr20:44520260_44520261delTG	ENST00000372459.2	+	1	246_247	c.53_54delTG	c.(52-54)ctgfs	p.L19fs	CTSA_ENST00000354880.5_Frame_Shift_Del_p.L37fs|CTSA_ENST00000191018.5_Frame_Shift_Del_p.L19fs|CTSA_ENST00000372484.3_Frame_Shift_Del_p.L37fs|RP3-337O18.9_ENST00000607703.1_RNA|NEURL2_ENST00000372518.4_5'Flank			P10619	PPGB_HUMAN	cathepsin A	19				Missing (in Ref. 4; AAH00597). {ECO:0000305}.	glycosphingolipid metabolic process (GO:0006687)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|enzyme activator activity (GO:0008047)|serine-type carboxypeptidase activity (GO:0004185)	p.L36fs*121(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				ctgctgctgctgctAGTGTCCT	0.698														215	0.0429313	0.0106	0.0303	5008	,	,		13385	0.129		0.007	False		,,,				2504	0.044				p.36_36del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.107_108del	20						.																																			43953668	SO:0001589	frameshift_variant	5476	exon2			M22960	CCDS13385.2, CCDS46609.1, CCDS54467.1	20q13.12	2012-02-10	2006-12-05	2006-12-05	ENSG00000064601	ENSG00000064601	3.4.16.5	"""Cathepsins"""	9251	protein-coding gene	gene with protein product	"""carboxypeptidase C"", ""lysosomal protective protein"", ""carboxypeptidase-L"", ""carboxypeptidase Y-like kininase"", ""deamidase"", ""lysosomal carboxypeptidase A"", ""urinary kininase"""	613111	"""protective protein for beta-galactosidase (galactosialidosis)"""	GSL, PPGB		2071143	Standard	NM_000308		Approved		uc002xqh.3	P10619	OTTHUMG00000033078	ENST00000372459.2:c.53_54delTG	20.37:g.44520260_44520261delTG	ENSP00000361537:p.Leu19fs		43953667	NM_000308	B2R798|Q561W6|Q5JZH1|Q96KJ2|Q9BR08|Q9BW68	Frame_Shift_Del	DEL	ENST00000372459.2	37	CCDS46609.1																																																																																				0.698	CTSA-012	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471297.2	NM_000308	
COL18A1	80781	broad.mit.edu	37	21	46900643	46900644	+	Frame_Shift_Ins	INS	-	-	C	rs375739796		TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	-	-	-	-	-	-	Unknown	Wildtype	None	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr21:46900643_46900644insC	ENST00000359759.4	+	12	2748_2749	c.2727_2728insC	c.(2728-2730)cccfs	p.P910fs	COL18A1_ENST00000400337.2_Frame_Shift_Ins_p.P495fs|COL18A1_ENST00000355480.5_Frame_Shift_Ins_p.P675fs			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	910	Triple-helical region 3 (COL3).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GACCTCCCGGACCCCCCGGTGT	0.698																																					p.G494fs												.	.	0			c.1482_1483insC	21						.																																			45725072	SO:0001589	frameshift_variant	80781	exon13				CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.2733dupC	21.37:g.46900649_46900649dupC	ENSP00000352798:p.Pro910fs		45725071	NM_130445	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Frame_Shift_Ins	INS	ENST00000359759.4	37																																																																																					0.698	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
BRD1	23774	broad.mit.edu	37	22	50181213	50181214	+	Intron	INS	-	-	G	rs552160357		TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr22:50181213_50181214insG	ENST00000216267.8	-	7	2846				BRD1_ENST00000542442.1_Intron|BRD1_ENST00000457780.2_Intron|BRD1_ENST00000404760.1_Frame_Shift_Ins_p.P894fs|BRD1_ENST00000404034.1_Intron|BRD1_ENST00000342989.5_Frame_Shift_Ins_p.P489fs	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1						histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)	p.S491fs*6(1)		endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		TGGCAGACTTTGGGGGGCTTAC	0.554																																					.												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	.	22						.																																			48567218	SO:0001627	intron_variant	23774	.			AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"""BR140-like"""	604589	"""bromodomain-containing 1"""			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.2360-71->C	22.37:g.50181219_50181219dupG			48567217	.	A6ZJA4	Frame_Shift_Ins	INS	ENST00000216267.8	37	CCDS14080.1																																																																																				0.554	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577	
PIWIL3	440822	broad.mit.edu	37	22	25144892	25144892	+	Silent	SNP	G	G	A	rs201406937		TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr22:25144892G>A	ENST00000332271.5	-	12	1847	c.1431C>T	c.(1429-1431)atC>atT	p.I477I	PIWIL3_ENST00000527701.1_Silent_p.I368I|PIWIL3_ENST00000532537.2_5'UTR|PIWIL3_ENST00000533313.1_Silent_p.I368I	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	477					cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)	p.I477I(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						TGCCTTGCACGATGTTTGCGT	0.373																																					p.I477I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1431T	22						.						133.0	113.0	119.0					22																	25144892		2203	4300	6503	23474892	SO:0001819	synonymous_variant	440822	exon12			AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"""Argonaute/PIWI family"""	18443	protein-coding gene	gene with protein product		610314	"""piwi-like 3 (Drosophila)"""			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.1431C>T	22.37:g.25144892G>A			23474892	NM_001008496		Silent	SNP	ENST00000332271.5	37	CCDS33623.1																																																																																				0.373	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2	NM_001008496	
SEZ6L	23544	broad.mit.edu	37	22	26693012	26693012	+	Silent	SNP	C	C	T	rs371203903		TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr22:26693012C>T	ENST00000248933.6	+	4	1223	c.1128C>T	c.(1126-1128)gaC>gaT	p.D376D	SEZ6L_ENST00000343706.4_Silent_p.D376D|SEZ6L_ENST00000402979.1_Silent_p.D149D|SEZ6L_ENST00000360929.3_Silent_p.D376D|SEZ6L_ENST00000403121.1_Silent_p.D149D|SEZ6L_ENST00000404234.3_Silent_p.D376D|SEZ6L_ENST00000529632.2_Silent_p.D376D			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	376	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)		p.D376D(2)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						CCTTCCAGGACGACGGCCTTG	0.577																																					p.D376D												.	.	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	c.C1128T	22						.	C	,,,,,	0,4406		0,0,2203	49.0	43.0	45.0		1128,1128,1128,1128,1128,1128	-10.5	0.0	22		45	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEZ6L	NM_001184773.1,NM_001184774.1,NM_001184775.1,NM_001184776.1,NM_001184777.1,NM_021115.4	,,,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,,,	376/1024,376/1014,376/1012,376/950,376/949,376/1025	26693012	1,13005	2203	4300	6503	25023012	SO:0001819	synonymous_variant	23544	exon4			AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"""seizure related gene 6 (mouse)-like"""				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.1128C>T	22.37:g.26693012C>T			25023012	NM_001184776	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Silent	SNP	ENST00000248933.6	37	CCDS13833.1																																																																																				0.577	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		
