#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_BAM_File	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_Mutation_Status	i_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_deletion_substructures	i_domain	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_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
PLOD1	5351	genome.wustl.edu	37	1	12024810	12024810	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2860-03B-01W-0728-08	TCGA-AB-2860-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3b8b7cea-9e19-426f-9e58-d40de477ce12	a9f714a7-2581-4ce0-b077-3db990730b27	g.chr1:12024810G>A	ENST00000196061.4	+	13	1465	c.1438G>A	c.(1438-1440)Gac>Aac	p.D480N	PLOD1_ENST00000376369.3_Missense_Mutation_p.D527N	NM_000302.3	NP_000293.2	Q02809	PLOD1_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	480					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|extracellular matrix organization (GO:0030198)|hydroxylysine biosynthetic process (GO:0046947)|oxidation-reduction process (GO:0055114)|response to hypoxia (GO:0001666)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	29	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000809)|KIRC - Kidney renal clear cell carcinoma(229;0.00267)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)	Succinic acid(DB00139)|Vitamin C(DB00126)	GCTGGACCCCGACATGGCCTT	0.612																																						dbGAP											0			1											81.0	82.0	82.0					1																	12024810		2203	4300	6503	11947397	SO:0001583	missense	0			BC016657	CCDS142.1	1p36.22	2011-08-25	2011-08-24	2004-12-14	ENSG00000083444	ENSG00000083444	1.14.11.4		9081	protein-coding gene	gene with protein product	"""lysyl hydroxlase 1"""	153454	"""procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase, Ehlers-Danlos syndrome type VI)"""	LLH, PLOD		1577494	Standard	NM_000302		Approved	LH1	uc001atm.3	Q02809	OTTHUMG00000002393	ENST00000196061.4:c.1438G>A	1.37:g.12024810G>A	ENSP00000196061:p.Asp480Asn	Somatic	26	0.00	0		40	43.66	31	WXS	Illumina HiSeq	Phase_IV	11947397	8	38.46	5	B4DR87|Q96AV9|Q9H132	Missense_Mutation	SNP	PatternScan_LYS_HYDROXYLASE,HMMPfam_2OG-FeII_Oxy,HMMSmart_P4Hc	p.D480N	ENST00000196061.4	37	c.1438	CCDS142.1	1	.	.	.	.	.	.	.	.	.	.	G	32	5.109114	0.94292	.	.	ENSG00000083444	ENST00000376369;ENST00000196061	D;D	0.95690	-3.78;-3.78	5.02	5.02	0.67125	.	0.100479	0.64402	D	0.000003	D	0.98027	0.9350	M	0.88842	2.985	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.982;0.997	D	0.99153	1.0859	10	0.87932	D	0	.	17.3226	0.87240	0.0:0.0:1.0:0.0	.	527;480	B4DR87;Q02809	.;PLOD1_HUMAN	N	527;480	ENSP00000365548:D527N;ENSP00000196061:D480N	ENSP00000196061:D480N	D	+	1	0	PLOD1	11947397	1.000000	0.71417	0.937000	0.37676	0.802000	0.45316	9.869000	0.99810	2.331000	0.79229	0.655000	0.94253	GAC	-	NULL		0.612	PLOD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	PLOD1	protein_coding	OTTHUMT00000006865.1	G	NM_000302		11947397	+1	no_errors	NM_000302.2	genbank	human	reviewed	54_36p	missense	SNP	0.997	A
