#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
PIGG	54872	hgsc.bcm.edu	37	4	520847	520864	+	In_Frame_Del	DEL	CTCTCTGTCCTGGCTGCC	CTCTCTGTCCTGGCTGCC	-	rs13114026	byFrequency	TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	CTCTCTGTCCTGGCTGCC	CTCTCTGTCCTGGCTGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_III	WXS	none			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr4:520847_520864delCTCTCTGTCCTGGCTGCC	ENST00000453061.2	+	10	2195_2212	c.2089_2106delCTCTCTGTCCTGGCTGCC	c.(2089-2106)ctctctgtcctggctgccdel	p.LSVLAA697del	PIGG_ENST00000296306.7_3'UTR|PIGG_ENST00000383028.4_In_Frame_Del_p.LSVLAA564del|PIGG_ENST00000504346.1_In_Frame_Del_p.LSVLAA608del|PIGG_ENST00000310340.5_In_Frame_Del_p.LSVLAA689del	NM_001127178.1	NP_001120650.1	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class G	697					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CP2 mannose-ethanolamine phosphotransferase activity (GO:0051267)|phosphotransferase activity, for other substituted phosphate groups (GO:0016780)	p.L689_A694delLSVLAA(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	39						CAAAGCCGAGCTCTCTGTCCTGGCTGCCCTCTCCCTCC	0.56																																																1	Deletion - In frame(1)	ovary(1)	4																																								510864	SO:0001651	inframe_deletion	54872				CCDS3336.1, CCDS46992.1, CCDS75080.1, CCDS75081.1, CCDS75082.1, CCDS75083.1	4p16.3	2013-02-26	2006-06-28		ENSG00000174227	ENSG00000174227		"""Phosphatidylinositol glycan anchor biosynthesis"""	25985	protein-coding gene	gene with protein product			"""phosphatidylinositol glycan, class G"""			15632136	Standard	XM_005272287		Approved	FLJ20265, GPI7, LAS21	uc003gak.4	Q5H8A4	OTTHUMG00000112457	ENST00000453061.2:c.2089_2106delCTCTCTGTCCTGGCTGCC	4.37:g.520847_520864delCTCTCTGTCCTGGCTGCC	ENSP00000415203:p.Leu697_Ala702del		510847	B4DKC7|Q2TAK5|Q6UX31|Q7L5Y4|Q8N866|Q8NCC9|Q96SY9|Q9BVT7|Q9NXG5	In_Frame_Del	DEL	ENST00000453061.2	37	CCDS46992.1																																																																																				0.560	PIGG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357494.1	NM_017733	
RBM43	375287	hgsc.bcm.edu	37	2	152108088	152108088	+	Frame_Shift_Del	DEL	T	T	-			TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_III	WXS	none			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr2:152108088delT	ENST00000331426.5	-	4	557	c.406delA	c.(406-408)atcfs	p.I136fs		NM_198557.2	NP_940959.1	Q6ZSC3	RBM43_HUMAN	RNA binding motif protein 43	136							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.I136fs*4(1)		endometrium(2)|large_intestine(3)|lung(2)|ovary(1)	8				BRCA - Breast invasive adenocarcinoma(221;0.131)		AAACTCGGGATTTTTTTTTTC	0.388																																																1	Deletion - Frameshift(1)	ovary(1)	2								67,49,4116		3,1,60,6,36,2010	81.0	90.0	87.0			4.3	0.8	2	dbSNP_134	89	115,71,8038		0,1,114,8,54,3935	no	codingComplex	RBM43	NM_198557.2		3,2,174,14,90,5945	A1A1,A1A2,A1R,A2A2,A2R,RR		2.2617,2.741,2.4245			152108088	182,120,12154	2198	4292	6490	151816334	SO:0001589	frameshift_variant	375287			AK127552	CCDS2191.1	2q23.3	2007-01-30	2007-01-30	2007-01-30	ENSG00000184898	ENSG00000184898		"""RNA binding motif (RRM) containing"""	24790	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 38"""	C2orf38			Standard	NM_198557		Approved	FLJ45645	uc002txh.3	Q6ZSC3	OTTHUMG00000131866	ENST00000331426.5:c.406delA	2.37:g.152108088delT	ENSP00000331211:p.Ile136fs		151816334	B2RMT5	Frame_Shift_Del	DEL	ENST00000331426.5	37	CCDS2191.1																																																																																				0.388	RBM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254816.2	NM_198557	
TMCO5A	145942	hgsc.bcm.edu	37	15	38235571	38235571	+	Missense_Mutation	SNP	A	A	G			TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_III	WXS	none			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr15:38235571A>G	ENST00000319669.4	+	9	701	c.599A>G	c.(598-600)gAa>gGa	p.E200G	TMCO5A_ENST00000540944.1_Missense_Mutation_p.E200G|TMCO5A_ENST00000559502.1_Missense_Mutation_p.E200G|TMCO5A_ENST00000558158.1_3'UTR	NM_152453.2	NP_689666.2	Q8N6Q1	TMC5A_HUMAN	transmembrane and coiled-coil domains 5A	200						integral component of membrane (GO:0016021)		p.E200G(1)		central_nervous_system(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	15						AACCCTGTGGAAAAAGAGCAT	0.393																																																1	Substitution - Missense(1)	ovary(1)	15											175.0	150.0	158.0					15																	38235571		2200	4297	6497	36022863	SO:0001583	missense	145942			BC029221	CCDS10046.1	15q14	2008-06-10	2008-06-10	2008-06-10	ENSG00000166069	ENSG00000166069			28558	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 5"""	TMCO5		12477932	Standard	NM_152453		Approved	MGC35118	uc001zjw.3	Q8N6Q1	OTTHUMG00000129787	ENST00000319669.4:c.599A>G	15.37:g.38235571A>G	ENSP00000327234:p.Glu200Gly		36022863	Q8NA63	Missense_Mutation	SNP	ENST00000319669.4	37	CCDS10046.1	.	.	.	.	.	.	.	.	.	.	A	4.937	0.174113	0.09391	.	.	ENSG00000166069	ENST00000540944;ENST00000319669	.	.	.	4.95	-1.58	0.08479	.	1.239810	0.05568	N	0.570647	T	0.28034	0.0691	L	0.29908	0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.19063	-1.0317	9	0.28530	T	0.3	-8.7042	5.6116	0.17408	0.332:0.0:0.5371:0.1309	.	200;200	Q8N6Q1;Q8N6Q1-2	TMC5A_HUMAN;.	G	200	.	ENSP00000327234:E200G	E	+	2	0	TMCO5A	36022863	0.002000	0.14202	0.000000	0.03702	0.002000	0.02628	0.442000	0.21628	-0.379000	0.07906	-2.424000	0.00217	GAA		0.393	TMCO5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252012.1	NM_152453	
