#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_Start_position_hg18	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
PAPPA2	60676	broad.mit.edu	37	1	176664927	176664927	+	Missense_Mutation	SNP	A	A	G			TCGA-23-1116-01A-01W-0486-08	TCGA-23-1116-10A-01W-0486-08	A	A	G	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	a7a5ba23-a4bb-4224-9e67-36866679f583	c1171469-248f-4cd9-9af0-1356bbaf4b60	g.chr1:176664927A>G	ENST00000367662.3	+	7	3842	c.2678A>G	c.(2677-2679)tAt>tGt	p.Y893C		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	893					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.Y893C(1)		NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						TTTCGTCAGTATGTGCACACA	0.537																																																1	Substitution - Missense(1)	ovary(1)	1											83.0	86.0	85.0					1																	176664927		2086	4234	6320	174931550	SO:0001583	missense	60676			BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"""placenta-specific 3"""	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.2678A>G	1.37:g.176664927A>G	ENSP00000356634:p.Tyr893Cys		174931550	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	37	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.165435	0.78339	.	.	ENSG00000116183	ENST00000367662	T	0.04706	3.57	5.51	5.51	0.81932	Fibronectin, type III (2);	0.000000	0.85682	D	0.000000	T	0.24470	0.0593	M	0.82823	2.61	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.01218	-1.1415	10	0.87932	D	0	-22.1286	15.2975	0.73922	1.0:0.0:0.0:0.0	.	893	Q9BXP8	PAPP2_HUMAN	C	893	ENSP00000356634:Y893C	ENSP00000356634:Y893C	Y	+	2	0	PAPPA2	174931550	1.000000	0.71417	0.986000	0.45419	0.958000	0.62258	7.137000	0.77295	2.098000	0.63641	0.460000	0.39030	TAT		0.537	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1		
LAMC1	3915	broad.mit.edu	37	1	183111876	183111876	+	Missense_Mutation	SNP	A	A	C			TCGA-23-1116-01A-01W-0486-08	TCGA-23-1116-10A-01W-0486-08	A	A	C	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture;Sequenom			Illumina GAIIx	a7a5ba23-a4bb-4224-9e67-36866679f583	c1171469-248f-4cd9-9af0-1356bbaf4b60	g.chr1:183111876A>C	ENST00000258341.4	+	28	5038	c.4781A>C	c.(4780-4782)aAg>aCg	p.K1594T	RP11-181K3.4_ENST00000457852.3_RNA	NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	1594	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.K1594T(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						GACATCAGGAAGACCTTACCA	0.522																																																1	Substitution - Missense(1)	ovary(1)	1											126.0	110.0	115.0					1																	183111876		2203	4300	6503	181378499	SO:0001583	missense	3915			J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.4781A>C	1.37:g.183111876A>C	ENSP00000258341:p.Lys1594Thr		181378499	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	37	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	A	13.04	2.119317	0.37436	.	.	ENSG00000135862	ENST00000258341	T	0.31247	1.5	5.57	3.28	0.37604	.	0.159267	0.53938	D	0.000041	T	0.25975	0.0633	L	0.56769	1.78	0.43317	D	0.995334	B	0.29716	0.255	B	0.24394	0.053	T	0.03566	-1.1024	10	0.25106	T	0.35	.	9.517	0.39111	0.8577:0.0:0.1423:0.0	.	1594	P11047	LAMC1_HUMAN	T	1594	ENSP00000258341:K1594T	ENSP00000258341:K1594T	K	+	2	0	LAMC1	181378499	1.000000	0.71417	0.973000	0.42090	0.997000	0.91878	5.465000	0.66725	0.415000	0.25817	0.533000	0.62120	AAG		0.522	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