MNDA	4332	genome.wustl.edu	37	1	158815449	158815449	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2860-03B-01W-0728-08	TCGA-AB-2860-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3b8b7cea-9e19-426f-9e58-d40de477ce12	a9f714a7-2581-4ce0-b077-3db990730b27	g.chr1:158815449G>A	ENST00000368141.4	+	5	904	c.643G>A	c.(643-645)Gtg>Atg	p.V215M		NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	215	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				B cell receptor signaling pathway (GO:0050853)|cellular defense response (GO:0006968)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of B cell proliferation (GO:0030889)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(26)|ovary(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	all_hematologic(112;0.0378)					AGTGACAGTGGTGGTACTGAA	0.458																																						dbGAP											0			1											84.0	79.0	81.0					1																	158815449		2203	4300	6503	157082073	SO:0001583	missense	0			BC032319	CCDS1177.1	1q22	2008-02-05			ENSG00000163563	ENSG00000163563			7183	protein-coding gene	gene with protein product		159553				1644857, 7512843	Standard	NM_002432		Approved	PYHIN3	uc001fsz.1	P41218	OTTHUMG00000022776	ENST00000368141.4:c.643G>A	1.37:g.158815449G>A	ENSP00000357123:p.Val215Met	Somatic	76	0.00	0		124	51.18	130	WXS	Illumina HiSeq	Phase_IV	157082073	73	29.13	30		Missense_Mutation	SNP	HMMPfam_PAAD_DAPIN,HMMPfam_HIN	p.V215M	ENST00000368141.4	37	c.643	CCDS1177.1	1	.	.	.	.	.	.	.	.	.	.	G	0.328	-0.958108	0.02267	.	.	ENSG00000163563	ENST00000368141	T	0.12774	2.65	4.15	-3.13	0.05266	HIN-200/IF120x (2);Nucleic acid-binding, OB-fold (1);	0.742224	0.11651	N	0.542801	T	0.00412	0.0013	N	0.00157	-1.96	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.38499	-0.9658	10	0.02654	T	1	-3.1394	0.9426	0.01358	0.3565:0.3093:0.1843:0.1499	.	215	P41218	MNDA_HUMAN	M	215	ENSP00000357123:V215M	ENSP00000357123:V215M	V	+	1	0	MNDA	157082073	0.211000	0.23529	0.127000	0.21898	0.283000	0.27025	-0.788000	0.04614	-0.752000	0.04728	-0.294000	0.09567	GTG	-	HMMPfam_HIN		0.458	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MNDA	protein_coding	OTTHUMT00000059069.1	G	NM_002432		157082073	+1	no_errors	NM_002432.1	genbank	human	reviewed	54_36p	missense	SNP	0.003	A
LINC01122	400955	genome.wustl.edu	37	2	58688100	58688100	+	lincRNA	SNP	C	C	T			TCGA-AB-2860-03B-01W-0728-08	TCGA-AB-2860-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3b8b7cea-9e19-426f-9e58-d40de477ce12	a9f714a7-2581-4ce0-b077-3db990730b27	g.chr2:58688100C>T	ENST00000452840.1	+	0	127																											ctcccgttcccgatatctctc	0.542																																						dbGAP											0			2																																								58541604			0																															2.37:g.58688100C>T		Somatic	75	2.60	2		18	0.00	0	WXS	Illumina HiSeq	Phase_IV	58541604	162	23.36	50		RNA	SNP	-	NULL	ENST00000452840.1	37	NULL		2																																																																																			-	-		0.542	AC007092.1-001	KNOWN	basic	lincRNA	LOC644456	lincRNA	OTTHUMT00000327022.1	C			58541604	-1	pseudogene	XR_039438.1	genbank	human	model	54_36p	rna	SNP	0.005	T
VN2R1P	344760	genome.wustl.edu	37	3	155754637	155754637	+	IGR	SNP	G	G	A			TCGA-AB-2860-03B-01W-0728-08	TCGA-AB-2860-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3b8b7cea-9e19-426f-9e58-d40de477ce12	a9f714a7-2581-4ce0-b077-3db990730b27	g.chr3:155754637G>A								GMPS (92822 upstream) : KCNAB1 (83699 downstream)																							GTGATACACAGGCACACTCCC	0.493																																						dbGAP											0			3																																								157237331	SO:0001628	intergenic_variant	0																															3.37:g.155754637G>A		Somatic	27	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	157237331	77	27.36	29		Missense_Mutation	SNP	HMMPfam_ANF_receptor,HMMPfam_NCD3G,HMMPfam_7tm_3,PatternScan_G_PROTEIN_RECEP_F3_1,PatternScan_G_PROTEIN_RECEP_F3_2,PatternScan_G_PROTEIN_RECEP_F3_3,superfamily_SSF53822	p.R477K		37	c.1430		3																																																																																			-	HMMPfam_7tm_3	0	0.493					CASRL1			G			157237331	+1	no_errors	ENST00000312652	ensembl	human	known	54_36p	missense	SNP	0.173	A