ANO4	121601	hgsc.bcm.edu	37	12	101477519	101477519	+	Missense_Mutation	SNP	G	G	C			TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr12:101477519G>C	ENST00000392977.3	+	16	1669	c.1459G>C	c.(1459-1461)Gga>Cga	p.G487R	ANO4_ENST00000550015.1_Intron|ANO4_ENST00000299222.9_Intron|ANO4_ENST00000392979.3_Missense_Mutation_p.G452R			Q32M45	ANO4_HUMAN	anoctamin 4	487					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)	p.G452R(1)		NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						TCCAATTTCTGGAAAGCCAGA	0.348										HNSCC(74;0.22)																																						1	Substitution - Missense(1)	ovary(1)	12											98.0	101.0	100.0					12																	101477519		2203	4300	6503	100001650	SO:0001583	missense	121601			AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	23837	protein-coding gene	gene with protein product		610111	"""transmembrane protein 16D"""	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.1459G>C	12.37:g.101477519G>C	ENSP00000376703:p.Gly487Arg		100001650	Q8NAJ0|Q8NB39|Q8NB53	Missense_Mutation	SNP	ENST00000392977.3	37		.	.	.	.	.	.	.	.	.	.	G	23.0	4.356867	0.82243	.	.	ENSG00000151572	ENST00000392979;ENST00000392977	T;T	0.66460	-0.21;-0.21	5.78	5.78	0.91487	.	0.130338	0.50627	D	0.000112	T	0.77718	0.4172	M	0.62723	1.935	0.80722	D	1	D;D	0.61697	0.985;0.99	D;P	0.64506	0.926;0.878	T	0.69221	-0.5202	10	0.09338	T	0.73	.	20.3668	0.98882	0.0:0.0:1.0:0.0	.	487;452	Q32M45;Q32M45-2	ANO4_HUMAN;.	R	452;487	ENSP00000376705:G452R;ENSP00000376703:G487R	ENSP00000376703:G487R	G	+	1	0	ANO4	100001650	1.000000	0.71417	0.977000	0.42913	0.928000	0.56348	9.813000	0.99286	2.894000	0.99253	0.655000	0.94253	GGA		0.348	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826	
BHMT2	23743	hgsc.bcm.edu	37	5	78379052	78379052	+	Silent	SNP	C	C	T	rs151238476		TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	C	C	T	T	C	C	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr5:78379052C>T	ENST00000255192.3	+	6	702	c.636C>T	c.(634-636)ccC>ccT	p.P212P	BHMT2_ENST00000521567.1_Silent_p.P148P|DMGDH_ENST00000520388.1_Intron	NM_017614.4	NP_060084.2	Q9H2M3	BHMT2_HUMAN	betaine--homocysteine S-methyltransferase 2	212	Hcy-binding. {ECO:0000255|PROSITE- ProRule:PRU00333}.				L-methionine salvage (GO:0071267)|S-adenosylmethionine metabolic process (GO:0046500)|S-methylmethionine metabolic process (GO:0033477)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|S-methylmethionine-homocysteine S-methyltransferase activity (GO:0061627)|zinc ion binding (GO:0008270)	p.P212P(2)		endometrium(2)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|urinary_tract(1)	15		all_lung(232;0.00063)|Lung NSC(167;0.00171)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;2.09e-45)|Epithelial(54;9.3e-41)|all cancers(79;4.09e-36)	L-Methionine(DB00134)	GCTTTGGGCCCGACACCAGCT	0.483													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17532	0.0		0.0	False		,,,				2504	0.0															2	Substitution - coding silent(2)	ovary(1)|large_intestine(1)	5						C	,	16,4390	23.3+/-48.9	0,16,2187	53.0	52.0	52.0		444,636	-3.8	0.0	5	dbSNP_134	52	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	BHMT2	NM_001178005.1,NM_017614.4	,	0,16,6487	TT,TC,CC		0.0,0.3631,0.123	,	148/300,212/364	78379052	16,12990	2203	4300	6503	78414808	SO:0001819	synonymous_variant	23743				CCDS4045.1, CCDS54871.1	5q13	2010-04-28	2010-04-28		ENSG00000132840	ENSG00000132840	2.1.1.5		1048	protein-coding gene	gene with protein product		605932				11087663, 18230605	Standard	NM_017614		Approved		uc003kft.3	Q9H2M3	OTTHUMG00000108158	ENST00000255192.3:c.636C>T	5.37:g.78379052C>T			78414808	B7Z516|Q9NXX7	Silent	SNP	ENST00000255192.3	37	CCDS4045.1																																																																																				0.483	BHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226962.2	NM_017614	
