#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_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_EVS_AA	i_EVS_All	i_EVS_EA	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	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_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	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_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
BAHCC1	57597	genome.wustl.edu	37	17	79414760	79414760	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chr17:79414760delG	ENST00000307745.7	+	15	3862	c.3862delG	c.(3862-3864)gggfs	p.G1288fs																								AGCGGCCTCTGGGCCCCCCAG	0.682																																						dbGAP											0													10.0	13.0	12.0					17																	79414760		1953	4100	6053	-	-	-	SO:0001589	frameshift_variant	0																														ENST00000307745.7:c.3862delG	17.37:g.79414760delG	ENSP00000303486:p.Gly1288fs			Frame_Shift_Del	DEL	pfam_BAH_dom,smart_BAH_dom,pfscan_BAH_dom	p.S1291fs	ENST00000307745.7	37	c.3862		17																																																																																			BAHCC1	-	NULL	ENSG00000171282		0.682	RP11-1055B8.7-201	KNOWN	basic|appris_principal	protein_coding	BAHCC1	HGNC	protein_coding		11	0.00	0	G			79414760	79414760	+1	no_errors	ENST00000307745	ensembl	human	known	69_37n	frame_shift_del	27	25.00	9	DEL	0.000	-
BCO1	53630	genome.wustl.edu	37	16	81303769	81303769	+	Nonsense_Mutation	SNP	T	T	A			TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chr16:81303769T>A	ENST00000258168.2	+	7	1310	c.849T>A	c.(847-849)taT>taA	p.Y283*	BCMO1_ENST00000425577.2_Nonsense_Mutation_p.Y214*	NM_017429.2	NP_059125.2														breast(2)|endometrium(1)|large_intestine(4)|lung(9)|prostate(3)|skin(3)|stomach(1)	23						TTCAGACTTATATCCACATCA	0.552																																						dbGAP											0													153.0	138.0	143.0					16																	81303769		2202	4300	6502	-	-	-	SO:0001587	stop_gained	0																														ENST00000258168.2:c.849T>A	16.37:g.81303769T>A	ENSP00000258168:p.Tyr283*			Nonsense_Mutation	SNP	pfam_Carotenoid_Oase	p.Y283*	ENST00000258168.2	37	c.849	CCDS10934.1	16	.	.	.	.	.	.	.	.	.	.	T	36	5.693582	0.96793	.	.	ENSG00000135697	ENST00000258168;ENST00000425577	.	.	.	5.62	1.34	0.21922	.	0.832987	0.11355	N	0.572516	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.7623	6.1271	0.20186	0.0:0.4747:0.216:0.3093	.	.	.	.	X	283;214	.	ENSP00000258168:Y283X	Y	+	3	2	BCMO1	79861270	0.988000	0.35896	0.644000	0.29465	0.303000	0.27691	0.151000	0.16283	0.063000	0.16370	-0.977000	0.02584	TAT	BCMO1	-	pfam_Carotenoid_Oase	ENSG00000135697		0.552	BCMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BCMO1	HGNC	protein_coding	OTTHUMT00000269056.1	99	0.00	0	T			81303769	81303769	+1	no_errors	ENST00000258168	ensembl	human	known	69_37n	nonsense	83	12.63	12	SNP	0.965	A
BRPF1	7862	genome.wustl.edu	37	3	9783065	9783065	+	Missense_Mutation	SNP	A	A	C			TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chr3:9783065A>C	ENST00000457855.1	+	4	1807	c.1796A>C	c.(1795-1797)gAg>gCg	p.E599A	BRPF1_ENST00000383829.2_Missense_Mutation_p.E599A|BRPF1_ENST00000424362.1_Missense_Mutation_p.E599A|BRPF1_ENST00000433861.2_Missense_Mutation_p.E599A|BRPF1_ENST00000302054.3_Missense_Mutation_p.E599A			P55201	BRPF1_HUMAN	bromodomain and PHD finger containing, 1	599	Interaction with MEAF6 and ING5.|Required for RUNX1 and RUNX2 transcriptional activation.				chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	49	Medulloblastoma(99;0.227)					CATGACTTGGAGCGAGCTCGG	0.512																																						dbGAP											0													62.0	70.0	67.0					3																	9783065		2203	4300	6503	-	-	-	SO:0001583	missense	0			M91585	CCDS2575.1, CCDS33692.1	3p26-p25	2008-07-18			ENSG00000156983	ENSG00000156983			14255	protein-coding gene	gene with protein product	"""peregrin"", ""bromodomain-containing protein, 140kD"""	602410				8946209, 7906940	Standard	NM_001003694		Approved	BR140	uc003bsf.3	P55201	OTTHUMG00000097033	ENST00000457855.1:c.1796A>C	3.37:g.9783065A>C	ENSP00000410210:p.Glu599Ala		B4DEZ6|Q7Z6E0|Q8TCM6|Q9UHI0	Missense_Mutation	SNP	pfam_Enhancer_polycomb-like_N,pfam_Bromodomain,pfam_PWWP,superfamily_Bromodomain,superfamily_Znf_FYVE_PHD,smart_Znf_PHD,smart_Bromodomain,smart_PWWP,prints_Bromodomain,pfscan_PWWP,pfscan_Znf_PHD-finger,pfscan_Znf_C2H2,pfscan_Bromodomain	p.E599A	ENST00000457855.1	37	c.1796	CCDS2575.1	3	.	.	.	.	.	.	.	.	.	.	A	32	5.113447	0.94339	.	.	ENSG00000156983	ENST00000433861;ENST00000424362;ENST00000383829;ENST00000302054;ENST00000457855	T;T;T;T;T	0.23552	1.93;1.9;3.29;1.9;1.9	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.58524	0.2128	M	0.88570	2.965	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.80764	0.994;0.994;0.994;0.987	T	0.67264	-0.5714	10	0.87932	D	0	.	16.0204	0.80478	1.0:0.0:0.0:0.0	.	599;599;599;599	P55201-4;P55201-3;P55201-2;P55201	.;.;.;BRPF1_HUMAN	A	599	ENSP00000402485:E599A;ENSP00000398863:E599A;ENSP00000373340:E599A;ENSP00000306297:E599A;ENSP00000410210:E599A	ENSP00000306297:E599A	E	+	2	0	BRPF1	9758065	1.000000	0.71417	0.999000	0.59377	0.933000	0.57130	9.339000	0.96797	2.174000	0.68829	0.533000	0.62120	GAG	BRPF1	-	NULL	ENSG00000156983		0.512	BRPF1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	BRPF1	HGNC	protein_coding	OTTHUMT00000338485.1	69	0.00	0	A	NM_001003694		9783065	9783065	+1	no_errors	ENST00000383829	ensembl	human	known	69_37n	missense	84	17.48	18	SNP	1.000	C