OR2M5	127059	broad.mit.edu	37	1	248308539	248308539	+	Silent	SNP	G	G	T			TCGA-23-1116-01A-01W-0486-08	TCGA-23-1116-10A-01W-0486-08	G	G	T	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	a7a5ba23-a4bb-4224-9e67-36866679f583	c1171469-248f-4cd9-9af0-1356bbaf4b60	g.chr1:248308539G>T	ENST00000366476.1	+	1	90	c.90G>T	c.(88-90)ctG>ctT	p.L30L		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	30						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L30L(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)			TCTTCTTTCTGGTCCTGGCCA	0.507																																																1	Substitution - coding silent(1)	ovary(1)	1											220.0	222.0	222.0					1																	248308539		2203	4297	6500	246375162	SO:0001819	synonymous_variant	127059				CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"""GPCR / Class A : Olfactory receptors"""	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.90G>T	1.37:g.248308539G>T			246375162		Silent	SNP	ENST00000366476.1	37	CCDS31105.1																																																																																				0.507	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690	
CPAMD8	27151	broad.mit.edu	37	19	17039019	17039019	+	Missense_Mutation	SNP	T	T	C	rs375296622		TCGA-23-1116-01A-01W-0486-08	TCGA-23-1116-10A-01W-0486-08	T	T	C	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom			Illumina GAIIx	a7a5ba23-a4bb-4224-9e67-36866679f583	c1171469-248f-4cd9-9af0-1356bbaf4b60	g.chr19:17039019T>C	ENST00000443236.1	-	25	3342	c.3311A>G	c.(3310-3312)aAt>aGt	p.N1104S		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	1057						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.N1104S(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						GACAGACTCATTGGATGGCTC	0.587																																																1	Substitution - Missense(1)	ovary(1)	19						T	SER/ASN	0,3938		0,0,1969	35.0	39.0	38.0		3311	3.1	0.8	19		38	1,8309		0,1,4154	no	missense	CPAMD8	NM_015692.2	46	0,1,6123	CC,CT,TT		0.012,0.0,0.0082	possibly-damaging	1104/1933	17039019	1,12247	1969	4155	6124	16900019	SO:0001583	missense	27151			AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.3311A>G	19.37:g.17039019T>C	ENSP00000402505:p.Asn1104Ser		16900019	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.558|4.558	0.103578|0.103578	0.08731|0.08731	0.0|0.0	1.2E-4|1.2E-4	ENSG00000160111|ENSG00000160111	ENST00000443236|ENST00000291440	.|.	.|.	.|.	3.13|3.13	3.13|3.13	0.36017|0.36017	.|Farnesoic acid O-methyl transferase (1);	.|0.462648	.|0.17924	.|U	.|0.157387	T|T	0.35970|0.35970	0.0950|0.0950	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	.|P	.|0.38420	.|0.63	.|B	.|0.34873	.|0.191	T|T	0.09185|0.09185	-1.0686|-1.0686	5|9	.|0.27082	.|T	.|0.32	.|.	11.38|11.38	0.49752|0.49752	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1057	.|Q8IZJ3	.|CPMD8_HUMAN	V|S	1115|1104	.|.	.|ENSP00000291440:N1104S	M|N	-|-	1|2	0|0	CPAMD8|CPAMD8	16900019|16900019	1.000000|1.000000	0.71417|0.71417	0.819000|0.819000	0.32651|0.32651	0.075000|0.075000	0.17131|0.17131	2.111000|2.111000	0.41883|0.41883	1.072000|1.072000	0.40860|0.40860	0.533000|0.533000	0.62120|0.62120	ATG|AAT		0.587	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