C10orf113	387638	hgsc.bcm.edu	37	10	21414853	21414853	+	Missense_Mutation	SNP	C	C	T			TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr10:21414853C>T	ENST00000534331.1	-	2	417	c.367G>A	c.(367-369)Gga>Aga	p.G123R	NEBL_ENST00000417816.2_Intron|C10orf113_ENST00000377118.4_Missense_Mutation_p.G113R|C10orf113_ENST00000529198.1_3'UTR	NM_001010896.2	NP_001010896.2	Q5VZT2	CJ113_HUMAN	chromosome 10 open reading frame 113	123								p.G113R(2)		endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|pancreas(1)	7						CCTTCTGGTCCCAGAGACAGC	0.488																																																2	Substitution - Missense(2)	ovary(2)	10											90.0	90.0	90.0					10																	21414853		2203	4300	6503	21454859	SO:0001583	missense	387638				CCDS31162.1, CCDS31162.2, CCDS53496.1	10p12.31	2012-06-12			ENSG00000204683	ENSG00000204683			31447	protein-coding gene	gene with protein product							Standard	NM_001010896		Approved	bA165O3.1	uc001iqm.3	Q5VZT2	OTTHUMG00000017786	ENST00000534331.1:c.367G>A	10.37:g.21414853C>T	ENSP00000433646:p.Gly123Arg		21454859	B9EIM9|E9PRX7	Missense_Mutation	SNP	ENST00000534331.1	37	CCDS31162.2	.	.	.	.	.	.	.	.	.	.	C	13.80	2.346167	0.41599	.	.	ENSG00000204683	ENST00000534331;ENST00000377118	T;T	0.46451	0.87;0.87	4.81	2.47	0.30058	.	.	.	.	.	T	0.22085	0.0532	N	0.08118	0	0.24878	N	0.99224	B	0.32800	0.385	B	0.32583	0.148	T	0.15925	-1.0420	9	0.87932	D	0	-0.7563	6.2531	0.20859	0.0:0.7146:0.0:0.2854	.	123	Q5VZT2	CJ113_HUMAN	R	123;113	ENSP00000433646:G123R;ENSP00000366322:G113R	ENSP00000366322:G113R	G	-	1	0	C10orf113	21454859	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.270000	0.33086	0.527000	0.28560	0.460000	0.39030	GGA		0.488	C10orf113-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047108.3	NM_001010896	
CALCOCO2	10241	hgsc.bcm.edu	37	17	46937737	46937737	+	Missense_Mutation	SNP	C	C	T	rs369142528		TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr17:46937737C>T	ENST00000258947.3	+	11	1171	c.1070C>T	c.(1069-1071)cCg>cTg	p.P357L	CALCOCO2_ENST00000509507.1_Missense_Mutation_p.P378L|CALCOCO2_ENST00000416445.2_Missense_Mutation_p.P315L|CALCOCO2_ENST00000448105.2_Missense_Mutation_p.P381L|CALCOCO2_ENST00000508679.1_Missense_Mutation_p.P285L	NM_001261390.1|NM_001261391.1|NM_001261393.1|NM_001261395.1|NM_005831.4	NP_001248319.1|NP_001248320.1|NP_001248322.1|NP_001248324.1|NP_005822.1	Q13137	CACO2_HUMAN	calcium binding and coiled-coil domain 2	357					response to interferon-gamma (GO:0034341)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)	p.P357L(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	15						AATTCTTTGCCGTATCAAGTA	0.408																																																1	Substitution - Missense(1)	ovary(1)	17						C	LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	143.0	138.0	140.0		1070	-0.7	0.0	17		140	0,8600		0,0,4300	no	missense	CALCOCO2	NM_005831.3	98	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	357/447	46937737	1,13005	2203	4300	6503	44292736	SO:0001583	missense	10241			BC004130	CCDS11538.1, CCDS58558.1, CCDS58559.1, CCDS58560.1, CCDS58561.1	17q21.32	2006-02-09				ENSG00000136436			29912	protein-coding gene	gene with protein product		604587				7540613	Standard	NM_001261390		Approved	MGC17318, NDP52	uc010wlr.3	Q13137		ENST00000258947.3:c.1070C>T	17.37:g.46937737C>T	ENSP00000258947:p.Pro357Leu		44292736	B2RBT0|B4DDC4|B4DDT4|B4DP36|B4E0C0|E7ENK0|E7ETP5|E9PBE5|Q53FQ5|Q53HB5|Q6IBN9|Q9BTF7	Missense_Mutation	SNP	ENST00000258947.3	37	CCDS11538.1	.	.	.	.	.	.	.	.	.	.	C	12.86	2.065872	0.36470	2.27E-4	0.0	ENSG00000136436	ENST00000258947;ENST00000509507;ENST00000448105;ENST00000416445;ENST00000508679	T;T;T;T;T	0.16073	2.73;2.62;2.73;2.6;2.37	5.56	-0.676	0.11361	.	0.499687	0.18587	N	0.136849	T	0.12178	0.0296	L	0.50333	1.59	0.09310	N	1	B;B;B;B	0.13594	0.008;0.002;0.001;0.001	B;B;B;B	0.06405	0.002;0.0;0.001;0.001	T	0.18335	-1.0340	10	0.39692	T	0.17	-0.1299	3.9568	0.09393	0.2842:0.4493:0.0:0.2665	.	315;381;378;357	E7ETP5;B4DP36;E9PBE5;Q13137	.;.;.;CACO2_HUMAN	L	357;378;381;315;285	ENSP00000258947:P357L;ENSP00000424352:P378L;ENSP00000398523:P381L;ENSP00000406974:P315L;ENSP00000423437:P285L	ENSP00000258947:P357L	P	+	2	0	CALCOCO2	44292736	0.000000	0.05858	0.000000	0.03702	0.131000	0.20780	0.027000	0.13621	0.029000	0.15352	-0.158000	0.13435	CCG		0.408	CALCOCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360866.1	NM_005831	
CDH4	1002	hgsc.bcm.edu	37	20	60419770	60419770	+	Missense_Mutation	SNP	C	C	T			TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr20:60419770C>T	ENST00000360469.5	+	5	711	c.623C>T	c.(622-624)aCg>aTg	p.T208M	CDH4_ENST00000543233.1_Missense_Mutation_p.T134M	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	208	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T208M(1)		NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			TACAGCATCACGGGAGTGGGC	0.612																																																1	Substitution - Missense(1)	ovary(1)	20											90.0	78.0	82.0					20																	60419770		2203	4300	6503	59853165	SO:0001583	missense	1002			L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"""Cadherins / Major cadherins"""	1763	protein-coding gene	gene with protein product	"""R-Cadherin"""	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.623C>T	20.37:g.60419770C>T	ENSP00000353656:p.Thr208Met		59853165	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	37	CCDS13488.1	.	.	.	.	.	.	.	.	.	.	C	15.71	2.912930	0.52439	.	.	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.53206	0.63;0.63	3.68	3.68	0.42216	Cadherin (4);Cadherin-like (1);	0.117348	0.56097	D	0.000023	T	0.69931	0.3166	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.75593	-0.3264	9	.	.	.	.	15.7299	0.77792	0.0:1.0:0.0:0.0	.	208	P55283	CADH4_HUMAN	M	208;116;134	ENSP00000353656:T208M;ENSP00000443301:T134M	.	T	+	2	0	CDH4	59853165	1.000000	0.71417	0.998000	0.56505	0.063000	0.16089	7.491000	0.81471	1.753000	0.51906	0.313000	0.20887	ACG		0.612	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794	