ELOVL5	60481	genome.wustl.edu	37	6	53156612	53156612	+	Missense_Mutation	SNP	G	G	A			TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chr6:53156612G>A	ENST00000542638.1	-	3	655	c.208C>T	c.(208-210)Ctt>Ttt	p.L70F	ELOVL5_ENST00000541407.1_Missense_Mutation_p.L70F|ELOVL5_ENST00000486973.1_5'UTR|ELOVL5_ENST00000370918.4_Splice_Site|ELOVL5_ENST00000304434.6_Missense_Mutation_p.L70F			Q9NYP7	ELOV5_HUMAN	ELOVL fatty acid elongase 5	70					alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid elongation, monounsaturated fatty acid (GO:0034625)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|linoleic acid metabolic process (GO:0043651)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	fatty acid elongase activity (GO:0009922)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7	Lung NSC(77;0.116)					GTGAGTCCAAGGTTATACACC	0.393																																						dbGAP											0													121.0	114.0	117.0					6																	53156612		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF052129	CCDS4951.1, CCDS56433.1, CCDS56434.1, CCDS75470.1	6p21.1-p12.1	2014-07-30	2011-05-25		ENSG00000012660	ENSG00000012660			21308	protein-coding gene	gene with protein product		611805	"""ELOVL family member 5, elongation of long chain fatty acids (FEN1/Elo2, SUR4/Elo3-like, yeast)"", ""spinocerebellar ataxia 38"""	SCA38		10970790, 25065913	Standard	NM_021814		Approved	HELO1, dJ483K16.1	uc011dwx.2	Q9NYP7	OTTHUMG00000016249	ENST00000542638.1:c.208C>T	6.37:g.53156612G>A	ENSP00000440728:p.Leu70Phe		B4DZJ2|F6SH78|Q59EL3|Q5TGH5|Q6NXE7|Q7L2S5|Q8NCG4|Q9UI22	Splice_Site	SNP	-	e2+2	ENST00000542638.1	37	c.206+2	CCDS4951.1	6	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.90|19.90	3.912753|3.912753	0.72983|0.72983	.|.	.|.	ENSG00000012660|ENSG00000012660	ENST00000370918|ENST00000304434;ENST00000542638;ENST00000541407	.|T;T;T	.|0.27104	.|1.69;1.69;1.69	5.94|5.94	5.05|5.05	0.67936|0.67936	.|.	.|0.060364	.|0.64402	.|D	.|0.000003	.|T	.|0.07458	.|0.0188	L|L	0.35793|0.35793	1.09|1.09	0.80722|0.80722	D|D	1|1	.|B;B;B	.|0.24368	.|0.028;0.005;0.102	.|B;B;B	.|0.30495	.|0.053;0.03;0.116	.|T	.|0.13602	.|-1.0503	.|10	.|0.10902	.|T	.|0.67	.|-8.0063	6.2413|6.2413	0.20793|0.20793	0.0698:0.135:0.6549:0.1403|0.0698:0.135:0.6549:0.1403	.|.	.|70;70;70	.|F6SH78;B3KWH9;Q9NYP7	.|.;.;ELOV5_HUMAN	.|F	-1|70	.|ENSP00000306640:L70F;ENSP00000440728:L70F;ENSP00000438095:L70F	.|ENSP00000306640:L70F	.|L	-|-	.|1	.|0	ELOVL5|ELOVL5	53264571|53264571	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	2.449000|2.449000	0.44935|0.44935	1.463000|1.463000	0.47967|0.47967	0.591000|0.591000	0.81541|0.81541	.|CTT	ELOVL5	-	-	ENSG00000012660		0.393	ELOVL5-203	KNOWN	basic|appris_principal|CCDS	protein_coding	ELOVL5	HGNC	protein_coding	OTTHUMT00000043566.1	172	0.00	0	G	NM_021814		53156612	53156612	-1	no_errors	ENST00000370918	ensembl	human	known	69_37n	splice_site	196	12.50	28	SNP	1.000	A
GNAS	2778	genome.wustl.edu	37	20	57485019	57485019	+	Missense_Mutation	SNP	A	A	G			TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chr20:57485019A>G	ENST00000371085.3	+	11	1277	c.853A>G	c.(853-855)Atc>Gtc	p.I285V	GNAS_ENST00000371100.4_Missense_Mutation_p.I928V|GNAS_ENST00000313949.7_3'UTR|GNAS_ENST00000265620.7_Missense_Mutation_p.I270V|GNAS_ENST00000354359.7_Missense_Mutation_p.I286V|GNAS_ENST00000371095.3_Missense_Mutation_p.I271V|GNAS_ENST00000306090.10_Missense_Mutation_p.I271V|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371102.4_Missense_Mutation_p.I914V|GNAS_ENST00000371075.3_3'UTR	NM_000516.4	NP_000507.1	P63092	GNAS2_HUMAN	GNAS complex locus	285					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			GCTGCGCACCATCTCTGTGAT	0.517			Mis		pituitary adenoma		"""McCune-Albright syndrome; pseudohypoparathyroidism, type IA"""			TSP Lung(22;0.16)																											Colon(117;935 1597 6045 8307 46442)	dbGAP		Dom	yes		20	20q13.2	2778	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	yes	E	0													83.0	79.0	80.0					20																	57485019		2203	4300	6503	-	-	-	SO:0001583	missense	0			M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"""secretogranin VI"""	139320	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371085.3:c.853A>G	20.37:g.57485019A>G	ENSP00000360126:p.Ile285Val		A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	pfam_Gprotein_alpha_su,pfam_Small_GTPase_ARF/SAR,superfamily_GproteinA_insert,smart_Gprotein_alpha_su,prints_Gprotein_alpha_S,prints_Gprotein_alpha_su	p.I286V	ENST00000371085.3	37	c.856	CCDS13472.1	20	.	.	.	.	.	.	.	.	.	.	A	17.87	3.494619	0.64186	.	.	ENSG00000087460	ENST00000371100;ENST00000371102;ENST00000371095;ENST00000371085;ENST00000354359;ENST00000265620;ENST00000306090;ENST00000371082	D;D;D;D;D;D;D	0.87179	-2.22;-2.22;-2.22;-2.22;-2.22;-2.22;-2.22	5.29	4.19	0.49359	.	0.049272	0.85682	D	0.000000	D	0.88559	0.6469	L	0.33293	1	0.80722	D	1	B;B;B;D	0.54964	0.022;0.045;0.036;0.969	B;B;B;D	0.67103	0.056;0.122;0.052;0.949	D	0.88509	0.3088	10	0.72032	D	0.01	.	11.2941	0.49267	0.9275:0.0:0.0725:0.0	.	285;286;270;928	P63092;A6NI00;P63092-3;Q5JWF2	GNAS2_HUMAN;.;.;GNAS1_HUMAN	V	928;914;271;285;286;270;271;51	ENSP00000360141:I928V;ENSP00000360143:I914V;ENSP00000360136:I271V;ENSP00000360126:I285V;ENSP00000346328:I286V;ENSP00000265620:I270V;ENSP00000304472:I271V	ENSP00000265620:I270V	I	+	1	0	GNAS	56918414	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	6.986000	0.76200	0.940000	0.37473	0.482000	0.46254	ATC	GNAS	-	pfam_Gprotein_alpha_su,pfam_Small_GTPase_ARF/SAR,smart_Gprotein_alpha_su,prints_Gprotein_alpha_S	ENSG00000087460		0.517	GNAS-015	KNOWN	basic|CCDS	protein_coding	GNAS	HGNC	protein_coding	OTTHUMT00000080431.2	103	0.00	0	A	NM_000516		57485019	57485019	+1	no_errors	ENST00000354359	ensembl	human	known	69_37n	missense	97	20.49	25	SNP	1.000	G