HOXD11	3237	broad.mit.edu	37	2	176973647	176973647	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr2:176973647G>A	ENST00000249504.5	+	2	864	c.794G>A	c.(793-795)cGg>cAg	p.R265Q	HOXD11_ENST00000498438.1_3'UTR|HOXD10_ENST00000490088.2_3'UTR|AC009336.1_ENST00000401374.2_RNA	NM_021192.2	NP_067015.2	P31277	HXD11_HUMAN	homeobox D11	265					anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|developmental growth (GO:0048589)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint morphogenesis (GO:0060272)|metanephros development (GO:0001656)|organ induction (GO:0001759)|positive regulation of cell development (GO:0010720)|positive regulation of chondrocyte differentiation (GO:0032332)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|single fertilization (GO:0007338)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.R265Q(1)						OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678)		GCCCCCCAGCGGTCCCGGAAA	0.592			T	NUP98	AML																																p.R265Q			Dom	yes		2	2q31-q32	3237	homeo box D11		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G794A	2						.						71.0	79.0	76.0					2																	176973647		2203	4300	6503	176681893	SO:0001583	missense	3237	exon2				CCDS2265.1	2q31.1	2011-06-20	2005-12-22		ENSG00000128713	ENSG00000128713		"""Homeoboxes / ANTP class : HOXL subclass"""	5134	protein-coding gene	gene with protein product		142986	"""homeo box D11"""	HOX4, HOX4F		1973146, 1358459	Standard	NM_021192		Approved		uc002uki.3	P31277	OTTHUMG00000132510	ENST00000249504.5:c.794G>A	2.37:g.176973647G>A	ENSP00000249504:p.Arg265Gln		176681893	NM_021192	A6NIS4|Q9NS02	Missense_Mutation	SNP	ENST00000249504.5	37	CCDS2265.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.278715	0.80692	.	.	ENSG00000128713	ENST00000249504;ENST00000392538	D	0.95853	-3.83	5.39	5.39	0.77823	Homeodomain-related (1);Homeobox (1);Homeodomain-like (1);	0.000000	0.31847	U	0.006963	D	0.95322	0.8482	M	0.62723	1.935	0.80722	D	1	D	0.67145	0.996	P	0.47015	0.534	D	0.95147	0.8269	10	0.49607	T	0.09	.	19.2002	0.93708	0.0:0.0:1.0:0.0	.	265	P31277	HXD11_HUMAN	Q	265;86	ENSP00000249504:R265Q	ENSP00000249504:R265Q	R	+	2	0	HOXD11	176681893	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.019000	0.64060	2.548000	0.85928	0.597000	0.82753	CGG		0.592	HOXD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359250.2		
TTN	7273	broad.mit.edu	37	2	179500701	179500701	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr2:179500701A>G	ENST00000591111.1	-	176	36898	c.36674T>C	c.(36673-36675)gTa>gCa	p.V12225A	TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000418062.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V11298A|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V4993A|TTN_ENST00000460472.2_Missense_Mutation_p.V4801A|TTN_ENST00000359218.5_Missense_Mutation_p.V4926A|TTN_ENST00000589042.1_Missense_Mutation_p.V13866A|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12225					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.V11298A(1)|p.V4801A(1)|p.V4926A(1)|p.V4993A(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TACTACTTTTACGCAAGATGA	0.423																																					p.V4801A												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.T14402C	2						.						110.0	112.0	111.0					2																	179500701		1935	4137	6072	179208946	SO:0001583	missense	7273	exon54			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.36674T>C	2.37:g.179500701A>G	ENSP00000465570:p.Val12225Ala		179208946	NM_003319	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	13.72	2.320073	0.41096	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.05855	3.38;3.38;3.38;3.38	5.66	5.66	0.87406	Immunoglobulin subtype (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.29652	0.0740	M	0.85197	2.74	0.54753	D	0.999984	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.80764	0.994;0.994;0.994;0.994	T	0.06338	-1.0832	9	0.87932	D	0	.	15.8786	0.79185	1.0:0.0:0.0:0.0	.	4801;4926;4993;12225	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	11298;4801;4993;4926;4801	ENSP00000343764:V11298A;ENSP00000434586:V4801A;ENSP00000340554:V4993A;ENSP00000352154:V4926A	ENSP00000340554:V4993A	V	-	2	0	TTN	179208946	1.000000	0.71417	0.247000	0.24249	0.940000	0.58332	9.051000	0.93849	2.156000	0.67533	0.477000	0.44152	GTA		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
AQP12B	653437	broad.mit.edu	37	2	241622318	241622318	+	5'Flank	SNP	C	C	T	rs201727958		TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr2:241622318C>T	ENST00000407834.3	-	0	0					NM_001102467.1	NP_001095937.1	A6NM10	AQ12B_HUMAN	aquaporin 12B							integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|lung(8)|ovary(1)	13		all_epithelial(40;1.71e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		AGGAGCTGGCCGGTTCCCACA	0.672																																					.												.	.	0			.	2						.																																			241270991	SO:0001631	upstream_gene_variant	653437	.			BC041460	CCDS46560.1	2q37.3	2007-12-14	2005-05-26	2005-05-26	ENSG00000185176	ENSG00000185176		"""Ion channels / Aquaporins"""	6096	protein-coding gene	gene with protein product			"""insulin synthesis associated 3"""	INSSA3			Standard	NM_001102467		Approved		uc010fzj.3	A6NM10	OTTHUMG00000152263		2.37:g.241622318C>T	Exception_encountered		241270991	.	A4QPB9	Splice_Site	SNP	ENST00000407834.3	37	CCDS46560.1																																																																																				0.672	AQP12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325625.1		