CHSY3	337876	hgsc.bcm.edu	37	5	129520720	129520720	+	Missense_Mutation	SNP	G	G	A	rs145272862	byFrequency	TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr5:129520720G>A	ENST00000305031.4	+	3	2243	c.1885G>A	c.(1885-1887)Gga>Aga	p.G629R		NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	629					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)	p.G629R(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		TCCTCTCATCGGAAGGTATGA	0.353																																																1	Substitution - Missense(1)	ovary(1)	5						G	ARG/GLY	0,4406	2.1+/-5.4	0,0,2203	73.0	74.0	74.0		1885	4.1	1.0	5	dbSNP_134	74	4,8596	3.7+/-12.6	0,4,4296	yes	missense	CHSY3	NM_175856.4	125	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	probably-damaging	629/883	129520720	4,13002	2203	4300	6503	129548619	SO:0001583	missense	337876			AB086062	CCDS34223.1	5q13	2013-02-19			ENSG00000198108	ENSG00000198108	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	24293	protein-coding gene	gene with protein product		609963				12907687	Standard	XM_005271982		Approved	CSS3, CHSY-2	uc003kvd.3	Q70JA7	OTTHUMG00000163043	ENST00000305031.4:c.1885G>A	5.37:g.129520720G>A	ENSP00000302629:p.Gly629Arg		129548619	B2RP97|Q76L22|Q86Y52	Missense_Mutation	SNP	ENST00000305031.4	37	CCDS34223.1	.	.	.	.	.	.	.	.	.	.	G	18.34	3.601961	0.66445	0.0	4.65E-4	ENSG00000198108	ENST00000305031	T	0.35048	1.33	4.12	4.12	0.48240	.	0.000000	0.53938	D	0.000054	T	0.61652	0.2364	M	0.77406	2.37	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.64681	-0.6350	9	.	.	.	-5.0315	17.6798	0.88239	0.0:0.0:1.0:0.0	.	629	Q70JA7	CHSS3_HUMAN	R	629	ENSP00000302629:G629R	.	G	+	1	0	CHSY3	129548619	1.000000	0.71417	0.953000	0.39169	0.931000	0.56810	9.597000	0.98273	2.559000	0.86315	0.650000	0.86243	GGA		0.353	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1	NM_175856	
DDHD2	23259	hgsc.bcm.edu	37	8	38110293	38110293	+	Missense_Mutation	SNP	T	T	G			TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr8:38110293T>G	ENST00000397166.2	+	14	2196	c.1671T>G	c.(1669-1671)ttT>ttG	p.F557L	DDHD2_ENST00000529845.1_Missense_Mutation_p.F8L|DDHD2_ENST00000520272.2_Missense_Mutation_p.F557L|DDHD2_ENST00000517385.1_Missense_Mutation_p.F176L	NM_015214.2	NP_056029.2	O94830	DDHD2_HUMAN	DDHD domain containing 2	557	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|microtubule organizing center (GO:0005815)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.F557L(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)|urinary_tract(2)	28	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			GAGTGGAATTTGAGCCAATGC	0.448																																																1	Substitution - Missense(1)	ovary(1)	8											143.0	126.0	132.0					8																	38110293		2203	4300	6503	38229450	SO:0001583	missense	23259			AK056525	CCDS34883.1	8p11.23	2014-03-03	2004-04-05	2004-04-07				"""Sterile alpha motif (SAM) domain containing"""	29106	protein-coding gene	gene with protein product		615003	"""SAM, WWE and DDHD domain containing 1"""	SAMWD1		9872452, 11788596, 19632984, 20932832	Standard	NM_015214		Approved	KIAA0725, SPG54	uc003xlc.3	O94830		ENST00000397166.2:c.1671T>G	8.37:g.38110293T>G	ENSP00000380352:p.Phe557Leu		38229450	B3KWV2|B3KXB5|Q9H8X7	Missense_Mutation	SNP	ENST00000397166.2	37	CCDS34883.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	6.592|6.592	0.477568|0.477568	0.12521|0.12521	.|.	.|.	ENSG00000085788|ENSG00000085788	ENST00000397166;ENST00000520272;ENST00000517385;ENST00000529845|ENST00000526144	T;T|.	0.26518|.	1.73;1.73|.	5.34|5.34	4.19|4.19	0.49359|0.49359	DDHD (2);|.	0.242758|.	0.43747|.	D|.	0.000521|.	T|T	0.31702|0.31702	0.0805|0.0805	N|N	0.04880|0.04880	-0.145|-0.145	0.47123|0.47123	D|D	0.999328|0.999328	B|.	0.09022|.	0.002|.	B|.	0.14023|.	0.01|.	T|T	0.08249|0.08249	-1.0731|-1.0731	10|5	0.02654|.	T|.	1|.	-23.7336|-23.7336	9.2995|9.2995	0.37835|0.37835	0.0:0.1515:0.0:0.8485|0.0:0.1515:0.0:0.8485	.|.	557|.	O94830|.	DDHD2_HUMAN|.	L|W	557;557;176;8|59	ENSP00000380352:F557L;ENSP00000429932:F557L|.	ENSP00000380352:F557L|.	F|L	+|+	3|2	2|0	DDHD2|DDHD2	38229450|38229450	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.962000|0.962000	0.63368|0.63368	1.132000|1.132000	0.31418|0.31418	0.978000|0.978000	0.38470|0.38470	0.260000|0.260000	0.18958|0.18958	TTT|TTG		0.448	DDHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377251.2	XM_291291	