HLA-A	3105	genome.wustl.edu	37	6	29910604	29910604	+	Silent	SNP	C	C	A	rs12721675	byFrequency	TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chr6:29910604C>A	ENST00000396634.1	+	4	485	c.144C>A	c.(142-144)gcC>gcA	p.A48A	HLA-A_ENST00000376802.2_Silent_p.A48A|HLA-A_ENST00000376806.5_Silent_p.A48A|HLA-A_ENST00000376809.5_Silent_p.A48A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	48	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GCTTCATCGCCGTGGGCTACG	0.701									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			c|||	1915	0.382388	0.4425	0.4597	5008	,	,		15112	0.3899		0.3807	False		,,,				2504	0.2403					dbGAP											0													33.0	29.0	30.0					6																	29910604		2201	4298	6499	-	-	-	SO:0001819	synonymous_variant	0	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.144C>A	6.37:g.29910604C>A			O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	pfam_MHC_I_a_a1/a2,pfam_Ig_C1-set,pfam_MHC_I_a_C,superfamily_MHC_I/II-like_Ag-recog,smart_Ig_C1-set,pfscan_Ig-like,prints_MHC_I_a_a1/a2	p.A48	ENST00000396634.1	37	c.144	CCDS34373.1	6																																																																																			HLA-A	-	pfam_MHC_I_a_a1/a2,superfamily_MHC_I/II-like_Ag-recog	ENSG00000206503		0.701	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HLA-A	HGNC	protein_coding	OTTHUMT00000252909.1	17	0.00	0	C	NM_002116		29910604	29910604	+1	no_errors	ENST00000376806	ensembl	human	known	69_37n	silent	49	22.22	14	SNP	0.000	A
HLA-DRB6	3128	genome.wustl.edu	37	6	32521160	32521160	+	RNA	SNP	C	C	G	rs62621247	byFrequency	TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chr6:32521160C>G	ENST00000411500.1	-	0	867					NR_001298.1				major histocompatibility complex, class II, DR beta 6 (pseudogene)																		TACCTGTTGGCTGAAGTCCAG	0.408																																						dbGAP											0																																										-	-	-			0			L76566		6p21.3	2011-07-08			ENSG00000229391	ENSG00000229391		"""Histocompatibility complex"""	4954	pseudogene	pseudogene						1529427, 10436177	Standard	NR_001298		Approved		uc003obn.1		OTTHUMG00000031028		6.37:g.32521160C>G				RNA	SNP	-	NULL	ENST00000411500.1	37	NULL		6																																																																																			HLA-DRB6	-	-	ENSG00000229391		0.408	HLA-DRB6-002	KNOWN	basic	processed_transcript	HLA-DRB6	HGNC	pseudogene	OTTHUMT00000272900.1	13	0.00	0	C	NR_001298		32521160	32521160	-1	no_errors	ENST00000411500	ensembl	human	known	69_37n	rna	44	31.25	20	SNP	0.953	G
LILRA1	11024	genome.wustl.edu	37	19	55107152	55107152	+	Missense_Mutation	SNP	C	C	T			TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chr19:55107152C>T	ENST00000251372.3	+	6	892	c.710C>T	c.(709-711)gCc>gTc	p.A237V	LILRA1_ENST00000473156.1_Intron|LILRB1_ENST00000396321.2_Intron|LILRA1_ENST00000453777.1_Intron|LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000418536.2_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	237	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		CCTATAGTGGCCCCTGGGGAG	0.552																																						dbGAP											0													128.0	129.0	129.0					19																	55107152		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.710C>T	19.37:g.55107152C>T	ENSP00000251372:p.Ala237Val		O75018|Q3MJA6	Missense_Mutation	SNP	smart_Ig_sub,smart_Ig_sub2,pirsf_A1B_glyco/leuk_Ig-like_rcpt,pfscan_Ig-like	p.A237V	ENST00000251372.3	37	c.710	CCDS12901.1	19	.	.	.	.	.	.	.	.	.	.	C	8.431	0.848530	0.17034	.	.	ENSG00000104974	ENST00000251372	T	0.12465	2.68	1.58	-3.16	0.05217	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.15609	0.0376	M	0.76433	2.335	0.09310	N	1	P	0.35192	0.489	B	0.39935	0.314	T	0.26643	-1.0097	9	0.56958	D	0.05	.	2.5948	0.04851	0.4887:0.3279:0.0:0.1835	.	237	O75019	LIRA1_HUMAN	V	237	ENSP00000251372:A237V	ENSP00000251372:A237V	A	+	2	0	LILRA1	59798964	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.762000	0.01803	-0.707000	0.05022	0.194000	0.17425	GCC	LILRA1	-	smart_Ig_sub,smart_Ig_sub2,pirsf_A1B_glyco/leuk_Ig-like_rcpt	ENSG00000104974		0.552	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LILRA1	HGNC	protein_coding	OTTHUMT00000140807.2	210	0.00	0	C	NM_006863		55107152	55107152	+1	no_errors	ENST00000251372	ensembl	human	known	69_37n	missense	249	20.63	65	SNP	0.000	T
MAGEA11	4110	genome.wustl.edu	37	X	148798316	148798316	+	Silent	SNP	C	C	G			TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chrX:148798316C>G	ENST00000355220.5	+	5	1272	c.1170C>G	c.(1168-1170)gcC>gcG	p.A390A	MAGEA11_ENST00000333104.4_Silent_p.A361A	NM_005366.4	NP_005357.2	P43364	MAGAB_HUMAN	melanoma antigen family A, 11	390	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|skin(1)	9	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					GTCCAAGGGCCCACGCTGAGA	0.532																																						dbGAP											0													151.0	131.0	138.0					X																	148798316		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS48180.1	Xq28	2009-03-13			ENSG00000185247	ENSG00000185247			6798	protein-coding gene	gene with protein product	"""MAGE-11 antigen"", ""melanoma-associated antigen 11"", ""cancer/testis antigen family 1, member 11"""	300344		MAGE11		8575766	Standard	NM_001011544		Approved	MAGE-11, MAGEA-11, MGC10511, CT1.11	uc004fdq.3	P43364	OTTHUMG00000022633	ENST00000355220.5:c.1170C>G	X.37:g.148798316C>G			Q5ETU4|Q6ZRZ5	Silent	SNP	pfam_MAGE,pfam_Melanoma_ass_antigen_N,pfscan_MAGE	p.A390	ENST00000355220.5	37	c.1170	CCDS48180.1	X																																																																																			MAGEA11	-	pfam_MAGE,pfscan_MAGE	ENSG00000185247		0.532	MAGEA11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	MAGEA11	HGNC	protein_coding	OTTHUMT00000058725.4	50	0.00	0	C	NM_005366		148798316	148798316	+1	no_errors	ENST00000355220	ensembl	human	known	69_37n	silent	69	11.54	9	SNP	0.116	G