HS3ST1	9957	genome.wustl.edu	37	4	11401018	11401018	+	Silent	SNP	C	C	T			TCGA-AB-2860-03B-01W-0728-08	TCGA-AB-2860-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3b8b7cea-9e19-426f-9e58-d40de477ce12	a9f714a7-2581-4ce0-b077-3db990730b27	g.chr4:11401018C>T	ENST00000002596.5	-	2	1786	c.612G>A	c.(610-612)ctG>ctA	p.L204L		NM_005114.2	NP_005105.1	O14792	HS3S1_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	204					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|sulfotransferase activity (GO:0008146)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(3)	15						GGAAAAAGCGCAGCCAGTTCT	0.592																																						dbGAP											0			4											52.0	48.0	50.0					4																	11401018		2203	4300	6503	11010116	SO:0001819	synonymous_variant	0			AF019386	CCDS3408.1	4p16	2008-02-05			ENSG00000002587	ENSG00000002587	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5194	protein-coding gene	gene with protein product		603244				9988767	Standard	NM_005114		Approved	3OST1	uc003gmq.3	O14792	OTTHUMG00000090547	ENST00000002596.5:c.612G>A	4.37:g.11401018C>T		Somatic	23	0.00	0		13	38.10	8	WXS	Illumina HiSeq	Phase_IV	11010116	31	38.00	19	B3KUA6|Q6PEY8	Silent	SNP	HMMPfam_Sulfotransfer_1,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.L204	ENST00000002596.5	37	c.612	CCDS3408.1	4																																																																																			-	HMMPfam_Sulfotransfer_1,superfamily_P-loop containing nucleoside triphosphate hydrolases		0.592	HS3ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HS3ST1	protein_coding	OTTHUMT00000207073.3	C	NM_005114		11010116	-1	no_errors	NM_005114.2	genbank	human	reviewed	54_36p	silent	SNP	0.999	T
FRAS1	80144	genome.wustl.edu	37	4	79188550	79188550	+	Silent	SNP	C	C	T			TCGA-AB-2860-03B-01W-0728-08	TCGA-AB-2860-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3b8b7cea-9e19-426f-9e58-d40de477ce12	a9f714a7-2581-4ce0-b077-3db990730b27	g.chr4:79188550C>T	ENST00000325942.6	+	9	1385	c.945C>T	c.(943-945)tgC>tgT	p.C315C	FRAS1_ENST00000264899.6_Silent_p.C315C|FRAS1_ENST00000264895.6_Silent_p.C315C	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	315	VWFC 5. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						AAGTGACCTGCCAGACTGGAG	0.562																																						dbGAP											0			4											74.0	79.0	78.0					4																	79188550		2123	4219	6342	79407574	SO:0001819	synonymous_variant	0			AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.945C>T	4.37:g.79188550C>T		Somatic	49	2.00	1		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	79407574	141	23.78	44	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	HMMPfam_VWC,HMMSmart_SM00214,PatternScan_VWFC_1,HMMPfam_Calx-beta,HMMSmart_SM00237,HMMSmart_SM00181,HMMSmart_SM00261,HMMSmart_SM00215,superfamily_Growth factor receptor domain	p.C315	ENST00000325942.6	37	c.945	CCDS54772.1	4	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.530|8.530	0.870768|0.870768	0.17322|0.17322	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000502446|ENST00000508900	.|.	.|.	.|.	5.19|5.19	3.43|3.43	0.39272|0.39272	.|.	.|.	.|.	.|.	.|.	