CELSR3	1951	broad.mit.edu	37	3	48689430	48689431	+	Frame_Shift_Ins	INS	-	-	G	rs372105067		TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	-	-	-	-	-	-	Unknown	Wildtype	None	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr3:48689430_48689431insG	ENST00000164024.4	-	12	6082_6083	c.5802_5803insC	c.(5800-5805)cccagcfs	p.S1935fs	CELSR3_ENST00000544264.1_Frame_Shift_Ins_p.S1935fs	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	1935	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		ACTCGGTGGCTGGGGGGTAGCA	0.663																																					p.S1935fs												.	.	0			c.5803_5804insC	3						.																																			48664435	SO:0001589	frameshift_variant	1951	exon12			AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3230	protein-coding gene	gene with protein product	"""flamingo homolog 1 (Drosophila)"""	604264	"""cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"""	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.5803dupC	3.37:g.48689436_48689436dupG	ENSP00000164024:p.Ser1935fs		48664434	NM_001407	O75092	Frame_Shift_Ins	INS	ENST00000164024.4	37	CCDS2775.1																																																																																				0.663	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407	
CAND2	23066	broad.mit.edu	37	3	12858015	12858015	+	Silent	SNP	C	C	T			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr3:12858015C>T	ENST00000456430.2	+	10	1625	c.1584C>T	c.(1582-1584)gcC>gcT	p.A528A	CAND2_ENST00000295989.5_Silent_p.A435A	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	528					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)		p.A435A(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CTGTGATGGCCTGTGTGGCTG	0.647																																					p.A528A	GBM(43;676 868 1633 6395 37496)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1584T	3						.						45.0	51.0	49.0					3																	12858015		2099	4206	6305	12833015	SO:0001819	synonymous_variant	23066	exon10				CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.1584C>T	3.37:g.12858015C>T			12833015	NM_001162499	B9EGM9|E9KL24	Silent	SNP	ENST00000456430.2	37	CCDS54554.1																																																																																				0.647	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
SH3BP5	9467	broad.mit.edu	37	3	15298363	15298363	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr3:15298363G>A	ENST00000383791.3	-	8	1367	c.1147C>T	c.(1147-1149)Cga>Tga	p.R383*	SH3BP5-AS1_ENST00000413977.1_RNA|SH3BP5-AS1_ENST00000436602.1_RNA|SH3BP5-AS1_ENST00000420195.1_RNA|SH3BP5_ENST00000426925.1_Nonsense_Mutation_p.R226*|SH3BP5_ENST00000408919.3_Nonsense_Mutation_p.R226*|SH3BP5_ENST00000253688.5_Nonsense_Mutation_p.R226*	NM_004844.4	NP_004835.2	O60239	3BP5_HUMAN	SH3-domain binding protein 5 (BTK-associated)	383	Ser-rich.				intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	protein kinase inhibitor activity (GO:0004860)	p.R383*(1)		NS(1)|endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	12						TACTCACCTCGTTCTACTTCA	0.597																																					p.R226X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C676T	3						.						35.0	32.0	33.0					3																	15298363		2203	4300	6503	15273367	SO:0001587	stop_gained	9467	exon8			AB005047	CCDS2625.2, CCDS43055.1	3p24.3	2008-07-10			ENSG00000131370	ENSG00000131370			10827	protein-coding gene	gene with protein product	"""SH3 binding protein"""	605612				9571151, 10339589	Standard	NM_004844		Approved	Sab	uc003bzp.2	O60239	OTTHUMG00000129859	ENST00000383791.3:c.1147C>T	3.37:g.15298363G>A	ENSP00000373301:p.Arg383*		15273367	NM_001018009	B3KQW6|Q5JWV9	Nonsense_Mutation	SNP	ENST00000383791.3	37	CCDS2625.2	.	.	.	.	.	.	.	.	.	.	G	41	8.924643	0.99004	.	.	ENSG00000131370	ENST00000383791;ENST00000426925;ENST00000253688;ENST00000408919	.	.	.	5.43	3.44	0.39384	.	0.050712	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.5152	0.56028	0.0:0.0:0.6599:0.3401	.	.	.	.	X	383;226;226;226	.	ENSP00000253688:R226X	R	-	1	2	SH3BP5	15273367	0.998000	0.40836	0.996000	0.52242	0.860000	0.49131	2.849000	0.48286	2.566000	0.86566	0.456000	0.33151	CGA		0.597	SH3BP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340740.2	NM_004844	
PEX5L	51555	broad.mit.edu	37	3	179597740	179597740	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr3:179597740G>A	ENST00000467460.1	-	5	812	c.482C>T	c.(481-483)cCg>cTg	p.P161L	PEX5L_ENST00000392649.3_Intron|PEX5L_ENST00000476138.1_Missense_Mutation_p.P118L|PEX5L_ENST00000485199.1_Missense_Mutation_p.P126L|PEX5L_ENST00000263962.8_Missense_Mutation_p.P159L|PEX5L_ENST00000472994.1_Missense_Mutation_p.P102L|PEX5L_ENST00000464614.1_Intron|PEX5L-AS1_ENST00000466064.1_RNA|PEX5L_ENST00000465751.1_Missense_Mutation_p.P137L|PEX5L_ENST00000467440.2_Intron|PEX5L_ENST00000468741.1_5'UTR	NM_001256751.1|NM_016559.2	NP_001243680.1|NP_057643.1	Q8IYB4	PEX5R_HUMAN	peroxisomal biogenesis factor 5-like	161					maintenance of protein location (GO:0045185)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of membrane potential (GO:0042391)	cytosol (GO:0005829)|dendrite (GO:0030425)|peroxisomal membrane (GO:0005778)|receptor complex (GO:0043235)	peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|small GTPase binding (GO:0031267)	p.P161L(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	all_cancers(143;3.94e-14)|Ovarian(172;0.0338)|Breast(254;0.183)		OV - Ovarian serous cystadenocarcinoma(80;1.75e-26)|GBM - Glioblastoma multiforme(14;0.000518)			TGAAGTCTCCGGGACTCTGAG	0.507																																					p.P161L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C482T	3						.						136.0	133.0	134.0					3																	179597740		2203	4300	6503	181080434	SO:0001583	missense	51555	exon5			AJ245503	CCDS3236.1, CCDS58861.1, CCDS58862.1, CCDS58863.1, CCDS58864.1, CCDS58865.1, CCDS58866.1, CCDS58867.1	3q27.1	2013-01-10			ENSG00000114757	ENSG00000114757		"""Tetratricopeptide (TTC) repeat domain containing"""	30024	protein-coding gene	gene with protein product		611058				11463335	Standard	NM_016559		Approved	PEX5R, PXR2	uc003fki.2	Q8IYB4	OTTHUMG00000157363	ENST00000467460.1:c.482C>T	3.37:g.179597740G>A	ENSP00000419975:p.Pro161Leu		181080434	NM_016559	B7Z2A5|B7Z305|B7Z318|B7Z5Z5|B7Z8P2|E7EUV8|E7EUZ0|E9PEC1|E9PH97|Q9NQD1|Q9P2U3|Q9P2U4	Missense_Mutation	SNP	ENST00000467460.1	37	CCDS3236.1	.	.	.	.	.	.	.	.	.	.	G	17.66	3.444549	0.63178	.	.	ENSG00000114757	ENST00000467460;ENST00000263962;ENST00000485199;ENST00000382596;ENST00000476138;ENST00000472994;ENST00000465751;ENST00000469198;ENST00000463761	D;D;D;D;D;D	0.90069	-2.6;-2.61;-2.54;-2.56;-2.57;-2.57	5.62	5.62	0.85841	.	0.309586	0.35555	N	0.003139	D	0.84147	0.5408	L	0.27053	0.805	0.80722	D	1	P;P;P;P;P	0.48589	0.569;0.569;0.854;0.912;0.858	B;B;B;B;B	0.41466	0.141;0.141;0.358;0.358;0.196	T	0.83156	-0.0101	10	0.30854	T	0.27	-1.2949	20.0149	0.97475	0.0:0.0:1.0:0.0	.	102;137;159;126;161	E7EUZ0;E9PH97;Q8IYB4-2;Q8IYB4-3;Q8IYB4	.;.;.;.;PEX5R_HUMAN	L	161;159;126;159;118;102;137;150;185	ENSP00000419975:P161L;ENSP00000263962:P159L;ENSP00000418440:P126L;ENSP00000420555:P118L;ENSP00000418054:P102L;ENSP00000419348:P137L	ENSP00000263962:P159L	P	-	2	0	PEX5L	181080434	0.997000	0.39634	0.012000	0.15200	0.687000	0.40016	5.941000	0.70195	2.793000	0.96121	0.650000	0.86243	CCG		0.507	PEX5L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348577.1	NM_016559	