FLRT2	23768	hgsc.bcm.edu	37	14	86089196	86089196	+	Silent	SNP	C	C	T	rs142242956		TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr14:86089196C>T	ENST00000330753.4	+	2	2105	c.1338C>T	c.(1336-1338)acC>acT	p.T446T	FLRT2_ENST00000554746.1_Silent_p.T446T	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	446	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)	p.T446T(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		CTCTCTTCACCGTGATGGCAT	0.498																																																1	Substitution - coding silent(1)	ovary(1)	14						C		0,4406		0,0,2203	80.0	74.0	76.0		1338	-8.0	0.7	14	dbSNP_134	76	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FLRT2	NM_013231.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		446/661	86089196	1,13005	2203	4300	6503	85158949	SO:0001819	synonymous_variant	23768			AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"""Fibronectin type III domain containing"""	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1338C>T	14.37:g.86089196C>T			85158949	A0AV84|B7ZLP3	Silent	SNP	ENST00000330753.4	37	CCDS9877.1																																																																																				0.498	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1		
GJC3	349149	hgsc.bcm.edu	37	7	99526508	99526508	+	Missense_Mutation	SNP	C	C	T	rs191464858		TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr7:99526508C>T	ENST00000312891.2	-	1	735	c.736G>A	c.(736-738)Gat>Aat	p.D246N	RP4-604G5.1_ENST00000456499.1_RNA	NM_181538.2	NP_853516.1	Q8NFK1	CXG3_HUMAN	gap junction protein, gamma 3, 30.2kDa	246					cell communication (GO:0007154)|myelination (GO:0042552)|sensory perception of sound (GO:0007605)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)		p.D246N(2)		breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)	9	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					GGGAGGCTATCGGTTGCTTTC	0.478													C|||	1	0.000199681	0.0	0.0	5008	,	,		19703	0.001		0.0	False		,,,				2504	0.0															2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	7											133.0	130.0	131.0					7																	99526508		2203	4300	6503	99364444	SO:0001583	missense	349149			AF503615	CCDS34697.1	7q22.1	2008-09-04	2007-11-06	2007-11-06	ENSG00000176402	ENSG00000176402		"""Ion channels / Gap junction proteins (connexins)"""	17495	protein-coding gene	gene with protein product	"""connexin 30.2"""	611925	"""gap junction protein, epsilon 1, 29kDa"""	GJE1			Standard	NM_181538		Approved	CX30.2	uc011kjd.2	Q8NFK1	OTTHUMG00000156649	ENST00000312891.2:c.736G>A	7.37:g.99526508C>T	ENSP00000325775:p.Asp246Asn		99364444	A4D296|Q86XI9	Missense_Mutation	SNP	ENST00000312891.2	37	CCDS34697.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	4.624	0.116041	0.08831	.	.	ENSG00000176402	ENST00000312891	D	0.97941	-4.62	3.75	0.763	0.18459	.	2.765090	0.01548	N	0.019552	D	0.92205	0.7528	N	0.08118	0	0.09310	N	1	B	0.15473	0.013	B	0.04013	0.001	D	0.87471	0.2414	10	0.17369	T	0.5	.	5.4255	0.16423	0.0:0.5913:0.0:0.4087	.	246	Q8NFK1	CXG3_HUMAN	N	246	ENSP00000325775:D246N	ENSP00000325775:D246N	D	-	1	0	GJC3	99364444	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.166000	0.09954	0.143000	0.18926	0.655000	0.94253	GAT		0.478	GJC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345052.1	NM_181538	
LRRC15	131578	hgsc.bcm.edu	37	3	194080112	194080112	+	Missense_Mutation	SNP	G	G	C			TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr3:194080112G>C	ENST00000347624.3	-	2	1746	c.1661C>G	c.(1660-1662)tCc>tGc	p.S554C	LRRC15_ENST00000439944.2_Missense_Mutation_p.S560C|LRRC15_ENST00000428839.1_Missense_Mutation_p.S560C	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	554					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)	p.S554C(1)		biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		GGCAGCCAGGGAGCAGGCCAG	0.597																																																1	Substitution - Missense(1)	ovary(1)	3											62.0	62.0	62.0					3																	194080112		2203	4300	6503	195561407	SO:0001583	missense	131578			AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.1661C>G	3.37:g.194080112G>C	ENSP00000306276:p.Ser554Cys		195561407	Q495Q6|Q7RTN7	Missense_Mutation	SNP	ENST00000347624.3	37	CCDS3306.1	.	.	.	.	.	.	.	.	.	.	G	17.42	3.385289	0.61956	.	.	ENSG00000172061	ENST00000347624;ENST00000439944;ENST00000428839	T;T;T	0.57273	0.41;0.44;0.44	5.48	5.48	0.80851	.	0.511250	0.18877	N	0.128694	T	0.60521	0.2275	N	0.24115	0.695	0.37541	D	0.918315	D;D	0.89917	0.999;1.0	D;D	0.69479	0.921;0.964	T	0.64097	-0.6487	10	0.48119	T	0.1	.	17.9172	0.88955	0.0:0.0:1.0:0.0	.	554;560	Q8TF66;Q8TF66-2	LRC15_HUMAN;.	C	554;560;560	ENSP00000306276:S554C;ENSP00000389128:S560C;ENSP00000413707:S560C	ENSP00000306276:S554C	S	-	2	0	LRRC15	195561407	1.000000	0.71417	0.988000	0.46212	0.936000	0.57629	6.013000	0.70776	2.758000	0.94735	0.563000	0.77884	TCC		0.597	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2		