T|T	0.62295|0.62295	0.2416|0.2416	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.60855|0.60855	-0.7180|-0.7180	4|4	.|.	.|.	.|.	.|.	11.6734|11.6734	0.51415|0.51415	0.0:0.7949:0.0:0.2051|0.0:0.7949:0.0:0.2051	.|.	.|.	.|.	.|.	V|S	244|158	.|.	.|.	A|P	+|+	2|1	0|0	FRAS1|FRAS1	79407574|79407574	0.949000|0.949000	0.32298|0.32298	1.000000|1.000000	0.80357|0.80357	0.791000|0.791000	0.44710|0.44710	0.515000|0.515000	0.22801|0.22801	1.312000|1.312000	0.45043|0.45043	0.655000|0.655000	0.94253|0.94253	GCC|CCA	-	HMMPfam_VWC,HMMSmart_SM00214,PatternScan_VWFC_1		0.562	FRAS1-001	NOVEL	basic|CCDS	protein_coding	FRAS1	protein_coding	OTTHUMT00000362706.2	C			79407574	+1	no_errors	ENST00000380674	ensembl	human	known	54_36p	silent	SNP	1.000	T
DCHS2	54798	genome.wustl.edu	37	4	155253840	155253840	+	Missense_Mutation	SNP	T	T	A			TCGA-AB-2860-03B-01W-0728-08	TCGA-AB-2860-11B-01W-0729-08	T	T	T	A	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3b8b7cea-9e19-426f-9e58-d40de477ce12	a9f714a7-2581-4ce0-b077-3db990730b27	g.chr4:155253840T>A	ENST00000357232.4	-	9	2022	c.2023A>T	c.(2023-2025)Agc>Tgc	p.S675C	DCHS2_ENST00000339452.1_Missense_Mutation_p.S1174C|DCHS2_ENST00000507542.1_5'Flank	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	675	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		ACTGTAGTGCTCACATTTTGC	0.443																																						dbGAP											0			4											117.0	121.0	120.0					4																	155253840		2203	4300	6503	155473290	SO:0001583	missense	0			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.2023A>T	4.37:g.155253840T>A	ENSP00000349768:p.Ser675Cys	Somatic	29	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	155473290	50	41.18	35	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,superfamily_Cadherin-like	p.S675C	ENST00000357232.4	37	c.2023	CCDS3785.1	4	.	.	.	.	.	.	.	.	.	.	T	16.94	3.261843	0.59431	.	.	ENSG00000197410	ENST00000357232;ENST00000339452;ENST00000544161	T;T	0.63744	-0.06;-0.06	4.89	4.89	0.63831	Cadherin (3);Cadherin-like (1);	0.384518	0.24854	N	0.035069	T	0.81781	0.4895	M	0.88570	2.965	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.98	D	0.85594	0.1248	10	0.72032	D	0.01	.	14.7966	0.69881	0.0:0.0:0.0:1.0	.	1174;675	E9PC11;Q6V1P9	.;PCD23_HUMAN	C	675;1174;1174	ENSP00000349768:S675C;ENSP00000345062:S1174C	ENSP00000345062:S1174C	S	-	1	0	DCHS2	155473290	1.000000	0.71417	1.000000	0.80357	0.456000	0.32438	5.737000	0.68606	1.944000	0.56390	0.482000	0.46254	AGC	-	HMMSmart_SM00112,superfamily_Cadherin-like		0.443	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DCHS2	protein_coding	OTTHUMT00000365281.2	T	NM_001142552		155473290	-1	no_errors	NM_017639.1	genbank	human	validated	54_36p	missense	SNP	1.000	A
RPL35P4	100271006	genome.wustl.edu	37	7	27309104	27309104	+	IGR	SNP	C	C	T			TCGA-AB-2860-03B-01W-0728-08	TCGA-AB-2860-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3b8b7cea-9e19-426f-9e58-d40de477ce12	a9f714a7-2581-4ce0-b077-3db990730b27	g.chr7:27309104C>T								EVX1 (18992 upstream) : AC004009.3 (92357 downstream)																							GGTCCAGGGGCTTATACTTCT	0.502																																						dbGAP											0			7																																								27275629	SO:0001628	intergenic_variant	0																															7.37:g.27309104C>T		Somatic	38	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	27275629	48	36.84	28		RNA	SNP	-	NULL		37	NULL		7																																																																																			-	-	0	0.502					LOC392008			C			27275629	-1	no_errors	XR_017366.1	genbank	human	model	54_36p	rna	SNP	1.000	T