GYS1	2997	broad.mit.edu	37	19	49489140	49489140	+	Silent	SNP	G	G	A	rs371721154		TCGA-23-1116-01A-01W-0486-08	TCGA-23-1116-10A-01W-0486-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	a7a5ba23-a4bb-4224-9e67-36866679f583	c1171469-248f-4cd9-9af0-1356bbaf4b60	g.chr19:49489140G>A	ENST00000323798.3	-	4	841	c.645C>T	c.(643-645)gcC>gcT	p.A215A	GYS1_ENST00000541188.1_Silent_p.A135A|GYS1_ENST00000540532.1_Silent_p.A135A|GYS1_ENST00000263276.6_Silent_p.A151A|GYS1_ENST00000457974.1_5'Flank|GYS1_ENST00000544287.1_Intron	NM_002103.4	NP_002094.2	P13807	GYS1_HUMAN	glycogen synthase 1 (muscle)	215					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|heart development (GO:0007507)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|inclusion body (GO:0016234)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein kinase binding (GO:0019901)	p.A215A(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286)		CCACGGCACCGGCACACAGGT	0.632																																																1	Substitution - coding silent(1)	ovary(1)	19						G	,	0,4406		0,0,2203	68.0	61.0	64.0		453,645	-7.9	0.0	19		64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	GYS1	NM_001161587.1,NM_002103.4	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	151/674,215/738	49489140	1,13005	2203	4300	6503	54180952	SO:0001819	synonymous_variant	2997				CCDS12747.1, CCDS54292.1	19q13.3	2013-02-22			ENSG00000104812	ENSG00000104812	2.4.1.11	"""Glycosyltransferase group 1 domain containing"""	4706	protein-coding gene	gene with protein product		138570		GYS			Standard	NM_002103		Approved	GSY	uc002plp.3	P13807	OTTHUMG00000150723	ENST00000323798.3:c.645C>T	19.37:g.49489140G>A			54180952	Q9BTT9	Silent	SNP	ENST00000323798.3	37	CCDS12747.1																																																																																				0.632	GYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319791.1	NM_002103	
DDX1	1653	broad.mit.edu	37	2	15760383	15760383	+	Missense_Mutation	SNP	G	G	A			TCGA-23-1116-01A-01W-0486-08	TCGA-23-1116-10A-01W-0486-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	a7a5ba23-a4bb-4224-9e67-36866679f583	c1171469-248f-4cd9-9af0-1356bbaf4b60	g.chr2:15760383G>A	ENST00000381341.2	+	18	1647	c.1258G>A	c.(1258-1260)Gag>Aag	p.E420K	DDX1_ENST00000233084.3_Missense_Mutation_p.E420K			Q92499	DDX1_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 1	420	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|Necessary for interaction with RELA.				ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|multicellular organismal development (GO:0007275)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translational initiation (GO:0006446)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	cleavage body (GO:0071920)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|tRNA-splicing ligase complex (GO:0072669)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA/RNA helicase activity (GO:0033677)|double-stranded RNA binding (GO:0003725)|exonuclease activity (GO:0004527)|nuclease activity (GO:0004518)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|transcription