EPHB3	2049	broad.mit.edu	37	3	184290594	184290594	+	Silent	SNP	C	C	T			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr3:184290594C>T	ENST00000330394.2	+	3	938	c.486C>T	c.(484-486)ccC>ccT	p.P162P	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	162	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)	p.P162P(1)		breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			CCATTGCACCCGATGAGAGCT	0.597																																					p.P162P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C486T	3						.						72.0	72.0	72.0					3																	184290594		2203	4300	6503	185773288	SO:0001819	synonymous_variant	2049	exon3			X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3394	protein-coding gene	gene with protein product		601839	"""EphB3"""	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.486C>T	3.37:g.184290594C>T			185773288	NM_004443	Q7Z740	Silent	SNP	ENST00000330394.2	37	CCDS3268.1																																																																																				0.597	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443	
TADA2B	93624	broad.mit.edu	37	4	7056538	7056538	+	Silent	SNP	C	C	T			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr4:7056538C>T	ENST00000310074.7	+	2	1209	c.1020C>T	c.(1018-1020)gcC>gcT	p.A340A	TADA2B_ENST00000515646.1_Silent_p.A248A|TADA2B_ENST00000512388.1_Silent_p.A265A	NM_152293.2	NP_689506.2	Q86TJ2	TAD2B_HUMAN	transcriptional adaptor 2B	340					chromatin organization (GO:0006325)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	SAGA-type complex (GO:0070461)|STAGA complex (GO:0030914)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.A340A(1)		breast(3)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)	18						GCGAGTTCGCCGCCATTGAGA	0.557																																					p.A340A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1020T	4						.						65.0	72.0	70.0					4																	7056538		1967	4152	6119	7107439	SO:0001819	synonymous_variant	93624	exon2			AK026299	CCDS47007.1	4p16.1	2009-10-02			ENSG00000173011	ENSG00000173011			30781	protein-coding gene	gene with protein product		608790				12972612, 18936164	Standard	NM_152293		Approved	MGC21874	uc003gjw.4	Q86TJ2	OTTHUMG00000159983	ENST00000310074.7:c.1020C>T	4.37:g.7056538C>T			7107439	NM_152293	A0AUJ8|A4QMR7|B3KSN0|B3KU86|Q6MZG9	Silent	SNP	ENST00000310074.7	37	CCDS47007.1																																																																																				0.557	TADA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358687.2	NM_152293	
TRPC3	7222	broad.mit.edu	37	4	122853727	122853727	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr4:122853727C>T	ENST00000379645.3	-	2	759	c.686G>A	c.(685-687)cGc>cAc	p.R229H	TRPC3_ENST00000513531.1_Missense_Mutation_p.R156H|TRPC3_ENST00000264811.5_Missense_Mutation_p.R156H	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	144					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.R156H(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						CGGCGAGAAGCGCGTGCCGTC	0.632																																					p.R156H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G467A	4						.						83.0	77.0	79.0					4																	122853727		2203	4300	6503	123073177	SO:0001583	missense	7222	exon1			Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.686G>A	4.37:g.122853727C>T	ENSP00000368966:p.Arg229His		123073177	NM_003305	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Missense_Mutation	SNP	ENST00000379645.3	37	CCDS47130.1	.	.	.	.	.	.	.	.	.	.	C	35	5.433675	0.96150	.	.	ENSG00000138741	ENST00000264811;ENST00000379645;ENST00000513531	T;T;T	0.75938	-0.77;-0.98;-0.89	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.83207	0.5204	L	0.43152	1.355	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.943;0.999	D	0.84025	0.0356	10	0.72032	D	0.01	-15.4956	19.7417	0.96234	0.0:1.0:0.0:0.0	.	156;229	E9PCJ9;Q5G1L5	.;.	H	156;229;156	ENSP00000264811:R156H;ENSP00000368966:R229H;ENSP00000426899:R156H	ENSP00000264811:R156H	R	-	2	0	TRPC3	123073177	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.755000	0.85180	2.661000	0.90470	0.655000	0.94253	CGC		0.632	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305	
PCDHA10	56139	broad.mit.edu	37	5	140236526	140236526	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr5:140236526C>T	ENST00000307360.5	+	1	893	c.893C>T	c.(892-894)aCg>aTg	p.T298M	PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.T298M|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	298	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.T298M(2)		NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACGAAAGGACGGGAGAAATA	0.373																																					p.T298M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C893T	5						.						80.0	78.0	78.0					5																	140236526		2196	4269	6465	140216710	SO:0001583	missense	56139	exon1			AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"""Cadherins / Protocadherins : Clustered"""	8664	other	complex locus constituent	"""KIAA0345-like 4"", ""ortholog to mouse CNR8"""	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.893C>T	5.37:g.140236526C>T	ENSP00000304234:p.Thr298Met		140216710	NM_031860	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	.	.	.	.	.	.	.	.	.	.	C	10.62	1.401146	0.25291	.	.	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.58060	0.36;0.36	4.29	3.4	0.38934	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.76478	0.3993	M	0.92367	3.3	0.29087	N	0.882325	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.72338	0.977;0.961;0.944	T	0.72200	-0.4362	9	0.87932	D	0	.	10.8576	0.46808	0.1459:0.7133:0.1408:0.0	.	298;298;298	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	M	298	ENSP00000421030:T298M;ENSP00000304234:T298M	ENSP00000304234:T298M	T	+	2	0	PCDHA10	140216710	0.006000	0.16342	0.010000	0.14722	0.251000	0.25915	0.339000	0.19875	1.114000	0.41781	0.561000	0.74099	ACG		0.373	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901	