CLIP2	7461	genome.wustl.edu	37	7	73790978	73790978	+	Silent	SNP	C	C	T			TCGA-AB-2860-03B-01W-0728-08	TCGA-AB-2860-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3b8b7cea-9e19-426f-9e58-d40de477ce12	a9f714a7-2581-4ce0-b077-3db990730b27	g.chr7:73790978C>T	ENST00000395060.1	+	9	2247	c.2247C>T	c.(2245-2247)atC>atT	p.I749I	CLIP2_ENST00000361545.5_Silent_p.I714I|CLIP2_ENST00000223398.6_Silent_p.I749I			Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	749						cytoplasmic microtubule (GO:0005881)|microtubule associated complex (GO:0005875)|microtubule plus-end (GO:0035371)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|pancreas(1)|prostate(2)|skin(3)	30						CGCAGGCTATCGAGTTCCTCA	0.632																																						dbGAP											0			7											30.0	38.0	35.0					7																	73790978		2203	4300	6503	73428914	SO:0001819	synonymous_variant	0			AB006629	CCDS5569.1, CCDS5570.1	7q11.23	2008-06-12	2007-01-04	2007-01-04	ENSG00000106665	ENSG00000106665			2586	protein-coding gene	gene with protein product		603432	"""cytoplasmic linker 2"", ""Williams-Beuren syndrome chromosome region 3"""	WBSCR4, CYLN2, WBSCR3		8812460, 9799601	Standard	NM_003388		Approved	CLIP-115, KIAA0291, WSCR4, CLIP, WSCR3	uc003uam.3	Q9UDT6	OTTHUMG00000022980	ENST00000395060.1:c.2247C>T	7.37:g.73790978C>T		Somatic	35	0.00	0		17	43.33	13	WXS	Illumina HiSeq	Phase_IV	73428914	46	22.03	13	O14527|O43611	Silent	SNP	HMMPfam_CAP_GLY,PatternScan_CAP_GLY_1,superfamily_Cap-Gly domain	p.I749	ENST00000395060.1	37	c.2247	CCDS5569.1	7																																																																																			-	NULL		0.632	CLIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	CLIP2	protein_coding	OTTHUMT00000252556.1	C	NM_003388		73428914	+1	no_errors	NM_003388.4	genbank	human	reviewed	54_36p	silent	SNP	0.992	T
ENTPD1	953	genome.wustl.edu	37	10	97607227	97607227	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2860-03B-01W-0728-08	TCGA-AB-2860-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3b8b7cea-9e19-426f-9e58-d40de477ce12	a9f714a7-2581-4ce0-b077-3db990730b27	g.chr10:97607227G>A	ENST00000371205.4	+	7	1121	c.838G>A	c.(838-840)Gac>Aac	p.D280N	ENTPD1_ENST00000453258.2_Missense_Mutation_p.D287N|ENTPD1_ENST00000371203.5_Missense_Mutation_p.D142N|ENTPD1_ENST00000539125.1_Missense_Mutation_p.D142N|ENTPD1_ENST00000371207.3_Missense_Mutation_p.D292N|ENTPD1_ENST00000543964.1_Missense_Mutation_p.D172N|ENTPD1-AS1_ENST00000416301.1_RNA|RP11-429G19.3_ENST00000433113.1_RNA			P49961	ENTP1_HUMAN	ectonucleoside triphosphate diphosphohydrolase 1	280					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|purine ribonucleoside diphosphate catabolic process (GO:0009181)	basal lamina (GO:0005605)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|skin(1)	16		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)		AATTCTCAGGGACCCATGCTT	0.408																																						dbGAP											0			10											120.0	117.0	118.0					10																	97607227		2203	4300	6503	97597217	SO:0001583	missense	0			S73813	CCDS7444.1, CCDS53556.1, CCDS53557.1, CCDS53558.1, CCDS41554.1	10q24.1	2014-03-03			ENSG00000138185	ENSG00000138185		"""CD molecules"""	3363	protein-coding gene	gene with protein product		601752		CD39		9226376, 24482476	Standard	NM_001098175		Approved	NTPDase-1, ATPDase, SPG64	uc010qoj.2	P49961	OTTHUMG00000018818	ENST00000371205.4:c.838G>A	10.37:g.97607227G>A	ENSP00000360248:p.Asp280Asn	Somatic	36	0.00	0		20	28.57	8	WXS	Illumina HiSeq	Phase_IV	97597217	71	19.10	17	A9Z1X8|B4DWB9|B4E1X1|B7Z599|G3XAF6|Q5T561|Q5T562|Q86VV3|Q9UQQ9|Q9Y3Q9	Missense_Mutation	SNP	HMMPfam_GDA1_CD39,PatternScan_GDA1_CD39_NTPASE	p.D287N	ENST00000371205.4	37	c.859	CCDS7444.1	10	.	