cofactor activity (GO:0003712)	p.E420K(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(13)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)		GAAACTGTCCGAGAAGATAAT	0.368																																																1	Substitution - Missense(1)	ovary(1)	2											130.0	126.0	128.0					2																	15760383		2203	4300	6503	15677834	SO:0001583	missense	1653			X70649	CCDS1686.1	2p24	2012-02-23	2012-02-23		ENSG00000079785	ENSG00000079785		"""DEAD-boxes"""	2734	protein-coding gene	gene with protein product		601257	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 1"""			1552844, 19058135	Standard	NM_004939		Approved	DBP-RB	uc002rce.4	Q92499	OTTHUMG00000090593	ENST00000381341.2:c.1258G>A	2.37:g.15760383G>A	ENSP00000370745:p.Glu420Lys		15677834	B4DME8|B4DPN6	Missense_Mutation	SNP	ENST00000381341.2	37	CCDS1686.1	.	.	.	.	.	.	.	.	.	.	G	32	5.141873	0.94560	.	.	ENSG00000079785	ENST00000381341;ENST00000233084;ENST00000543614	T;T	0.04454	3.62;3.62	6.07	6.07	0.98685	DEAD-like helicase (2);	0.000000	0.85682	D	0.000000	T	0.06735	0.0172	N	0.17872	0.535	0.80722	D	1	D	0.61697	0.99	P	0.46659	0.523	T	0.46992	-0.9151	10	0.33141	T	0.24	-29.4035	20.6525	0.99598	0.0:0.0:1.0:0.0	.	420	Q92499	DDX1_HUMAN	K	420;420;404	ENSP00000370745:E420K;ENSP00000233084:E420K	ENSP00000233084:E420K	E	+	1	0	DDX1	15677834	1.000000	0.71417	0.995000	0.50966	0.436000	0.31835	9.869000	0.99810	2.890000	0.99128	0.585000	0.79938	GAG		0.368	DDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207141.2	NM_004939	
ATP6V1E2	90423	broad.mit.edu	37	2	46739447	46739447	+	Missense_Mutation	SNP	C	C	T	rs142304043		TCGA-23-1116-01A-01W-0486-08	TCGA-23-1116-10A-01W-0486-08	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	a7a5ba23-a4bb-4224-9e67-36866679f583	c1171469-248f-4cd9-9af0-1356bbaf4b60	g.chr2:46739447C>T	ENST00000306448.4	-	2	1517	c.404G>A	c.(403-405)cGc>cAc	p.R135H	ATP6V1E2_ENST00000522587.1_Missense_Mutation_p.R135H	NM_080653.3	NP_542384.1	Q96A05	VATE2_HUMAN	ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E2	135					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|proton-transporting two-sector ATPase complex, catalytic domain (GO:0033178)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)	p.R135H(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)	13		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.151)			TGGCCGGCAGCGTACAATCAT	0.552													C|||	1	0.000199681	0.0	0.0	5008	,	,		19067	0.0		0.001	False		,,,				2504	0.0															1	Substitution - Missense(1)	ovary(1)	2						C	HIS/ARG	0,4406		0,0,2203	91.0	88.0	89.0		404	4.4	1.0	2	dbSNP_134	89	3,8597	3.0+/-9.4	0,3,4297	yes	missense	ATP6V1E2	NM_080653.3	29	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	possibly-damaging	135/227	46739447	3,13003	2203	4300	6503	46592951	SO:0001583	missense	90423			BC008981	CCDS1826.1	2p21	2011-02-10	2006-01-13	2002-06-21	ENSG00000250565	ENSG00000250565		"""ATPases / V-type"""	18125	protein-coding gene	gene with protein product			"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) 31kD-like 2"", ""ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E isoform 2"""	ATP6EL2, ATP6V1EL2		12036578	Standard	NM_080653		Approved	MGC9341, VMA4, ATP6E1	uc002ruy.3	Q96A05	OTTHUMG00000128819	ENST00000306448.4:c.404G>A	2.37:g.46739447C>T	ENSP00000304891:p.Arg135His		46592951		Missense_Mutation	SNP	ENST00000306448.4	37	CCDS1826.