APC	324	broad.mit.edu	37	5	112175346	112175346	+	Frame_Shift_Del	DEL	T	T	-	rs528724202		TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr5:112175346delT	ENST00000457016.1	+	16	4435	c.4055delT	c.(4054-4056)gttfs	p.V1352fs	APC_ENST00000508376.2_Frame_Shift_Del_p.V1352fs|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Frame_Shift_Del_p.V1352fs			P25054	APC_HUMAN	adenomatous polyposis coli	1352	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1353fs*62(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CACAAAGCTGTTGAATTTTCT	0.488		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.V1334fs	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	APC,large_intestine,right,Substitution - Nonsense,-2 	.	3	Deletion - Frameshift(2)|Unknown(1)	large_intestine(1)|soft_tissue(1)|skin(1)	c.4001delT	5	GRCh37	CM080063	APC	M		.						62.0	65.0	64.0					5																	112175346		2202	4300	6502	112203245	SO:0001589	frameshift_variant	324	exon14	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4055delT	5.37:g.112175346delT	ENSP00000413133:p.Val1352fs		112203245	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.488	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
PCDHB16	57717	broad.mit.edu	37	5	140563763	140563763	+	Missense_Mutation	SNP	C	C	A	rs17844658	byFrequency	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr5:140563763C>A	ENST00000361016.2	+	1	2784	c.1629C>A	c.(1627-1629)agC>agA	p.S543R		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	543	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.			S -> R (in Ref. 1; AAF81914/AAG10030 and 7; AAH36062). {ECO:0000305}.	calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S543R(2)		breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTTTGAGCAGCGAGGCGCTGG	0.692													C|||	1002	0.20008	0.1407	0.196	5008	,	,		12178	0.2133		0.2893	False		,,,				2504	0.1779				p.S543R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1629A	5						.						18.0	20.0	19.0					5																	140563763		1828	3387	5215	140543947	SO:0001583	missense	57717	exon1			AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"""Cadherins / Protocadherins : Clustered"""	14546	other	protocadherin	"""cadherin ME1"", ""protocadherin-3x"", ""PCDHbeta 16"""	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.1629C>A	5.37:g.140563763C>A	ENSP00000354293:p.Ser543Arg		140543947	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	690	0.3159340659340659	122	0.24796747967479674	135	0.3729281767955801	162	0.28321678321678323	271	0.3575197889182058	c	17.84	3.487245	0.63962	.	.	ENSG00000196963	ENST00000361016	T	0.54866	0.55	4.12	2.25	0.28309	Cadherin (5);Cadherin-like (1);	0.000000	0.40908	D	0.000982	T	0.00012	0.0000	H	0.95850	3.73	0.34623	P	0.281168	P	0.46064	0.872	P	0.48982	0.597	T	0.07158	-1.0787	9	0.72032	D	0.01	.	6.473	0.22020	0.1418:0.6907:0.0:0.1675	rs17844658;rs17857092	543	Q9NRJ7	PCDBG_HUMAN	R	543	ENSP00000354293:S543R	ENSP00000354293:S543R	S	+	3	2	PCDHB16	140543947	0.269000	0.24143	1.000000	0.80357	0.909000	0.53808	0.506000	0.22658	0.706000	0.31912	0.479000	0.44913	AGC		0.692	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
VARS	7407	broad.mit.edu	37	6	31746949	31746950	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr6:31746949_31746950insG	ENST00000375663.3	-	29	3960_3961	c.3520_3521insC	c.(3520-3522)cagfs	p.Q1174fs	VWA7_ENST00000375688.4_5'Flank|VWA7_ENST00000375686.3_5'Flank|VARS_ENST00000482996.1_5'Flank|VWA7_ENST00000447450.1_5'Flank|VWA7_ENST00000467576.1_5'Flank|Y_RNA_ENST00000364685.1_RNA	NM_006295.2	NP_006286.1	P26640	SYVC_HUMAN	valyl-tRNA synthetase	1174					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)	p.Q1174fs*10(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	30					L-Valine(DB00161)	AGCGCAACCCTGGGGGGCGGGA	0.703																																					p.Q1174fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.3521_3522insC	6						.																																			31854929	SO:0001589	frameshift_variant	7407	exon29			BC012808	CCDS34412.1	6p21.3	2011-07-01		2005-07-05	ENSG00000204394	ENSG00000204394	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	12651	protein-coding gene	gene with protein product	"""valine tRNA ligase 1, cytoplasmic"""	192150	"""valyl-tRNA synthetase 2"""	VARS2		15779907	Standard	XM_005249362		Approved		uc003nxe.3	P26640	OTTHUMG00000031286	ENST00000375663.3:c.3521dupC	6.37:g.31746955_31746955dupG	ENSP00000364815:p.Gln1174fs		31854928	NM_006295	B0V1N1|B4DZ61|Q5JQ90|Q96E77|Q9UQM2	Frame_Shift_Ins	INS	ENST00000375663.3	37	CCDS34412.1																																																																																				0.703	VARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076619.2	NM_006295	
LINC00336	401253	broad.mit.edu	37	6	33560979	33560980	+	RNA	INS	-	-	G			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr6:33560979_33560980insG	ENST00000477984.1	-	0	135_136					NR_027908.1		Q6ZUF6	NC336_HUMAN	long intergenic non-protein coding RNA 336									p.Q46fs*6(1)									TGGGCGCCTGCGGGGGGAGGGC	0.698																																					.												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	.	6						.																																			33668958			401253	.			AK125740		6p21.31	2012-10-12	2011-08-10	2011-08-10	ENSG00000197251	ENSG00000197251		"""Long non-coding RNAs"""	33813	non-coding RNA	RNA, long non-coding			"""chromosome 6 open reading frame 227"", ""non-protein coding RNA 336"""	C6orf227, NCRNA00336			Standard	NR_027908		Approved	FLJ43752	uc003oew.1	Q6ZUF6	OTTHUMG00000159733		6.37:g.33560985_33560985dupG			33668957	.		Frame_Shift_Ins	INS	ENST00000477984.1	37																																																																																					0.698	LINC00336-001	KNOWN	basic	antisense	antisense	OTTHUMT00000357085.1		