.	.	.	.	.	.	.	.	.	G	18.65	3.669847	0.67814	.	.	ENSG00000138185	ENST00000453258;ENST00000371207;ENST00000543964;ENST00000539125;ENST00000371203;ENST00000371205	T;T;T;T;T;T	0.14766	2.48;2.48;2.48;2.48;2.48;2.48	5.77	5.77	0.91146	.	0.178610	0.64402	D	0.000014	T	0.19927	0.0479	N	0.21097	0.63	0.80722	D	1	P;B;P	0.52061	0.939;0.017;0.95	P;B;P	0.58660	0.756;0.033;0.843	T	0.03403	-1.1040	10	0.14252	T	0.57	-16.1031	17.8363	0.88699	0.0:0.0:1.0:0.0	.	292;287;280	G3XAF6;P49961-2;P49961	.;.;ENTP1_HUMAN	N	287;292;172;142;142;280	ENSP00000390955:D287N;ENSP00000360250:D292N;ENSP00000442968:D172N;ENSP00000440027:D142N;ENSP00000360246:D142N;ENSP00000360248:D280N	ENSP00000360246:D142N	D	+	1	0	ENTPD1	97597217	1.000000	0.71417	0.942000	0.38095	0.226000	0.24999	7.007000	0.76335	2.890000	0.99128	0.650000	0.86243	GAC	-	HMMPfam_GDA1_CD39		0.408	ENTPD1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	ENTPD1	protein_coding	OTTHUMT00000049566.1	G	NM_001776		97597217	+1	no_errors	NM_001098175.1	genbank	human	validated	54_36p	missense	SNP	0.005	A
NPAS4	266743	genome.wustl.edu	37	11	66192415	66192415	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2860-03B-01W-0728-08	TCGA-AB-2860-11B-01W-0729-08	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3b8b7cea-9e19-426f-9e58-d40de477ce12	a9f714a7-2581-4ce0-b077-3db990730b27	g.chr11:66192415A>G	ENST00000311034.2	+	7	2230	c.2054A>G	c.(2053-2055)gAc>gGc	p.D685G		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	685					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						CTCAGCCTGGACCTGAAACCC	0.602																																						dbGAP											0			11											82.0	89.0	87.0					11																	66192415		2200	4295	6495	65948991	SO:0001583	missense	0			AB049469	CCDS8138.1	11q13.2	2013-05-21			ENSG00000174576	ENSG00000174576		"""Basic helix-loop-helix proteins"""	18983	protein-coding gene	gene with protein product		608554				14701734	Standard	NM_178864		Approved	PASD10, NXF, Le-PAS, bHLHe79	uc001ohx.1	Q8IUM7	OTTHUMG00000167045	ENST00000311034.2:c.2054A>G	11.37:g.66192415A>G	ENSP00000311196:p.Asp685Gly	Somatic	57	3.39	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	65948991	13	40.91	9	B7ZL81|Q8N8S5|Q8N9Q9	Missense_Mutation	SNP	HMMSmart_PAS,HMMPfam_PAS_3,superfamily_SSF55785	p.D685G	ENST00000311034.2	37	c.2054	CCDS8138.1	11	.	.	.	.	.	.	.	.	.	.	A	11.79	1.744261	0.30865	.	.	ENSG00000174576	ENST00000311034	T	0.46063	0.88	4.69	4.69	0.59074	.	0.102006	0.43579	D	0.000541	T	0.26702	0.0653	N	0.14661	0.345	0.39185	D	0.962859	B	0.17667	0.023	B	0.20955	0.032	T	0.11991	-1.0565	10	0.51188	T	0.08	-5.8488	10.4666	0.44611	1.0:0.0:0.0:0.0	.	685	Q8IUM7	NPAS4_HUMAN	G	685	ENSP00000311196:D685G	ENSP00000311196:D685G	D	+	2	0	NPAS4	65948991	1.000000	0.71417	0.995000	0.50966	0.956000	0.61745	2.798000	0.47884	1.978000	0.57642	0.533000	0.62120	GAC	-	NULL		0.602	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NPAS4	protein_coding	OTTHUMT00000392634.1	A	NM_178864		65948991	+1	no_errors	NM_178864.3	genbank	human	validated	54_36p	missense	SNP	0.874	G