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.48	3.633009	0.67015	0.0	3.49E-4	ENSG00000250565	ENST00000306448;ENST00000522587	.	.	.	4.37	4.37	0.52481	.	0.000000	0.85682	D	0.000000	T	0.68348	0.2991	M	0.80183	2.485	0.80722	D	1	B	0.24533	0.105	B	0.26969	0.075	T	0.71361	-0.4616	9	0.72032	D	0.01	-9.083	12.7449	0.57276	0.0:1.0:0.0:0.0	.	135	Q96A05	VATE2_HUMAN	H	135	.	ENSP00000304891:R135H	R	-	2	0	ATP6V1E2	46592951	1.000000	0.71417	0.994000	0.49952	0.975000	0.68041	3.920000	0.56446	2.713000	0.92767	0.655000	0.94253	CGC		0.552	ATP6V1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250753.1	NM_080653	
ALS2CR12	130540	broad.mit.edu	37	2	202208956	202208956	+	Missense_Mutation	SNP	T	T	G			TCGA-23-1116-01A-01W-0486-08	TCGA-23-1116-10A-01W-0486-08	T	T	G	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	a7a5ba23-a4bb-4224-9e67-36866679f583	c1171469-248f-4cd9-9af0-1356bbaf4b60	g.chr2:202208956T>G	ENST00000286190.5	-	5	445	c.399A>C	c.(397-399)caA>caC	p.Q133H	ALS2CR12_ENST00000392257.3_Missense_Mutation_p.Q133H|ALS2CR12_ENST00000448967.1_5'UTR|ALS2CR12_ENST00000439709.1_Missense_Mutation_p.Q133H|ALS2CR12_ENST00000405148.2_Missense_Mutation_p.Q133H			Q96Q35	AL2SB_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 12	133					regulation of GTPase activity (GO:0043087)	outer dense fiber (GO:0001520)|sperm fibrous sheath (GO:0035686)|sperm flagellum (GO:0036126)		p.Q133H(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)	21						GCTCTGAGATTTGCTCTTCTA	0.433																																																1	Substitution - Missense(1)	ovary(1)	2											271.0	255.0	261.0					2																	202208956		2203	4300	6503	201917201	SO:0001583	missense	130540			AB053314	CCDS2346.1, CCDS46488.1	2q33.1	2009-10-06			ENSG00000155749	ENSG00000155749			14439	protein-coding gene	gene with protein product							Standard	XM_006712272		Approved		uc002uya.4	Q96Q35	OTTHUMG00000132824	ENST00000286190.5:c.399A>C	2.37:g.202208956T>G	ENSP00000286190:p.Gln133His		201917201	G5E9S3|Q53TT6|Q8N1B6	Missense_Mutation	SNP	ENST00000286190.5	37	CCDS2346.1	.	.	.	.	.	.	.	.	.	.	T	14.26	2.481966	0.44147	.	.	ENSG00000155749	ENST00000286190;ENST00000405148;ENST00000392257;ENST00000439709	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	5.17	2.3	0.28687	.	0.136402	0.33959	N	0.004394	T	0.36744	0.0978	M	0.66939	2.045	0.28104	N	0.931296	B;B	0.32800	0.385;0.385	B;B	0.33295	0.161;0.099	T	0.38351	-0.9665	10	0.87932	D	0	-7.1569	4.8772	0.13662	0.1674:0.6461:0.0:0.1865	.	133;133	Q96Q35;G5E9S3	AL2SB_HUMAN;.	H	133	ENSP00000286190:Q133H;ENSP00000385098:Q133H;ENSP00000376086:Q133H;ENSP00000412073:Q133H	ENSP00000286190:Q133H	Q	-	3	2	ALS2CR12	201917201	1.000000	0.71417	1.000000	0.80357	0.325000	0.28411	0.620000	0.24403	0.240000	0.21263	-0.375000	0.07067	CAA		0.433	ALS2CR12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256286.1	NM_139163	