MPZL1	9019	genome.wustl.edu	37	1	167741689	167741689	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chr1:167741689C>T	ENST00000359523.2	+	3	638	c.436C>T	c.(436-438)Cag>Tag	p.Q146*	MPZL1_ENST00000474859.1_Nonsense_Mutation_p.Q146*|MPZL1_ENST00000392121.3_Intron	NM_003953.5|NM_024569.4	NP_003944.1|NP_078845.3	O95297	MPZL1_HUMAN	myelin protein zero-like 1	146	Ig-like V-type.				cell-cell signaling (GO:0007267)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	structural molecule activity (GO:0005198)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(2)	15	all_hematologic(923;0.215)					CATCGTTGTCCAGCCTGGACA	0.388																																						dbGAP											0													113.0	100.0	104.0					1																	167741689		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AF087020	CCDS1264.1, CCDS44273.1, CCDS53425.1	1q24.2	2013-01-11			ENSG00000197965	ENSG00000197965		"""Immunoglobulin superfamily / V-set domain containing"""	7226	protein-coding gene	gene with protein product		604376				9792637	Standard	NM_003953		Approved	PZR, FLJ21047	uc001geo.3	O95297	OTTHUMG00000034571	ENST00000359523.2:c.436C>T	1.37:g.167741689C>T	ENSP00000352513:p.Gln146*		B2REB9|B2REC0|Q5R332|Q8IX11|Q9BWZ3|Q9NYK4|Q9UL20	Nonsense_Mutation	SNP	pfam_Ig_V-set,smart_Ig_sub,smart_Ig_V-set_subgr,pfscan_Ig-like,prints_Myelin_P0	p.Q146*	ENST00000359523.2	37	c.436	CCDS1264.1	1	.	.	.	.	.	.	.	.	.	.	C	36	5.624928	0.96660	.	.	ENSG00000197965	ENST00000359523;ENST00000474859;ENST00000367853	.	.	.	4.81	3.9	0.45041	.	0.571167	0.19149	N	0.121492	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.9882	0.36008	0.1804:0.737:0.0:0.0827	.	.	.	.	X	146;146;120	.	ENSP00000352513:Q146X	Q	+	1	0	MPZL1	166008313	0.006000	0.16342	0.895000	0.35142	0.967000	0.64934	1.158000	0.31737	1.352000	0.45808	0.557000	0.71058	CAG	MPZL1	-	pfam_Ig_V-set,smart_Ig_sub,pfscan_Ig-like,prints_Myelin_P0	ENSG00000197965		0.388	MPZL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MPZL1	HGNC	protein_coding	OTTHUMT00000083655.2	164	0.00	0	C	NM_024569		167741689	167741689	+1	no_errors	ENST00000359523	ensembl	human	known	69_37n	nonsense	210	13.58	33	SNP	0.446	T
MUC16	94025	genome.wustl.edu	37	19	9007506	9007506	+	Silent	SNP	G	G	A			TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chr19:9007506G>A	ENST00000397910.4	-	43	39665	c.39462C>T	c.(39460-39462)tcC>tcT	p.S13154S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13156					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						TGGGGACGGGGGATGGAGTCC	0.473																																						dbGAP											0													58.0	58.0	58.0					19																	9007506		1890	4109	5999	-	-	-	SO:0001819	synonymous_variant	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.39462C>T	19.37:g.9007506G>A			Q6ZQW5|Q96RK2	Silent	SNP	pfam_SEA,smart_SEA,pfscan_SEA	p.S13154	ENST00000397910.4	37	c.39462	CCDS54212.1	19																																																																																			MUC16	-	NULL	ENSG00000181143		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MUC16	HGNC	protein_coding	OTTHUMT00000402806.1	109	0.00	0	G	NM_024690		9007506	9007506	-1	no_errors	ENST00000397910	ensembl	human	known	69_37n	silent	377	11.92	51	SNP	0.000	A
NF1	4763	genome.wustl.edu	37	17	29586058	29586058	+	Missense_Mutation	SNP	G	G	C			TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chr17:29586058G>C	ENST00000358273.4	+	33	4724	c.4341G>C	c.(4339-4341)caG>caC	p.Q1447H	NF1_ENST00000356175.3_Missense_Mutation_p.Q1426H	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1447	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(5)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AGATACTTCAGAGTATTGCCA	0.303			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												dbGAP	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	13	Whole gene deletion(8)|Unknown(5)	soft_tissue(7)|autonomic_ganglia(3)|central_nervous_system(2)|lung(1)											39.0	35.0	36.0					17																	29586058		2202	4298	6500	-	-	-	SO:0001583	missense	0	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.4341G>C	17.37:g.29586058G>C	ENSP00000351015:p.Gln1447His		O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	pfam_RasGAP,superfamily_Rho_GTPase_activation_prot,superfamily_ARM-type_fold,superfamily_CRAL-TRIO_dom,smart_RasGAP,smart_CRAL-TRIO_dom,pfscan_CRAL-TRIO_dom,pfscan_RasGAP	p.Q1447H	ENST00000358273.4	37	c.4341	CCDS42292.1	17	.	.	.	.	.	.	.	.	.	.	G	21.6	4.170015	0.78452	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	D;D;D	0.87412	-2.25;-2.25;-2.25	5.78	5.78	0.91487	Rho GTPase activation protein (1);Armadillo-type fold (1);Ras GTPase-activating protein (4);	0.056413	0.64402	N	0.000001	D	0.95802	0.8634	H	0.97783	4.075	0.80722	D	1	D;D;P	0.71674	0.998;0.988;0.947	D;D;P	0.74674	0.974;0.984;0.905	D	0.96725	0.9535	10	0.87932	D	0	.	13.2461	0.60024	0.0724:0.0:0.9276:0.0	.	476;1426;1447	Q59FX3;P21359-2;P21359	.;.;NF1_HUMAN	H	1447;1426;1092	ENSP00000351015:Q1447H;ENSP00000348498:Q1426H;ENSP00000389907:Q1092H	ENSP00000348498:Q1426H	Q	+	3	2	NF1	26610184	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	3.413000	0.52686	2.732000	0.93576	0.555000	0.69702	CAG	NF1	-	pfam_RasGAP,superfamily_Rho_GTPase_activation_prot,superfamily_ARM-type_fold,smart_RasGAP,pfscan_RasGAP	ENSG00000196712		0.303	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NF1	HGNC	protein_coding	OTTHUMT00000256351.2	246	0.00	0	G	NM_000267		29586058	29586058	+1	no_errors	ENST00000358273	ensembl	human	known	69_37n	missense	185	26.29	66	SNP	1.000	C