MUC16	94025	genome.wustl.edu	37	19	9060849	9060849	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2860-03B-01W-0728-08	TCGA-AB-2860-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3b8b7cea-9e19-426f-9e58-d40de477ce12	a9f714a7-2581-4ce0-b077-3db990730b27	g.chr19:9060849G>A	ENST00000397910.4	-	3	26800	c.26597C>T	c.(26596-26598)tCg>tTg	p.S8866L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8868	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ATAAAGTGGCGAAGGTGAGGT	0.512																																						dbGAP											0			19											117.0	116.0	117.0					19																	9060849		2001	4170	6171	8921849	SO:0001583	missense	0			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.26597C>T	19.37:g.9060849G>A	ENSP00000381008:p.Ser8866Leu	Somatic	176	1.64	3		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	8921849	110	24.83	37	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	HMMPfam_SEA,HMMSmart_SM00200,PatternScan_ATPASE_ALPHA_BETA,superfamily_SEA domain	p.S8866L	ENST00000397910.4	37	c.26597	CCDS54212.1	19	.	.	.	.	.	.	.	.	.	.	-	7.312	0.615210	0.14129	.	.	ENSG00000181143	ENST00000397910	T	0.27256	1.68	2.02	2.02	0.26589	.	.	.	.	.	T	0.32763	0.0840	L	0.29908	0.895	.	.	.	D	0.76494	0.999	D	0.68765	0.96	T	0.42447	-0.9451	8	0.87932	D	0	.	7.5796	0.27957	0.0:0.0:1.0:0.0	.	8866	B5ME49	.	L	8866	ENSP00000381008:S8866L	ENSP00000381008:S8866L	S	-	2	0	MUC16	8921849	0.000000	0.05858	0.004000	0.12327	0.006000	0.05464	-0.273000	0.08548	1.459000	0.47892	0.298000	0.19748	TCG	-	NULL		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MUC16	protein_coding	OTTHUMT00000402806.1	G	NM_024690		8921849	-1	no_errors	NM_024690.2	genbank	human	validated	54_36p	missense	SNP	0.000	A
RYR1	6261	genome.wustl.edu	37	19	38987175	38987175	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2860-03B-01W-0728-08	TCGA-AB-2860-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3b8b7cea-9e19-426f-9e58-d40de477ce12	a9f714a7-2581-4ce0-b077-3db990730b27	g.chr19:38987175G>A	ENST00000359596.3	+	41	6790	c.6790G>A	c.(6790-6792)Ggc>Agc	p.G2264S	RYR1_ENST00000355481.4_Missense_Mutation_p.G2264S|RYR1_ENST00000360985.3_Missense_Mutation_p.G2264S			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2264	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CAGTGGCATCGGCCTGGGTGA	0.622																																						dbGAP											0			19											40.0	45.0	43.0					19																	38987175		2203	4299	6502	43679015	SO:0001583	missense	0			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.6790G>A	19.37:g.38987175G>A	ENSP00000352608:p.Gly2264Ser	Somatic	18	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	43679015	10	37.50	6	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	HMMPfam_RYDR_ITPR,HMMPfam_RyR,HMMPfam_MIR,superfamily_MIR domain (Pfam 02815),HMMPfam_SPRY,HMMPfam_Ion_trans,HMMPfam_RR_TM4-6,HMMPfam_RIH_assoc,HMMPfam_Ins145_P3_rec,HMMSmart_SM00472,HMMSmart_SM00449,superfamily_EF-hand	p.G2264S	ENST00000359596.3	37	c.6790	CCDS33011.1	19	.	.	.	.	.	.	.	.	.	.	G	22.7	4.321396	0.81580	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.95272	-3.66;-3.66;-3.66	4.83	4.83	0.62350	Intracellular calcium-release channel (1);	0.000000	0.64402	U	0.000002	D	0.95620	0.8576	L	0.46157	1.445	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.93409	0.6767	10	0.15952	T	0.53	.	17.6847	0.88253	0.0:0.0:1.0:0.0	.	2264;2264	P21817-2;P21817	.;RYR1_HUMAN	S	2264	ENSP00000352608:G2264S;ENSP00000347667:G2264S;ENSP00000354254:G2264S	ENSP00000347667:G2264S	G	+	1	0	RYR1	43679015	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	9.612000	0.98347	2.499000	0.84300	0.555000	0.69702	GGC	-	HMMPfam_RYDR_ITPR		0.622	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RYR1	protein_coding	OTTHUMT00000462137.1	G			43679015	+1	no_errors	NM_000540.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