MC3R	4159	broad.mit.edu	37	20	54824044	54824044	+	Missense_Mutation	SNP	G	G	C			TCGA-23-1116-01A-01W-0486-08	TCGA-23-1116-10A-01W-0486-08	G	G	C	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	a7a5ba23-a4bb-4224-9e67-36866679f583	c1171469-248f-4cd9-9af0-1356bbaf4b60	g.chr20:54824044G>C	ENST00000243911.2	+	1	257	c.145G>C	c.(145-147)Ggc>Cgc	p.G49R		NM_019888.3	NP_063941.3	P41968	MC3R_HUMAN	melanocortin 3 receptor	49					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|homoiothermy (GO:0042309)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP biosynthetic process (GO:0030819)|regulation of blood pressure (GO:0008217)|regulation of heart rate (GO:0002027)|sodium ion homeostasis (GO:0055078)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)	p.G86R(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(3)|skin(1)	26			Colorectal(105;0.202)			CCTGTCTCTGGGCATCGTCAG	0.567																																																1	Substitution - Missense(1)	ovary(1)	20											105.0	90.0	95.0					20																	54824044		2203	4300	6503	54257451	SO:0001583	missense	4159				CCDS13449.2	20q13.2-q13.3	2012-08-10			ENSG00000124089	ENSG00000124089		"""GPCR / Class A : Melanocortin receptors"""	6931	protein-coding gene	gene with protein product		155540				8463333	Standard	NM_019888		Approved	MC3	uc002xxb.2	P41968	OTTHUMG00000032785	ENST00000243911.2:c.145G>C	20.37:g.54824044G>C	ENSP00000243911:p.Gly49Arg		54257451	Q4KN27|Q9H517	Missense_Mutation	SNP	ENST00000243911.2	37	CCDS13449.2	.	.	.	.	.	.	.	.	.	.	G	19.77	3.889499	0.72524	.	.	ENSG00000124089	ENST00000243911	T	0.02974	4.09	5.01	5.01	0.66863	.	0.000000	0.64402	D	0.000003	T	0.06600	0.0169	N	0.08118	0	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.56763	-0.7925	10	0.87932	D	0	.	17.9343	0.89008	0.0:0.0:1.0:0.0	.	86	P41968	MC3R_HUMAN	R	49	ENSP00000243911:G49R	ENSP00000243911:G49R	G	+	1	0	MC3R	54257451	1.000000	0.71417	0.999000	0.59377	0.518000	0.34316	9.618000	0.98365	2.317000	0.78254	0.650000	0.86243	GGC		0.567	MC3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079786.2		
ZCWPW2	152098	broad.mit.edu	37	3	28454696	28454696	+	Missense_Mutation	SNP	G	G	T			TCGA-23-1116-01A-01W-0486-08	TCGA-23-1116-10A-01W-0486-08	G	G	T	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Capture			Illumina GAIIx	a7a5ba23-a4bb-4224-9e67-36866679f583	c1171469-248f-4cd9-9af0-1356bbaf4b60	g.chr3:28454696G>T	ENST00000383768.2	+	3	325	c.137G>T	c.(136-138)aGt>aTt	p.S46I	ZCWPW2_ENST00000421010.1_Missense_Mutation_p.S46I			Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2	46							zinc ion binding (GO:0008270)	p.S46I(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(6)|ovary(2)	17						TTGTTATCAAGTGAGGATTCA	0.363																																																1	Substitution - Missense(1)	ovary(1)	3											138.0	132.0	134.0					3																	28454696		2203	4300	6503	28429700	SO:0001583	missense	152098			BC065764	CCDS33723.1	3p23	2005-08-22			ENSG00000206559	ENSG00000206559			23574	protein-coding gene	gene with protein product						14607086	Standard	XM_005264892		Approved	ZCW2	uc003cei.3	Q504Y3	OTTHUMG00000155705	ENST00000383768.2:c.137G>T	3.37:g.28454696G>T	ENSP00000373278:p.Ser46Ile		28429700		Missense_Mutation	SNP	ENST00000383768.2	37	CCDS33723.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.76|11.76	1.736214|1.736214	0.30774|0.30774	.|.	.|.	