NR3C1	2908	hgsc.bcm.edu	37	5	142678313	142678313	+	Missense_Mutation	SNP	C	C	G			TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr5:142678313C>G	ENST00000343796.2	-	6	2805	c.1812G>C	c.(1810-1812)atG>atC	p.M604I	NR3C1_ENST00000424646.2_Missense_Mutation_p.M578I|NR3C1_ENST00000503201.1_Missense_Mutation_p.M604I|NR3C1_ENST00000394464.2_Missense_Mutation_p.M604I|NR3C1_ENST00000416954.2_Missense_Mutation_p.M207I|NR3C1_ENST00000394466.2_Missense_Mutation_p.M605I|NR3C1_ENST00000415690.2_Missense_Mutation_p.M604I|NR3C1_ENST00000231509.3_Missense_Mutation_p.M605I|NR3C1_ENST00000504572.1_Missense_Mutation_p.M605I|NR3C1_ENST00000504336.1_5'Flank	NM_001018074.1|NM_001018075.1|NM_001018077.1	NP_001018084.1|NP_001018085.1|NP_001018087.1	P04150	GCR_HUMAN	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	604	Interaction with CLOCK.|Interaction with CRY1.|Steroid-binding.				adrenal gland development (GO:0030325)|chromatin modification (GO:0016568)|gene expression (GO:0010467)|glucocorticoid metabolic process (GO:0008211)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of glucocorticoid mediated signaling pathway (GO:1900170)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucocorticoid biosynthetic process (GO:0031946)|regulation of gluconeogenesis (GO:0006111)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	glucocorticoid receptor activity (GO:0004883)|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)|zinc ion binding (GO:0008270)	p.M605I(1)		breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Budesonide(DB01222)|Ciclesonide(DB01410)|Clobetasol propionate(DB01013)|Clocortolone(DB00838)|Cortisone acetate(DB01380)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Difluprednate(DB06781)|Fludrocortisone(DB00687)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Fluoxymesterone(DB01185)|Flurandrenolide(DB00846)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol(DB00873)|Medrysone(DB00253)|Megestrol acetate(DB00351)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Paramethasone(DB01384)|Prednicarbate(DB01130)|Prednisolone(DB00860)|Prednisone(DB00635)|Rimexolone(DB00896)|Spironolactone(DB00421)|Triamcinolone(DB00620)	GAGCAAATGCCATAAGAAACA	0.408																																																1	Substitution - Missense(1)	ovary(1)	5											128.0	116.0	120.0					5																	142678313		2203	4300	6503	142658506	SO:0001583	missense	2908			X03225	CCDS4278.1, CCDS34258.1, CCDS47298.1	5q31-q32	2013-01-16	2002-08-27		ENSG00000113580	ENSG00000113580		"""Nuclear hormone receptors"""	7978	protein-coding gene	gene with protein product		138040	"""nuclear receptor subfamily 3, group C, member 1"""	GRL		2867473	Standard	NM_001204258		Approved	GR	uc003lnb.3	P04150	OTTHUMG00000129677	ENST00000343796.2:c.1812G>C	5.37:g.142678313C>G	ENSP00000343205:p.Met604Ile		142658506	A0ZXF9|B0LPG8|D3DQF4|P04151|Q53EP5|Q6N0A4	Missense_Mutation	SNP	ENST00000343796.2	37	CCDS4278.1	.	.	.	.	.	.	.	.	.	.	C	33	5.278153	0.95459	.	.	ENSG00000113580	ENST00000394464;ENST00000343796;ENST00000415690;ENST00000424646;ENST00000504572;ENST00000394466;ENST00000231509;ENST00000416954;ENST00000503201	D;D;T;D;D;D;D;D;D	0.95447	-3.71;-3.71;1.37;-3.71;-3.71;-3.71;-3.71;-3.71;-3.71	5.88	5.88	0.94601	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.97854	0.9295	M	0.82056	2.57	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.995	D;D;D	0.76071	0.98;0.945;0.987	D	0.98003	1.0361	10	0.72032	D	0.01	.	20.2314	0.98350	0.0:1.0:0.0:0.0	.	604;604;605	E5KQF5;P04150;E5KQF6	.;GCR_HUMAN;.	I	604;604;604;578;605;605;605;207;604	ENSP00000377977:M604I;ENSP00000343205:M604I;ENSP00000387672:M604I;ENSP00000405282:M578I;ENSP00000422518:M605I;ENSP00000377979:M605I;ENSP00000231509:M605I;ENSP00000404218:M207I;ENSP00000427672:M604I	ENSP00000231509:M605I	M	-	3	0	NR3C1	142658506	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.818000	0.86416	2.789000	0.95967	0.591000	0.81541	ATG		0.408	NR3C1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370829.1		
SEMA3E	9723	hgsc.bcm.edu	37	7	83037703	83037703	+	Silent	SNP	G	G	A			TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr7:83037703G>A	ENST00000307792.3	-	6	1118	c.651C>T	c.(649-651)gaC>gaT	p.D217D	SEMA3E_ENST00000427262.1_Silent_p.D157D	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	217	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.D217D(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				GACGCTCATCGTCATGCTCAG	0.448																																																1	Substitution - coding silent(1)	ovary(1)	7											72.0	68.0	69.0					7																	83037703		2203	4300	6503	82875639	SO:0001819	synonymous_variant	9723			AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10727	protein-coding gene	gene with protein product	"""M-sema H"""	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.651C>T	7.37:g.83037703G>A			82875639	B4E1P1|Q75M94|Q75M97	Silent	SNP	ENST00000307792.3	37	CCDS34674.1																																																																																				0.448	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431	