TP53	7157	genome.wustl.edu	37	17	7579569	7579570	+	Frame_Shift_Ins	INS	-	-	CCATCCAG			TCGA-AB-2860-03B-01W-0728-08	TCGA-AB-2860-11B-01W-0729-08	-	-	-	CCATCCAG	-	-	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3b8b7cea-9e19-426f-9e58-d40de477ce12	a9f714a7-2581-4ce0-b077-3db990730b27	g.chr17:7579569_7579570insCCATCCAG	ENST00000269305.4	-	4	306_307	c.117_118insCTGGATGG	c.(115-120)gcaatgfs	p.M40fs	TP53_ENST00000413465.2_Frame_Shift_Ins_p.M40fs|TP53_ENST00000359597.4_Frame_Shift_Ins_p.M40fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Frame_Shift_Ins_p.M40fs|TP53_ENST00000455263.2_Frame_Shift_Ins_p.M40fs|TP53_ENST00000420246.2_Frame_Shift_Ins_p.M40fs	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	40	Interaction with HRMT1L2.|Transcription activation (acidic).				apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.P36fs*4(3)|p.S37fs*79(1)|p.P13fs*18(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)	AAATCATCCATTGCTTGGGACG	0.599		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	dbGAP	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	14	Whole gene deletion(8)|Deletion - Frameshift(6)	bone(4)|ovary(3)|central_nervous_system(2)|upper_aerodigestive_tract(1)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)|prostate(1)	17																																								7520295	SO:0001589	frameshift_variant	0	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.117_118insCTGGATGG	17.37:g.7579569_7579570insCCATCCAG	ENSP00000269305:p.Met40fs	Somatic	NA	NA	NA		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	7520294	NA	NA	NA	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Ins	INS	PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD	p.M39fs	ENST00000269305.4	37	c.118_117	CCDS11118.1	17																																																																																			-	NULL		0.599	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TP53	protein_coding	OTTHUMT00000367397.1	-	NM_000546		7520295	-1	no_errors	NM_000546.4	genbank	human	reviewed	54_36p	frame_shift_ins	INS	0.000:0.000	CCATCCAG
Unknown	0	genome.wustl.edu	37	Unknown	0	0	+	IGR	DEL	CA	CA	-			TCGA-AB-2860-03B-01W-0728-08	TCGA-AB-2860-11B-01W-0729-08	CA	CA	CA	-	CA	CA	Verified	Invalid:failed_liftOver	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3b8b7cea-9e19-426f-9e58-d40de477ce12	a9f714a7-2581-4ce0-b077-3db990730b27	g.chrUnknown:0delCA								None (None upstream) : None (None downstream)																								0.0																																						dbGAP											0			19																																								23719584	SO:0001628	intergenic_variant	0																															Unknown.37:g.0delCA		Somatic	0	0.00	0		0	0.00	0	WXS	Illumina HiSeq	Phase_IV	23719583	0	0.00	0		Frame_Shift_Del	DEL	HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352),HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers	p.C203fs		37	c.609_608		19																																																																																			-	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers	0	0					ZNF681			CA			23719584	-1	no_errors	NM_138286.2	genbank	human	validated	54_36p	frame_shift_del	DEL	1.000:0.998	-