ENSG00000206559|ENSG00000206559	ENST00000428875|ENST00000420223;ENST00000383768;ENST00000421010	.|T;T	.|0.32988	.|1.43;1.43	5.46|5.46	0.421|0.421	0.16451|0.16451	.|Zinc finger, CW-type (2);	.|0.425465	.|0.22405	.|N	.|0.060488	T|T	0.19725|0.19725	0.0474|0.0474	L|L	0.31578|0.31578	0.945|0.945	0.22842|0.22842	N|N	0.998661|0.998661	.|P	.|0.36789	.|0.57	.|B	.|0.39805	.|0.31	T|T	0.11108|0.11108	-1.0601|-1.0601	5|10	.|0.38643	.|T	.|0.18	-1.4113|-1.4113	5.0514|5.0514	0.14511|0.14511	0.2519:0.2965:0.4515:0.0|0.2519:0.2965:0.4515:0.0	.|.	.|46	.|Q504Y3	.|ZCPW2_HUMAN	N|I	29|46	.|ENSP00000373278:S46I;ENSP00000412386:S46I	.|ENSP00000373278:S46I	K|S	+|+	3|2	2|0	ZCWPW2|ZCWPW2	28429700|28429700	1.000000|1.000000	0.71417|0.71417	0.983000|0.983000	0.44433|0.44433	0.908000|0.908000	0.53690|0.53690	0.384000|0.384000	0.20668|0.20668	-0.226000|-0.226000	0.09899|0.09899	-0.216000|-0.216000	0.12614|0.12614	AAG|AGT		0.363	ZCWPW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341318.1	XM_087384	
SDC2	6383	broad.mit.edu	37	8	97620629	97620629	+	Missense_Mutation	SNP	G	G	A	rs200028820		TCGA-23-1116-01A-01W-0486-08	TCGA-23-1116-10A-01W-0486-08	G	G	A	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Sequenom;Capture			Illumina GAIIx	a7a5ba23-a4bb-4224-9e67-36866679f583	c1171469-248f-4cd9-9af0-1356bbaf4b60	g.chr8:97620629G>A	ENST00000302190.4	+	4	1294	c.373G>A	c.(373-375)Gaa>Aaa	p.E125K	SDC2_ENST00000518385.1_Missense_Mutation_p.E89K|SDC2_ENST00000522911.1_Missense_Mutation_p.E96K|SDC2_ENST00000519914.1_Missense_Mutation_p.E96K	NM_002998.3	NP_002989.2	P34741	SDC2_HUMAN	syndecan 2	125					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dendrite morphogenesis (GO:0048813)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|regulation of dendrite morphogenesis (GO:0048814)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)	p.E125K(1)		breast(1)|cervix(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|stomach(2)	16	Breast(36;3.41e-05)				Sargramostim(DB00020)	GGACCCAGCCGAAGAGGATAC	0.458																																																1	Substitution - Missense(1)	ovary(1)	8						G	LYS/GLU	0,4406		0,0,2203	94.0	91.0	92.0		373	4.4	0.1	8		92	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SDC2	NM_002998.3	56	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	125/202	97620629	2,13004	2203	4300	6503	97689805	SO:0001583	missense	6383			BC030133	CCDS6272.1	8q22-q23	2011-08-11	2007-02-15		ENSG00000169439	ENSG00000169439		"""Proteoglycans / Cell Surface : Syndecans"", ""CD molecules"""	10659	protein-coding gene	gene with protein product	"""syndecan proteoglycan 2"""	142460	"""heparan sulfate proteoglycan 1, cell surface-associated"""	HSPG, HSPG1		8187643	Standard	NM_002998		Approved	fibroglycan, SYND2, CD362	uc003yhv.1	P34741	OTTHUMG00000164689	ENST00000302190.4:c.373G>A	8.37:g.97620629G>A	ENSP00000307046:p.Glu125Lys		97689805	B3KQA3|Q6PIS6|Q9H6V1	Missense_Mutation	SNP	ENST00000302190.4	37	CCDS6272.1	.	.	.	.	.	.	.	.	.	.	G	9.959	1.222336	0.22457	0.0	2.33E-4	ENSG00000169439	ENST00000302190;ENST00000518385;ENST00000545117;ENST00000546193;ENST00000522911;ENST00000519914;ENST00000521590;ENST00000523877	T;T;T;T;T	0.31247	1.52;1.5;1.53;1.53;1.51	6.17	4.37	0.52481	.	