SOGA3	387104	broad.mit.edu	37	6	127796870	127796870	+	Silent	SNP	C	C	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr6:127796870C>A	ENST00000525778.1	-	6	3046	c.2301G>T	c.(2299-2301)cgG>cgT	p.R767R	SOGA3_ENST00000556132.1_Silent_p.R767R|SOGA3_ENST00000465909.2_Silent_p.R767R|SOGA3_ENST00000368268.2_Silent_p.R767R|SOGA3_ENST00000474293.2_5'Flank|SOGA3_ENST00000481848.2_Silent_p.R767R			Q5TF21	SOGA3_HUMAN	SOGA family member 3	767					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.R767R(1)									GGTGCGGAGGCCGCGAGTCGT	0.721																																					p.R767R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2301T	6						.						27.0	35.0	33.0					6																	127796870		2118	4212	6330	127838563	SO:0001819	synonymous_variant	387104	exon6			AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 174"""	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.2301G>T	6.37:g.127796870C>A			127838563	NM_001012279		Silent	SNP	ENST00000525778.1	37	CCDS43505.1																																																																																				0.721	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279	
NMBR	4829	broad.mit.edu	37	6	142409379	142409379	+	Silent	SNP	G	G	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr6:142409379G>A	ENST00000258042.1	-	1	557	c.417C>T	c.(415-417)gcC>gcT	p.A139A	RP11-137J7.2_ENST00000454401.1_RNA	NM_002511.2	NP_002502.2	P28336	NMBR_HUMAN	neuromedin B receptor	139					G-protein coupled receptor signaling pathway (GO:0007186)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bombesin receptor activity (GO:0004946)	p.A139A(1)		breast(2)|central_nervous_system(3)|endometrium(3)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23	Breast(32;0.155)			OV - Ovarian serous cystadenocarcinoma(155;9.93e-06)|GBM - Glioblastoma multiforme(68;0.0013)		CTTACCTGTCGGCGCTGAGGG	0.577																																					p.A139A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C417T	6						.						55.0	45.0	48.0					6																	142409379		2203	4300	6503	142451072	SO:0001819	synonymous_variant	4829	exon1				CCDS5196.1	6q24.1	2014-02-21			ENSG00000135577	ENSG00000135577		"""GPCR / Class A : Bombesin receptors"""	7843	protein-coding gene	gene with protein product	"""bombesin receptor 1"""	162341					Standard	NM_002511		Approved	BB1	uc003qiu.3	P28336	OTTHUMG00000015704	ENST00000258042.1:c.417C>T	6.37:g.142409379G>A			142451072	NM_002511	E9KL38|Q5VUK8	Silent	SNP	ENST00000258042.1	37	CCDS5196.1																																																																																				0.577	NMBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042479.1		
JARID2	3720	broad.mit.edu	37	6	15496485	15496485	+	Silent	SNP	G	G	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr6:15496485G>A	ENST00000341776.2	+	7	1273	c.1029G>A	c.(1027-1029)acG>acA	p.T343T	JARID2_ENST00000397311.3_Silent_p.T171T|JARID2_ENST00000541660.1_Silent_p.T305T	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	343					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.T343T(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				CCACGGTGACGAAGGGGGCTG	0.522																																					p.T343T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1029A	6						.						198.0	156.0	170.0					6																	15496485		2203	4300	6503	15604464	SO:0001819	synonymous_variant	3720	exon7			U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"""jumonji (mouse) homolog"", ""Jumonji, AT rich interactive domain 2"""	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.1029G>A	6.37:g.15496485G>A			15604464	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Silent	SNP	ENST00000341776.2	37	CCDS4533.1																																																																																				0.522	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973	
PRL	5617	broad.mit.edu	37	6	22290443	22290443	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr6:22290443G>A	ENST00000306482.1	-	4	970	c.452C>T	c.(451-453)aCc>aTc	p.T151I	RP3-404K8.2_ENST00000561912.1_RNA	NM_000948.5|NM_001163558.2	NP_000939.1|NP_001157030.1	P01236	PRL_HUMAN	prolactin	151					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|circadian rhythm (GO:0007623)|female pregnancy (GO:0007565)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|multicellular organismal response to stress (GO:0033555)|ovulation cycle (GO:0042698)|parturition (GO:0007567)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of JAK-STAT cascade (GO:0046427)|regulation of multicellular organism growth (GO:0040014)|regulation of ossification (GO:0030278)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|secretory granule (GO:0030141)	prolactin receptor binding (GO:0005148)	p.T151I(1)		NS(1)|endometrium(2)|large_intestine(6)|lung(6)|prostate(1)	16	Ovarian(93;0.163)					AAGCCGTTTGGTTTGCTCCTC	0.498																																					p.T151I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C452T	6						.						101.0	95.0	97.0					6																	22290443		2203	4300	6503	22398422	SO:0001583	missense	5617	exon4			D00411	CCDS4548.1	6p22.3	2013-09-16			ENSG00000172179	ENSG00000172179			9445	protein-coding gene	gene with protein product		176760					Standard	NM_000948		Approved		uc003ndq.3	P01236	OTTHUMG00000016111	ENST00000306482.1:c.452C>T	6.37:g.22290443G>A	ENSP00000302150:p.Thr151Ile		22398422	NM_000948	Q15199|Q92996	Missense_Mutation	SNP	ENST00000306482.1	37	CCDS4548.1	.	.	.	.	.	.	.	.	.	.	G	7.922	0.738761	0.15642	.	.	ENSG00000172179	ENST00000306482;ENST00000438606	D	0.87571	-2.27	5.76	3.35	0.38373	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.194311	0.56097	D	0.000031	T	0.81153	0.4763	L	0.33753	1.03	0.28132	N	0.930139	B;B	0.34181	0.001;0.44	B;P	0.51487	0.012;0.671	T	0.75525	-0.3287	10	0.37606	T	0.19	-4.3973	12.9641	0.58473	0.0:0.0:0.4105:0.5895	.	151;152	P01236;Q5I0G2	PRL_HUMAN;.	I	151;120	ENSP00000302150:T151I	ENSP00000302150:T151I	T	-	2	0	PRL	22398422	1.000000	0.71417	0.023000	0.16930	0.259000	0.26198	1.015000	0.29963	0.517000	0.28361	-0.262000	0.10625	ACC		0.498	PRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043327.1	NM_000948	