NRF1	4899	hgsc.bcm.edu	37	7	129350263	129350263	+	Missense_Mutation	SNP	A	A	T			TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr7:129350263A>T	ENST00000393232.1	+	7	932	c.815A>T	c.(814-816)cAg>cTg	p.Q272L	NRF1_ENST00000223190.4_Missense_Mutation_p.Q272L|NRF1_ENST00000393230.2_Missense_Mutation_p.Q272L|NRF1_ENST00000539636.1_Missense_Mutation_p.Q111L|NRF1_ENST00000393231.3_Missense_Mutation_p.Q272L|NRF1_ENST00000353868.4_Intron|NRF1_ENST00000311967.2_Missense_Mutation_p.Q272L	NM_005011.3	NP_005002.3	Q16656	NRF1_HUMAN	nuclear respiratory factor 1	272					cellular lipid metabolic process (GO:0044255)|generation of precursor metabolites and energy (GO:0006091)|mitochondrion organization (GO:0007005)|organ regeneration (GO:0031100)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	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)	p.Q272L(1)		breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	24						TGTTATAAACAGCATGGGCGG	0.443																																																1	Substitution - Missense(1)	ovary(1)	7											152.0	137.0	143.0					7																	129350263		2203	4300	6503	129137499	SO:0001583	missense	4899			L22454	CCDS5813.2	7q32	2008-07-18			ENSG00000106459	ENSG00000106459			7996	protein-coding gene	gene with protein product	"""alpha palindromic-binding protein"""	600879				2584221	Standard	NM_005011		Approved	EWG, ALPHA-PAL	uc003voz.3	Q16656	OTTHUMG00000143736	ENST00000393232.1:c.815A>T	7.37:g.129350263A>T	ENSP00000376924:p.Gln272Leu		129137499	A8K4C6|B4DDV6|Q15305|Q96AN2	Missense_Mutation	SNP	ENST00000393232.1	37	CCDS5813.2	.	.	.	.	.	.	.	.	.	.	A	18.30	3.592899	0.66219	.	.	ENSG00000106459	ENST00000393232;ENST00000539636;ENST00000223190;ENST00000311967;ENST00000393230;ENST00000393231	.	.	.	5.45	5.45	0.79879	Nuclear respiratory factor 1, NLS/DNA-binding, dimerisation domain (1);	0.102760	0.64402	D	0.000002	T	0.40423	0.1116	N	0.08118	0	0.80722	D	1	B;B	0.18610	0.017;0.029	B;B	0.24006	0.05;0.03	T	0.30937	-0.9961	9	0.46703	T	0.11	-12.0975	14.8657	0.70412	1.0:0.0:0.0:0.0	.	272;272	Q96AN2;Q16656	.;NRF1_HUMAN	L	272;111;272;272;272;272	.	ENSP00000223190:Q272L	Q	+	2	0	NRF1	129137499	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.084000	0.94076	2.288000	0.76882	0.528000	0.53228	CAG		0.443	NRF1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289813.1	NM_001040110	
TARSL2	123283	hgsc.bcm.edu	37	15	102226159	102226159	+	Missense_Mutation	SNP	A	A	C			TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr15:102226159A>C	ENST00000335968.3	-	11	1643	c.1427T>G	c.(1426-1428)tTt>tGt	p.F476C	snoU13_ENST00000458877.1_RNA	NM_152334.2	NP_689547.2	A2RTX5	SYTC2_HUMAN	threonyl-tRNA synthetase-like 2	476					threonyl-tRNA aminoacylation (GO:0006435)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)	p.F476C(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(14)|ovary(2)|skin(1)|urinary_tract(1)	29	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CTCAAAGGTAAACATGTTCTC	0.468																																																1	Substitution - Missense(1)	ovary(1)	15											158.0	145.0	149.0					15																	102226159		2203	4300	6503	100043682	SO:0001583	missense	123283			AL833188	CCDS10394.1	15q26.3	2008-02-05			ENSG00000185418	ENSG00000185418			24728	protein-coding gene	gene with protein product							Standard	NM_152334		Approved	FLJ25005	uc002bxm.3	A2RTX5	OTTHUMG00000149869	ENST00000335968.3:c.1427T>G	15.37:g.102226159A>C	ENSP00000338093:p.Phe476Cys		100043682	B2RMP7|Q6B0A1|Q6IS76|Q96LW3|Q96MP4	Missense_Mutation	SNP	ENST00000335968.3	37	CCDS10394.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.373173	0.82573	.	.	ENSG00000185418	ENST00000335968;ENST00000333018;ENST00000539112	T;T	0.69685	-0.42;-0.42	5.82	5.82	0.92795	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain (1);	0.000000	0.85682	D	0.000000	D	0.89729	0.6799	H	0.99425	4.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.93726	0.7037	10	0.87932	D	0	-20.4604	14.1334	0.65270	1.0:0.0:0.0:0.0	.	476;381	A2RTX5;A2RTX5-2	SYTC2_HUMAN;.	C	476;381;476	ENSP00000338093:F476C;ENSP00000439899:F476C	ENSP00000329291:F381C	F	-	2	0	TARSL2	100043682	1.000000	0.71417	0.987000	0.45799	0.959000	0.62525	9.103000	0.94232	2.234000	0.73211	0.533000	0.62120	TTT		0.468	TARSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313619.3	NM_152334	
TTR	7276	hgsc.bcm.edu	37	18	29175118	29175118	+	Missense_Mutation	SNP	C	C	T			TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_III	WXS	454_PCR_WGA			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr18:29175118C>T	ENST00000237014.3	+	3	413	c.236C>T	c.(235-237)aCa>aTa	p.T79I		NM_000371.3	NP_000362.1	P02766	TTHY_HUMAN	transthyretin	79			T -> K (in AMYL-TTR; amyloid cardiomyopathy). {ECO:0000269|PubMed:7850982}.		extracellular matrix organization (GO:0030198)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	hormone binding (GO:0042562)|identical protein binding (GO:0042802)	p.T79I(1)		cervix(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	13			OV - Ovarian serous cystadenocarcinoma(10;0.00523)		Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diflunisal(DB00861)|Dimethyl sulfoxide(DB01093)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	CATGGGCTCACAACTGAGGAG	0.443																																																1	Substitution - Missense(1)	ovary(1)	18	GRCh37	CM951252	TTR	M							89.0	76.0	80.0					18																	29175118		2203	4300	6503	27429116	SO:0001583	missense	7276			M10605	CCDS11899.1	18q12.1	2014-09-17	2008-07-31		ENSG00000118271	ENSG00000118271			12405	protein-coding gene	gene with protein product		176300	"""prealbumin, amyloidosis type I"", ""carpal tunnel syndrome 1"""	PALB, CTS1		8309582	Standard	NM_000371		Approved	HsT2651, CTS	uc002kwx.4	P02766	OTTHUMG00000131984	ENST00000237014.3:c.236C>T	18.37:g.29175118C>T	ENSP00000237014:p.Thr79Ile		27429116	Q549C7|Q6IB96|Q9UBZ6|Q9UCM9	Missense_Mutation	SNP	ENST00000237014.3	37	CCDS11899.1	.	