PCDH19	57526	genome.wustl.edu	37	X	99662740	99662740	+	Missense_Mutation	SNP	G	G	A			TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chrX:99662740G>A	ENST00000373034.4	-	1	2531	c.856C>T	c.(856-858)Cgc>Tgc	p.R286C	PCDH19_ENST00000255531.7_Missense_Mutation_p.R286C|PCDH19_ENST00000420881.2_Missense_Mutation_p.R286C	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	286	Cadherin 3. {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)			breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						AAGAGCTCGCGCGTGCGGTCG	0.602																																						dbGAP											0													102.0	107.0	106.0					X																	99662740		2164	4245	6409	-	-	-	SO:0001583	missense	0			AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"""Cadherins / Protocadherins : Non-clustered"""	14270	protein-coding gene	gene with protein product		300460	"""epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"""	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.856C>T	X.37:g.99662740G>A	ENSP00000362125:p.Arg286Cys		B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Missense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.R286C	ENST00000373034.4	37	c.856	CCDS55462.1	X	.	.	.	.	.	.	.	.	.	.	G	12.42	1.931469	0.34096	.	.	ENSG00000165194	ENST00000420881;ENST00000373034;ENST00000255531	T;T;T	0.52983	0.64;0.64;0.64	5.95	4.14	0.48551	Cadherin (4);Cadherin-like (1);	0.047828	0.85682	D	0.000000	T	0.73860	0.3641	M	0.92459	3.31	0.40468	D	0.98031	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.68483	0.958;0.921;0.953	T	0.80144	-0.1505	10	0.72032	D	0.01	.	13.6617	0.62372	0.0:0.0:0.4694:0.5305	.	286;286;286	Q8TAB3;Q8TAB3-2;E9PAM6	PCD19_HUMAN;.;.	C	286	ENSP00000400327:R286C;ENSP00000362125:R286C;ENSP00000255531:R286C	ENSP00000255531:R286C	R	-	1	0	PCDH19	99549396	0.984000	0.35163	0.027000	0.17364	0.789000	0.44602	2.155000	0.42301	0.599000	0.29845	0.513000	0.50165	CGC	PCDH19	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin	ENSG00000165194		0.602	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PCDH19	HGNC	protein_coding	OTTHUMT00000057479.2	107	0.00	0	G	NM_020766		99662740	99662740	-1	no_errors	ENST00000373034	ensembl	human	known	69_37n	missense	92	11.54	12	SNP	0.115	A
PHF6	84295	genome.wustl.edu	37	X	133559244	133559244	+	Missense_Mutation	SNP	A	A	T			TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chrX:133559244A>T	ENST00000332070.3	+	10	1184	c.982A>T	c.(982-984)Aat>Tat	p.N328Y	PHF6_ENST00000394292.1_Missense_Mutation_p.N329Y|PHF6_ENST00000370803.3_Missense_Mutation_p.N328Y|PHF6_ENST00000416404.2_Missense_Mutation_p.N294Y	NM_032458.2	NP_115834.1	Q8IWS0	PHF6_HUMAN	PHD finger protein 6	328	Extended PHD2 domain (ePHD2).				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|scaffold protein binding (GO:0097110)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(88)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(1)|skin(1)|urinary_tract(1)	103	Acute lymphoblastic leukemia(192;0.000127)					ATACTGTAAAAATCATAGTGG	0.393			"""F, N, Splice, Mis"""		ETP ALL																																Colon(100;666 1493 6344 21231 35807)	dbGAP		Rec	yes		X	Xq26.3	84295	PHD finger protein 6		L	0													107.0	100.0	102.0					X																	133559244		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB058726	CCDS14639.1, CCDS14640.1	Xq26	2014-09-17			ENSG00000156531	ENSG00000156531		"""Zinc fingers, PHD-type"""	18145	protein-coding gene	gene with protein product	"""centromere protein 31"""	300414	"""Borjeson-Forssman-Lehmann syndrome"""	BFLS, BORJ		12415272, 15466013	Standard	NM_032335		Approved	KIAA1823, MGC14797, CENP-31	uc004exk.3	Q8IWS0	OTTHUMG00000022453	ENST00000332070.3:c.982A>T	X.37:g.133559244A>T	ENSP00000329097:p.Asn328Tyr		A8K230|B4E0G4|D3DTG3|E9PC97|Q5JRC7|Q5JRC8|Q96JK3|Q9BRU0	Missense_Mutation	SNP	superfamily_Znf_FYVE_PHD,smart_Znf_PHD	p.N329Y	ENST00000332070.3	37	c.985	CCDS14639.1	X	.	.	.	.	.	.	.	.	.	.	A	16.48	3.135016	0.56828	.	.	ENSG00000156531	ENST00000370803;ENST00000332070;ENST00000394292;ENST00000416404	T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53	5.53	5.53	0.82687	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.72334	0.3447	N	0.14661	0.345	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	T	0.76664	-0.2876	10	0.56958	D	0.05	-13.2959	13.8256	0.63348	1.0:0.0:0.0:0.0	.	294;328	B4E0G4;Q8IWS0	.;PHF6_HUMAN	Y	328;328;329;294	ENSP00000359839:N328Y;ENSP00000329097:N328Y;ENSP00000377831:N329Y;ENSP00000394480:N294Y	ENSP00000329097:N328Y	N	+	1	0	PHF6	133386910	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	8.346000	0.90060	1.861000	0.53984	0.441000	0.28932	AAT	PHF6	-	smart_Znf_PHD	ENSG00000156531		0.393	PHF6-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	PHF6	HGNC	protein_coding	OTTHUMT00000058367.1	400	0.00	0	A	NM_032458		133559244	133559244	+1	no_errors	ENST00000394292	ensembl	human	known	69_37n	missense	319	15.61	59	SNP	1.000	T