EPHA7	2045	broad.mit.edu	37	6	93956553	93956553	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr6:93956553G>A	ENST00000369303.4	-	15	2867	c.2683C>T	c.(2683-2685)Cga>Tga	p.R895*		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	895					brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)	p.R895*(2)		NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		TTTGGGTTTCGAATCATTTTG	0.413																																					p.R895X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C2683T	6						.						135.0	129.0	131.0					6																	93956553		2203	4300	6503	94013274	SO:0001587	stop_gained	2045	exon15			L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3390	protein-coding gene	gene with protein product		602190	"""EphA7"""			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.2683C>T	6.37:g.93956553G>A	ENSP00000358309:p.Arg895*		94013274	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Nonsense_Mutation	SNP	ENST00000369303.4	37	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	G	40	8.444810	0.98815	.	.	ENSG00000135333	ENST00000369303	.	.	.	5.74	2.52	0.30459	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.5944	0.84792	0.0:0.0:0.609:0.391	.	.	.	.	X	895	.	ENSP00000358309:R895X	R	-	1	2	EPHA7	94013274	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.145000	0.50623	0.700000	0.31782	0.591000	0.81541	CGA		0.413	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1		
ESR1	2099	broad.mit.edu	37	6	152201827	152201827	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr6:152201827C>A	ENST00000206249.3	+	3	1043	c.681C>A	c.(679-681)tgC>tgA	p.C227*	ESR1_ENST00000443427.1_Nonsense_Mutation_p.C227*|ESR1_ENST00000338799.5_Nonsense_Mutation_p.C227*|ESR1_ENST00000427531.2_Nonsense_Mutation_p.C54*|ESR1_ENST00000456483.2_Nonsense_Mutation_p.C227*|ESR1_ENST00000440973.1_Nonsense_Mutation_p.C227*|ESR1_ENST00000406599.1_Intron	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	227	Mediates interaction with DNTTIP2.				androgen metabolic process (GO:0008209)|antral ovarian follicle growth (GO:0001547)|cellular response to estradiol stimulus (GO:0071392)|chromatin remodeling (GO:0006338)|epithelial cell development (GO:0002064)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|gene expression (GO:0010467)|intracellular estrogen receptor signaling pathway (GO:0030520)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|male gonad development (GO:0008584)|mammary gland alveolus development (GO:0060749)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of gene expression (GO:0010629)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcriptionally active chromatin (GO:0035327)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0038052)|identical protein binding (GO:0042802)|nitric-oxide synthase regulator activity (GO:0030235)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.C227*(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(19)|ovary(1)|prostate(2)|skin(1)	49		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Allylestrenol(DB01431)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Estropipate(DB04574)|Ethinyl Estradiol(DB00977)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Ospemifene(DB04938)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)|Trilostane(DB01108)	CCAACCAGTGCACCATTGATA	0.453																																					p.C227X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C681A	6						.						67.0	67.0	67.0					6																	152201827		2203	4300	6503	152243520	SO:0001587	stop_gained	2099	exon4			X03635	CCDS5234.1	6q24-q27	2013-01-16			ENSG00000091831	ENSG00000091831		"""Nuclear hormone receptors"""	3467	protein-coding gene	gene with protein product		133430		ESR		3754034	Standard	NM_000125		Approved	NR3A1, Era	uc003qon.4	P03372	OTTHUMG00000016103	ENST00000206249.3:c.681C>A	6.37:g.152201827C>A	ENSP00000206249:p.Cys227*		152243520	NM_001122740	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Nonsense_Mutation	SNP	ENST00000206249.3	37	CCDS5234.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	43|43	10.201264|10.201264	0.99358|0.99358	.|.	.|.	ENSG00000091831|ENSG00000091831	ENST00000427531|ENST00000440973;ENST00000338799;ENST00000456483;ENST00000431219;ENST00000443427;ENST00000206249;ENST00000347491;ENST00000431590;ENST00000544394;ENST00000415488	.|.	.|.	.|.	5.42|5.42	4.54|4.54	0.55810|0.55810	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.15869|.	0.0382|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.04796|.	-1.0926|.	3|.	.|0.02654	.|T	.|1	.|.	12.6928|12.6928	0.56985|0.56985	0.0:0.8648:0.0:0.1352|0.0:0.8648:0.0:0.1352	.|.	.|.	.|.	.|.	E|X	132|227;227;227;8;227;227;52;155;54;12	.|.	.|ENSP00000206249:C227X	A|C	+|+	2|3	0|2	ESR1|ESR1	152243520|152243520	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.575000|2.575000	0.46025|0.46025	2.563000|2.563000	0.86464|0.86464	0.655000|0.655000	0.94253|0.94253	GCA|TGC		0.453	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1		
OR2A12	346525	broad.mit.edu	37	7	143792250	143792250	+	Missense_Mutation	SNP	A	A	C	rs373022188		TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr7:143792250A>C	ENST00000408949.2	+	1	110	c.50A>C	c.(49-51)cAg>cCg	p.Q17P		NM_001004135.1	NP_001004135.1	Q8NGT7	O2A12_HUMAN	olfactory receptor, family 2, subfamily A, member 12	17						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q17P(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)	25	Melanoma(164;0.0783)					TTGGGATTCCAGGTGGACCCA	0.443																																					p.Q17P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A50C	7						.						130.0	126.0	127.0					7																	143792250		1876	4115	5991	143423183	SO:0001583	missense	346525	exon1				CCDS43670.1	7q35	2013-09-20	2002-11-13	2002-11-13	ENSG00000221858	ENSG00000221858		"""GPCR / Class A : Olfactory receptors"""	15082	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily A, member 12 pseudogene"""	OR2A12P			Standard	NM_001004135		Approved		uc011kty.2	Q8NGT7	OTTHUMG00000157996	ENST00000408949.2:c.50A>C	7.37:g.143792250A>C	ENSP00000386174:p.Gln17Pro		143423183	NM_001004135	Q6IF43	Missense_Mutation	SNP	ENST00000408949.2	37	CCDS43670.1	.	.	.	.	.	.	.	.	.	.	A	2.479	-0.320063	0.05386	.	.	ENSG00000221858	ENST00000408949	T	0.00491	7.02	4.42	0.486	0.16836	.	.	.	.	.	T	0.00178	0.0005	N	0.00980	-1.08	0.09310	N	0.999999	B	0.11235	0.004	B	0.08055	0.003	T	0.35699	-0.9778	9	0.44086	T	0.13	-8.4238	4.3525	0.11162	0.3827:0.3034:0.0:0.3139	.	17	Q8NGT7	O2A12_HUMAN	P	17	ENSP00000386174:Q17P	ENSP00000386174:Q17P	Q	+	2	0	OR2A12	143423183	0.000000	0.05858	0.922000	0.36590	0.163000	0.22366	-0.324000	0.07986	0.687000	0.31509	0.413000	0.27773	CAG		0.443	OR2A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349969.1		