.	.	.	.	.	.	.	.	.	C	9.607	1.130128	0.21041	.	.	ENSG00000118271	ENST00000237014;ENST00000432547;ENST00000541025	D	0.95205	-3.64	5.54	5.54	0.83059	Transthyretin/hydroxyisourate hydrolase, superfamily (4);	0.155567	0.56097	D	0.000026	D	0.92948	0.7756	N	0.20685	0.6	0.45378	D	0.998367	P	0.45396	0.857	P	0.61275	0.886	D	0.89039	0.3447	10	0.10902	T	0.67	-8.395	12.7675	0.57401	0.0:0.9242:0.0:0.0758	.	79	P02766	TTHY_HUMAN	I	79	ENSP00000237014:T79I	ENSP00000237014:T79I	T	+	2	0	TTR	27429116	0.998000	0.40836	0.999000	0.59377	0.406000	0.30931	4.117000	0.57877	2.764000	0.94973	0.655000	0.94253	ACA		0.443	TTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254948.1	NM_000371	
NRXN3	9369	hgsc.bcm.edu	37	14	79432697	79432697	+	Missense_Mutation	SNP	C	C	A			TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr14:79432697C>A	ENST00000554719.1	+	9	2097	c.1606C>A	c.(1606-1608)Ctc>Atc	p.L536I	NRXN3_ENST00000335750.5_Missense_Mutation_p.L536I	NM_004796.4	NP_004787.2	Q9HDB5	NRX3B_HUMAN	neurexin 3	127					adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)	p.L536I(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		TGGCTTCATTCTCTTCAATAG	0.473																																																1	Substitution - Missense(1)	ovary(1)	14											174.0	147.0	156.0					14																	79432697		2203	4300	6503	78502450	SO:0001583	missense	9369			AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"""chromosome 14 open reading frame 60"""	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000554719.1:c.1606C>A	14.37:g.79432697C>A	ENSP00000451648:p.Leu536Ile		78502450	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000554719.1	37	CCDS9870.1	.	.	.	.	.	.	.	.	.	.	C	16.99	3.273958	0.59649	.	.	ENSG00000021645	ENST00000330071;ENST00000332068;ENST00000554719;ENST00000335750	D;D	0.86956	-2.19;-2.19	5.73	5.73	0.89815	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.129992	0.52532	D	0.000070	D	0.83385	0.5243	.	.	.	0.48632	D	0.999686	B;B	0.13145	0.006;0.007	B;B	0.26094	0.066;0.049	T	0.76080	-0.3090	8	.	.	.	.	20.2786	0.98501	0.0:1.0:0.0:0.0	.	909;536	Q9Y4C0;Q9Y4C0-3	NRX3A_HUMAN;.	I	909;898;536;536	ENSP00000451648:L536I;ENSP00000338349:L536I	.	L	+	1	0	NRXN3	78502450	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.109000	0.50345	2.868000	0.98415	0.557000	0.71058	CTC		0.473	NRXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413787.1	NM_001105250	
TP53	7157	hgsc.bcm.edu	37	17	7579494	7579494	+	Nonsense_Mutation	SNP	T	T	A			TCGA-04-1517-01A-01W-0615-10	TCGA-04-1517-11A-01W-0615-10	T	T	A	A	T	T	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	44dbc3b1-d994-451b-9453-f2511ecafc59	9dbf43ee-1701-4045-892a-4ccc4c202d69	g.chr17:7579494T>A	ENST00000269305.4	-	4	382	c.193A>T	c.(193-195)Aga>Tga	p.R65*	TP53_ENST00000420246.2_Nonsense_Mutation_p.R65*|TP53_ENST00000445888.2_Nonsense_Mutation_p.R65*|TP53_ENST00000413465.2_Nonsense_Mutation_p.R65*|TP53_ENST00000359597.4_Nonsense_Mutation_p.R65*|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Nonsense_Mutation_p.R65*	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	65	Interaction with HRMT1L2.		R -> T (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R65*(11)|p.0?(8)|p.R65fs*84(3)|p.G59fs*23(3)|p.D48fs*55(1)|p.R65_P71delRMPEAAP(1)|p.P13fs*18(1)|p.R65fs*38(1)|p.D57_A76del20(1)|p.S33fs*23(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)	TCTGGCATTCTGGGAGCTTCA	0.617		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"""	31	Substitution - Nonsense(11)|Whole gene deletion(8)|Deletion - Frameshift(7)|Insertion - Frameshift(3)|Deletion - In frame(2)	lung(7)|urinary_tract(5)|bone(4)|upper_aerodigestive_tract(3)|central_nervous_system(3)|pancreas(3)|breast(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|prostate(1)	17											125.0	130.0	128.0					17																	7579494		2203	4300	6503	7520219	SO:0001587	stop_gained	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.193A>T	17.37:g.7579494T>A	ENSP00000269305:p.Arg65*		7520219	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	16.14	3.039059	0.55003	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	.	.	.	3.84	-2.61	0.06171	.	1.821500	0.02314	N	0.072344	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	5.1499	6.7205	0.23328	0.0:0.3628:0.4224:0.2149	.	.	.	.	X	65	.	ENSP00000269305:R65X	R	-	1	2	TP53	7520219	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.045000	0.14013	-0.480000	0.06803	0.459000	0.35465	AGA		0.617	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