PIK3CA	5290	genome.wustl.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279		TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chr3:178952085A>G	ENST00000263967.3	+	21	3297	c.3140A>G	c.(3139-3141)cAt>cGt	p.H1047R	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1047	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (in BC; unknown pathological significance). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16353168}.|H -> R (in CLOVE, KERSEB, CRC, BC and OC; also found in an endometrial carcinoma sample; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane). {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|H -> Y (in MCAP; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H1047R(1387)|p.H1047L(194)|p.H1047P(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AATGATGCACATCATGGTGGC	0.378	H1047L(EFM19_BREAST)|H1047R(BT20_BREAST)|H1047R(CAL29_URINARY_TRACT)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(HCC1954_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(MCAS_OVARY)|H1047R(MDAMB453_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(RKO_LARGE_INTESTINE)|H1047R(SKOV3_OVARY)|H1047R(T47D_BREAST)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	dbGAP		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	1582	Substitution - Missense(1582)	breast(961)|large_intestine(245)|endometrium(114)|ovary(77)|urinary_tract(36)|upper_aerodigestive_tract(26)|lung(19)|central_nervous_system(19)|stomach(19)|haematopoietic_and_lymphoid_tissue(11)|thyroid(10)|NS(9)|liver(7)|kidney(6)|soft_tissue(6)|skin(4)|prostate(4)|pituitary(3)|pancreas(3)|meninges(1)|cervix(1)|bone(1)											99.0	89.0	92.0					3																	178952085		1912	4130	6042	-	-	-	SO:0001583	missense	0				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3140A>G	3.37:g.178952085A>G	ENSP00000263967:p.His1047Arg		Q14CW1|Q99762	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,pfam_PI3K_adapt-bd_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.H1047R	ENST00000263967.3	37	c.3140	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506328	0.44558	.	.	ENSG00000121879	ENST00000263967	T	0.80214	-1.35	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.62466	0.2430	N	0.08118	0	0.80722	D	1	P	0.38597	0.639	B	0.28011	0.085	T	0.67526	-0.5648	10	0.40728	T	0.16	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	R	1047	ENSP00000263967:H1047R	ENSP00000263967:H1047R	H	+	2	0	PIK3CA	180434779	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	CAT	PIK3CA	-	superfamily_Kinase-like_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	ENSG00000121879		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	213	0.00	0	A			178952085	178952085	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	172	19.25	41	SNP	1.000	G
RASAL2	9462	genome.wustl.edu	37	1	178411925	178411925	+	Missense_Mutation	SNP	G	G	A			TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chr1:178411925G>A	ENST00000462775.1	+	6	724	c.599G>A	c.(598-600)cGt>cAt	p.R200H	RASAL2_ENST00000367649.3_Missense_Mutation_p.R348H|RASAL2_ENST00000448150.3_Missense_Mutation_p.R330H	NM_004841.3	NP_004832.1	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	200	C2.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Ras GTPase activator activity (GO:0005099)			biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						CTCTTTGCTCGTACAACCAGC	0.413																																						dbGAP											0													95.0	94.0	94.0					1																	178411925		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF047711	CCDS1321.1, CCDS1322.1, CCDS1321.2	1q25	2013-01-10			ENSG00000075391	ENSG00000075391		"""Pleckstrin homology (PH) domain containing"""	9874	protein-coding gene	gene with protein product	"""Ras GTPase activating protein-like"", ""Ras protein activator like 1"""	606136				9877179	Standard	NM_004841		Approved	nGAP	uc001glq.3	Q9UJF2	OTTHUMG00000035022	ENST00000462775.1:c.599G>A	1.37:g.178411925G>A	ENSP00000420558:p.Arg200His		F8W755|O95174|Q2TB22|Q5TFU9	Missense_Mutation	SNP	pfam_DUF3498,pfam_RasGAP,pfam_Pleckstrin_homology,pfam_C2_Ca-dep,superfamily_Rho_GTPase_activation_prot,superfamily_C2_Ca/lipid-bd_dom_CaLB,superfamily_PP1_inhibitor,smart_Pleckstrin_homology,smart_C2_Ca-dep,smart_RasGAP,pfscan_Pleckstrin_homology,pfscan_RasGAP	p.R348H	ENST00000462775.1	37	c.1043	CCDS1322.1	1	.	.	.	.	.	.	.	.	.	.	G	33	5.203157	0.95033	.	.	ENSG00000075391	ENST00000448150;ENST00000367649;ENST00000462775	T;T;T	0.73469	-0.75;-0.75;-0.75	5.75	5.75	0.90469	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.072630	0.64402	D	0.000016	D	0.89504	0.6734	M	0.90369	3.11	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	D	0.90839	0.4722	10	0.87932	D	0	.	19.9405	0.97159	0.0:0.0:1.0:0.0	.	200;348	Q9UJF2;F8W755	NGAP_HUMAN;.	H	330;348;200	ENSP00000407768:R330H;ENSP00000356621:R348H;ENSP00000420558:R200H	ENSP00000356621:R348H	R	+	2	0	RASAL2	176678548	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.731000	0.98807	2.716000	0.92895	0.650000	0.86243	CGT	RASAL2	-	pfam_C2_Ca-dep,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_C2_Ca-dep	ENSG00000075391		0.413	RASAL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	RASAL2	HGNC	protein_coding	OTTHUMT00000084758.3	216	0.00	0	G	NM_170692		178411925	178411925	+1	no_errors	ENST00000367649	ensembl	human	known	69_37n	missense	165	26.01	58	SNP	1.000	A