NEIL2	252969	broad.mit.edu	37	8	11637221	11637221	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr8:11637221G>T	ENST00000284503.6	+	3	852	c.253G>T	c.(253-255)Gac>Tac	p.D85Y	NEIL2_ENST00000436750.3_Missense_Mutation_p.D85Y|NEIL2_ENST00000455213.2_Missense_Mutation_p.D85Y|NEIL2_ENST00000403422.3_Missense_Mutation_p.D24Y|NEIL2_ENST00000528323.1_Intron	NM_145043.2	NP_659480.1	Q969S2	NEIL2_HUMAN	nei endonuclease VIII-like 2 (E. coli)	85					base-excision repair (GO:0006284)|nucleotide-excision repair (GO:0006289)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|zinc ion binding (GO:0008270)	p.D85Y(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	all_epithelial(15;0.103)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.166)		AGGGGCTGCGGACCCAAAGCA	0.557								Base excision repair (BER), DNA glycosylases																													p.D85Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G253T	8						.						60.0	71.0	67.0					8																	11637221		2203	4300	6503	11674630	SO:0001583	missense	252969	exon3			AK056206	CCDS5984.1, CCDS47802.1, CCDS47803.1	8p23.1	2010-04-27	2010-04-27		ENSG00000154328	ENSG00000154328			18956	protein-coding gene	gene with protein product		608933	"""nei like 2 (E. coli)"""			12097317, 17686777	Standard	NM_145043		Approved	NEH2, FLJ31644, MGC2832, MGC4505	uc003wue.2	Q969S2	OTTHUMG00000090753	ENST00000284503.6:c.253G>T	8.37:g.11637221G>T	ENSP00000284503:p.Asp85Tyr		11674630	NM_145043	B4DFR7|Q7Z3Q7|Q8N842|Q8NG52	Missense_Mutation	SNP	ENST00000284503.6	37	CCDS5984.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.729665	0.48833	.	.	ENSG00000154328	ENST00000530433;ENST00000455213;ENST00000403422;ENST00000436750;ENST00000284503	T;T;T;T	0.05996	3.45;3.36;3.45;3.45	5.31	0.699	0.18093	DNA glycosylase/AP lyase, catalytic domain (2);	1.787610	0.02876	N	0.132257	T	0.10852	0.0265	L	0.51422	1.61	0.09310	N	1	P	0.50369	0.934	P	0.47744	0.556	T	0.18713	-1.0328	10	0.72032	D	0.01	-41.8354	4.2028	0.10475	0.1681:0.1279:0.5734:0.1305	.	85	Q969S2	NEIL2_HUMAN	Y	85;85;24;85;85	ENSP00000397538:D85Y;ENSP00000384070:D24Y;ENSP00000394023:D85Y;ENSP00000284503:D85Y	ENSP00000284503:D85Y	D	+	1	0	NEIL2	11674630	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.102000	0.10956	0.193000	0.20303	0.462000	0.41574	GAC		0.557	NEIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207583.3	NM_145043	
DCAF10	79269	broad.mit.edu	37	9	37842161	37842161	+	Silent	SNP	C	C	T			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chr9:37842161C>T	ENST00000377724.3	+	3	1094	c.729C>T	c.(727-729)aaC>aaT	p.N243N	DCAF10_ENST00000242323.7_Silent_p.N243N|RP11-613M10.9_ENST00000540557.1_Intron	NM_024345.3	NP_077321.3	Q5QP82	DCA10_HUMAN	DDB1 and CUL4 associated factor 10	243					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)		p.N243N(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	12						GAAAATTGAACACCAAAGTAT	0.378																																					p.N243N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C729T	9						.						167.0	147.0	154.0					9																	37842161		2203	4300	6503	37832161	SO:0001819	synonymous_variant	79269	exon3			BC003520	CCDS6613.2, CCDS75835.1	9p13.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000122741	ENSG00000122741		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	23686	protein-coding gene	gene with protein product			"""WD repeat domain 32"""	WDR32			Standard	NM_001286810		Approved	MGC10765, FLJ23201	uc004aao.3	Q5QP82	OTTHUMG00000019934	ENST00000377724.3:c.729C>T	9.37:g.37842161C>T			37832161	NM_024345	A4VCJ5|Q32NE2|Q8N2Q5|Q96ET5|Q9BTQ5|Q9H5P6	Silent	SNP	ENST00000377724.3	37	CCDS6613.2																																																																																				0.378	DCAF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052485.2	NM_024345	
RGAG4	340526	broad.mit.edu	37	X	71350455	71350455	+	Silent	SNP	G	G	A			TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chrX:71350455G>A	ENST00000545866.1	-	1	1303	c.936C>T	c.(934-936)cgC>cgT	p.R312R	RGAG4_ENST00000609883.1_Silent_p.R312R|NHSL2_ENST00000540800.1_Intron	NM_001024455.3	NP_001019626.1	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4	312								p.R385R(1)		cervix(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|skin(1)	24	Renal(35;0.156)					GCTTGGGAACGCGCACTTTTC	0.483																																					p.R312R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C936T	X						.						108.0	102.0	104.0					X																	71350455		1918	4124	6042	71267180	SO:0001819	synonymous_variant	340526	exon1			AB082532	CCDS55446.1	Xq13.1	2008-02-05			ENSG00000242732	ENSG00000242732			29430	protein-coding gene	gene with protein product						12056414, 15716091, 16093683	Standard	NM_001024455		Approved	KIAA2001, Mar5, Mart5	uc004eaj.2	Q5HYW3	OTTHUMG00000021808	ENST00000545866.1:c.936C>T	X.37:g.71350455G>A			71267180	NM_001024455	A7E2W7|Q8NCM4|Q9NPX1	Silent	SNP	ENST00000545866.1	37	CCDS55446.1																																																																																				0.483	RGAG4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057171.1	NM_001024455	
GPR112	139378	broad.mit.edu	37	X	135431925	135431925	+	Silent	SNP	G	G	A	rs374261576		TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3858-01A-01W-0900-09	TCGA-AA-3858-10A-01W-0900-09	g.chrX:135431925G>A	ENST00000394143.1	+	6	6351	c.6060G>A	c.(6058-6060)ccG>ccA	p.P2020P	GPR112_ENST00000287534.4_Silent_p.P1957P|GPR112_ENST00000412101.1_Silent_p.P1815P|GPR112_ENST00000370652.1_Silent_p.P2020P|GPR112_ENST00000394141.1_Silent_p.P1815P	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	2020					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.P2020P(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					GCTCCCCTCCGGCAACTGTAT	0.453																																					p.P2020P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G6060A	X						.			0,3835		0,0,0,1632,571	117.0	100.0	106.0		6060	-0.5	0.0	X		106	3,6725		0,2,1,2426,1871	no	coding-synonymous	GPR112	NM_153834.3		0,2,1,4058,2442	AA,AG,A,GG,G		0.0446,0.0,0.0284		2020/3081	135431925	3,10560	2203	4300	6503	135259591	SO:0001819	synonymous_variant	139378	exon6			AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.6060G>A	X.37:g.135431925G>A			135259591	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	ENST00000394143.1	37	CCDS35409.1																																																																																				0.453	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