0.807226	0.12068	N	0.502522	T	0.13372	0.0324	N	0.08118	0	0.24271	N	0.995245	P	0.41524	0.753	B	0.35655	0.207	T	0.04522	-1.0945	10	0.07644	T	0.81	-3.8934	10.21	0.43134	0.2061:0.0:0.7939:0.0	.	125	P34741	SDC2_HUMAN	K	125;89;125;115;96;96;96;96	ENSP00000307046:E125K;ENSP00000429045:E89K;ENSP00000427784:E96K;ENSP00000428256:E96K;ENSP00000429121:E96K	ENSP00000307046:E125K	E	+	1	0	SDC2	97689805	1.000000	0.71417	0.082000	0.20525	0.178000	0.23041	3.450000	0.52957	0.918000	0.36919	-0.150000	0.13652	GAA		0.458	SDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379750.1	NM_002998	
TP53	7157	broad.mit.edu	37	17	7577146	7577156	+	Splice_Site	DEL	TAGATTACCAC	TAGATTACCAC	-	rs72661119|rs200579969		TCGA-23-1116-01A-01W-0486-08	TCGA-23-1116-10A-01W-0486-08	TAGATTACCAC	TAGATTACCAC	-	-	TAGATTACCAC	TAGATTACCAC	Unknown	Valid	Somatic	Phase_I	Capture	Illumina_Capture			Illumina GAIIx	a7a5ba23-a4bb-4224-9e67-36866679f583	c1171469-248f-4cd9-9af0-1356bbaf4b60	g.chr17:7577146_7577156delTAGATTACCAC	ENST00000269305.4	-	8	972_981	c.783_792delGTGGTAATCTA	c.(781-792)aggtggtaatct>ag	p.RW*S261fs	TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Splice_Site_p.RW*S261fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Splice_Site_p.RW*S261fs|TP53_ENST00000445888.2_Splice_Site_p.RW*S261fs|TP53_ENST00000455263.2_Splice_Site_p.RW*S261fs	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	261	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		S -> C (in a sporadic cancer; somatic mutation).|S -> G (in sporadic cancers; somatic mutation).|S -> I (in sporadic cancers; somatic mutation).|S -> N (in a sporadic cancer; somatic mutation).|S -> R (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.?(26)|p.G262V(19)|p.0?(8)|p.L264L(5)|p.G262fs*83(5)|p.G262D(4)|p.L264fs*81(4)|p.L264del(4)|p.S261R(4)|p.L264I(3)|p.N263fs*82(3)|p.G262_F270delGNLLGRNSF(2)|p.N263D(2)|p.N263H(2)|p.N263I(2)|p.G262S(2)|p.G262del(2)|p.S261S(2)|p.G262_S269delGNLLGRNS(2)|p.L265del(2)|p.264_265insSSGNL(1)|p.L265fs*81(1)|p.G262G(1)|p.E258fs*71(1)|p.S261_G262insX(1)|p.N263K(1)|p.G262fs*2(1)|p.L264V(1)|p.L264P(1)|p.L264R(1)|p.S261_L264>R(1)|p.N263fs*5(1)|p.G262H(1)|p.N263fs*84(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)	TCCGTCCCAGTAGATTACCACTACTCAGGAT	0.521		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	117	Substitution - Missense(43)|Unknown(26)|Deletion - Frameshift(15)|Deletion - In frame(12)|Whole gene deletion(8)|Substitution - coding silent(8)|Insertion - Frameshift(2)|Insertion - In frame(2)|Complex - deletion inframe(1)	lung(18)|upper_aerodigestive_tract(16)|large_intestine(16)|urinary_tract(14)|ovary(13)|haematopoietic_and_lymphoid_tissue(7)|central_nervous_system(6)|breast(6)|stomach(5)|bone(4)|endometrium(2)|liver(2)|pancreas(2)|oesophagus(2)|eye(1)|genital_tract(1)|kidney(1)|skin(1)	17																																								7517881	SO:0001630	splice_region_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.783-1GTGGTAATCTA>-	17.37:g.7577146_7577156delTAGATTACCAC			7517871	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	Splice_Site	DEL	ENST00000269305.4	37	CCDS11118.1																																																																																				0.521	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Frame_Shift_Del