SOCS4	122809	genome.wustl.edu	37	14	55510028	55510028	+	Missense_Mutation	SNP	C	C	A			TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chr14:55510028C>A	ENST00000395472.2	+	2	601	c.269C>A	c.(268-270)tCt>tAt	p.S90Y	SOCS4_ENST00000339298.2_Missense_Mutation_p.S90Y|SOCS4_ENST00000555846.1_Missense_Mutation_p.S90Y	NM_080867.2|NM_199421.1	NP_543143.1|NP_955453.1	Q8WXH5	SOCS4_HUMAN	suppressor of cytokine signaling 4	90					intracellular signal transduction (GO:0035556)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)					central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)	14						TTAGGCCGATCTCTTAAACAG	0.428																																						dbGAP											0													121.0	114.0	117.0					14																	55510028		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF424815	CCDS9722.1	14q22.1	2013-02-14	2004-02-25	2004-02-27	ENSG00000180008	ENSG00000180008		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	19392	protein-coding gene	gene with protein product			"""suppressor of cytokine signaling 7"""	SOCS7		12076535, 10500304	Standard	NM_080867		Approved		uc001xbp.3	Q8WXH5	OTTHUMG00000140311	ENST00000395472.2:c.269C>A	14.37:g.55510028C>A	ENSP00000378855:p.Ser90Tyr			Missense_Mutation	SNP	pfam_SOCS,pfam_SOCS_C,pfam_SH2,smart_SH2,smart_SOCS_C,pfscan_SOCS_C,pfscan_SH2	p.S90Y	ENST00000395472.2	37	c.269	CCDS9722.1	14	.	.	.	.	.	.	.	.	.	.	C	20.7	4.026278	0.75390	.	.	ENSG00000180008	ENST00000395472;ENST00000555846;ENST00000339298	T;T;T	0.48836	0.8;0.8;0.8	5.48	5.48	0.80851	.	0.000000	0.64402	D	0.000005	T	0.67344	0.2883	L	0.59436	1.845	0.58432	D	0.99999	D	0.76494	0.999	D	0.77004	0.989	T	0.69224	-0.5201	10	0.87932	D	0	-16.6133	19.3595	0.94431	0.0:1.0:0.0:0.0	.	90	Q8WXH5	SOCS4_HUMAN	Y	90	ENSP00000378855:S90Y;ENSP00000452522:S90Y;ENSP00000341327:S90Y	ENSP00000341327:S90Y	S	+	2	0	SOCS4	54579781	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.484000	0.81180	2.576000	0.86940	0.655000	0.94253	TCT	SOCS4	-	pfam_SOCS	ENSG00000180008		0.428	SOCS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SOCS4	HGNC	protein_coding	OTTHUMT00000276910.1	146	0.00	0	C			55510028	55510028	+1	no_errors	ENST00000339298	ensembl	human	known	69_37n	missense	144	13.25	22	SNP	1.000	A
SYTL4	94121	genome.wustl.edu	37	X	99936233	99936233	+	Missense_Mutation	SNP	G	G	A			TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chrX:99936233G>A	ENST00000372989.1	-	16	1880	c.1549C>T	c.(1549-1551)Cgg>Tgg	p.R517W	SYTL4_ENST00000491602.1_5'Flank|SYTL4_ENST00000455616.1_Missense_Mutation_p.R517W|SYTL4_ENST00000263033.5_Missense_Mutation_p.R517W|SYTL4_ENST00000454200.2_Missense_Mutation_p.R519W|SYTL4_ENST00000276141.6_Missense_Mutation_p.R517W	NM_080737.2	NP_542775.2	Q96C24	SYTL4_HUMAN	synaptotagmin-like 4	517	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|multivesicular body sorting pathway (GO:0071985)|negative regulation of insulin secretion (GO:0046676)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	neurexin family protein binding (GO:0042043)|phospholipid binding (GO:0005543)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(2)	27					"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	CTCTTTTTCCGGTCACCTCCA	0.517																																						dbGAP											0													63.0	56.0	58.0					X																	99936233		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS14472.1	Xq21.33	2008-07-31	2008-07-31		ENSG00000102362	ENSG00000102362			15588	protein-coding gene	gene with protein product	"""granuphilin-a"", ""exophilin-2"""	300723					Standard	NM_080737		Approved		uc010nnc.3	Q96C24	OTTHUMG00000022004	ENST00000372989.1:c.1549C>T	X.37:g.99936233G>A	ENSP00000362080:p.Arg517Trp		Q5H9J3|Q5JPG8|Q8N9P4|Q9H4R0|Q9H4R1	Missense_Mutation	SNP	pfam_C2_Ca-dep,superfamily_C2_Ca/lipid-bd_dom_CaLB,superfamily_Znf_FYVE_PHD,smart_C2_Ca-dep,pfscan_C2_membr_targeting,pfscan_Rab-bd_domain,prints_Synaptotagmin	p.R519W	ENST00000372989.1	37	c.1555	CCDS14472.1	X	.	.	.	.	.	.	.	.	.	.	G	13.09	2.134228	0.37630	.	.	ENSG00000102362	ENST00000372989;ENST00000455616;ENST00000454200;ENST00000276141;ENST00000263033	T;T;T;T;T	0.22539	1.95;1.95;1.95;1.95;1.95	4.98	4.12	0.48240	C2 calcium/lipid-binding domain, CaLB (1);	0.439888	0.23896	N	0.043482	T	0.15176	0.0366	L	0.47716	1.5	0.33148	D	0.545244	B	0.11235	0.004	B	0.06405	0.002	T	0.14144	-1.0483	9	.	.	.	-3.1743	3.4024	0.07328	0.0971:0.2259:0.5312:0.1458	.	517	Q96C24	SYTL4_HUMAN	W	517;517;519;517;517	ENSP00000362080:R517W;ENSP00000390252:R517W;ENSP00000403556:R519W;ENSP00000276141:R517W;ENSP00000263033:R517W	.	R	-	1	2	SYTL4	99822889	0.693000	0.27728	1.000000	0.80357	0.993000	0.82548	0.543000	0.23237	1.099000	0.41499	0.468000	0.43344	CGG	SYTL4	-	superfamily_C2_Ca/lipid-bd_dom_CaLB	ENSG00000102362		0.517	SYTL4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	SYTL4	HGNC	protein_coding	OTTHUMT00000057488.1	134	0.00	0	G	NM_080737		99936233	99936233	-1	no_errors	ENST00000454200	ensembl	human	known	69_37n	missense	168	13.40	26	SNP	0.997	A
TP53	7157	genome.wustl.edu	37	17	7577121	7577121	+	Missense_Mutation	SNP	G	G	A	rs121913343		TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chr17:7577121G>A	ENST00000269305.4	-	8	1006	c.817C>T	c.(817-819)Cgt>Tgt	p.R273C	TP53_ENST00000420246.2_Missense_Mutation_p.R273C|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R273C|TP53_ENST00000445888.2_Missense_Mutation_p.R273C|TP53_ENST00000359597.4_Missense_Mutation_p.R273C|TP53_ENST00000413465.2_Intron	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	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		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.R273C(481)|p.R273S(16)|p.R273G(9)|p.0?(8)|p.?(2)|p.R273fs*72(2)|p.R273fs*33(2)|p.R273fs*32(2)|p.V272>?(2)|p.F270fs*72(1)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.E258fs*71(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.E271_R273delEVR(1)|p.V272_K292del21(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)	GCACAAACACGCACCTCAAAG	0.542	R273C(8MGBA_CENTRAL_NERVOUS_SYSTEM)|R273C(BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(EFO27_OVARY)|R273C(KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(MFE319_ENDOMETRIUM)|R273C(NCIH1048_LUNG)|R273C(PANC0213_PANCREAS)|R273C(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(RDES_BONE)|R273C(RH30_SOFT_TISSUE)|R273C(RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SH10TC_STOMACH)|R273C(SJRH30_SOFT_TISSUE)|R273C(SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SW1710_URINARY_TRACT)|R273C(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273C(TT2609C02_THYROID)	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"""	533	Substitution - Missense(506)|Whole gene deletion(8)|Deletion - Frameshift(8)|Deletion - In frame(5)|Insertion - Frameshift(2)|Unknown(2)|Complex(2)	central_nervous_system(117)|large_intestine(108)|ovary(32)|haematopoietic_and_lymphoid_tissue(31)|upper_aerodigestive_tract(30)|stomach(25)|urinary_tract(23)|lung(21)|breast(21)|liver(20)|endometrium(17)|oesophagus(17)|bone(16)|pancreas(15)|prostate(8)|skin(7)|cervix(6)|biliary_tract(6)|kidney(3)|thyroid(3)|vulva(2)|genital_tract(1)|penis(1)|adrenal_gland(1)|salivary_gland(1)|small_intestine(1)	GRCh37	CM010471|CM010473|CM951233	TP53	M	rs121913343						65.0	56.0	59.0					17																	7577121		2203	4300	6503	-	-	-	SO:0001583	missense	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.817C>T	17.37:g.7577121G>A	ENSP00000269305:p.Arg273Cys		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	pfam_p53_DNA-bd,pfam_p53_tetrameristn,pfam_p53_transactivation_domain,superfamily_p53-like_TF_DNA-bd,superfamily_p53_tetrameristn,prints_p53_tumour_suppressor	p.R273C	ENST00000269305.4	37	c.817	CCDS11118.1	17	.	.	.	.	.	.	.	.	.	.	G	17.48	3.400216	0.62177	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.92	3.95	0.45737	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99851	0.9931	M	0.90759	3.145	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.999;0.996	D	0.96877	0.9643	10	0.87932	D	0	-11.9995	11.2235	0.48869	0.0895:0.0:0.9105:0.0	.	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	C	273;273;273;273;273;262;141	ENSP00000352610:R273C;ENSP00000269305:R273C;ENSP00000398846:R273C;ENSP00000391127:R273C;ENSP00000391478:R273C;ENSP00000425104:R141C	ENSP00000269305:R273C	R	-	1	0	TP53	7517846	1.000000	0.71417	0.066000	0.19879	0.723000	0.41478	4.540000	0.60664	1.299000	0.44798	0.462000	0.41574	CGT	TP53	-	pfam_p53_DNA-bd,superfamily_p53-like_TF_DNA-bd,prints_p53_tumour_suppressor	ENSG00000141510		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TP53	HGNC	protein_coding	OTTHUMT00000367397.1	135	0.00	0	G	NM_000546		7577121	7577121	-1	no_errors	ENST00000269305	ensembl	human	known	69_37n	missense	137	35.98	77	SNP	0.830	A
TRANK1	9881	genome.wustl.edu	37	3	36879889	36879889	+	Missense_Mutation	SNP	C	C	A			TCGA-AR-A1AW-01A-21D-A12Q-09	TCGA-AR-A1AW-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	33c6b6b5-1484-4002-8f84-ba67525a8777	e93c2d61-5212-4796-8a2c-950db804fddf	g.chr3:36879889C>A	ENST00000429976.2	-	19	5606	c.5359G>T	c.(5359-5361)Gcc>Tcc	p.A1787S	TRANK1_ENST00000428977.2_Missense_Mutation_p.A1237S|TRANK1_ENST00000301807.6_Missense_Mutation_p.A1237S	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1787							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						CACAGCTGGGCAGAGAGCTGG	0.532																																						dbGAP											0													108.0	106.0	107.0					3																	36879889		1951	4145	6096	-	-	-	SO:0001583	missense	0			AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29011	protein-coding gene	gene with protein product	"""lupus brain antigen 1"", ""KIAA0342"""					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.5359G>T	3.37:g.36879889C>A	ENSP00000416168:p.Ala1787Ser		Q8N8K0	Missense_Mutation	SNP	pfam_UvrD-like_ATP-bd,superfamily_Ankyrin_rpt-contain_dom,smart_TPR_repeat,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_TPR-contain_dom	p.A1787S	ENST00000429976.2	37	c.5359	CCDS46789.2	3	.	.	.	.	.	.	.	.	.	.	C	27.9	4.874074	0.91664	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.37411	1.2;1.62;1.2	4.99	4.99	0.66335	Tetratricopeptide-like helical (1);	0.000000	0.52532	D	0.000061	T	0.47192	0.1432	L	0.29908	0.895	0.43947	D	0.996618	D	0.67145	0.996	P	0.60541	0.876	T	0.47433	-0.9118	10	0.62326	D	0.03	.	19.1493	0.93481	0.0:1.0:0.0:0.0	.	1787	O15050	TRNK1_HUMAN	S	1237;1787;1237	ENSP00000416826:A1237S;ENSP00000416168:A1787S;ENSP00000301807:A1237S	ENSP00000301807:A1237S	A	-	1	0	TRANK1	36854893	1.000000	0.71417	0.970000	0.41538	0.887000	0.51463	4.000000	0.57039	2.686000	0.91538	0.655000	0.94253	GCC	TRANK1	-	NULL	ENSG00000168016		0.532	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	TRANK1	HGNC	protein_coding		150	0.00	0	C	NM_014831		36879889	36879889	-1	no_errors	ENST00000429976	ensembl	human	known	69_37n	missense	144	16.28	28	SNP	0.999	A
