#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
CLCNKA	1187	genome.wustl.edu	37	1	16360144	16360144	+	Silent	SNP	T	T	C	rs371202740		TCGA-OL-A5RY-01A-21D-A28B-09	TCGA-OL-A5RY-10A-01D-A28E-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	476465ea-63a7-49d0-8b85-25e02d69b78d	90710e07-11e4-4116-a955-3a58f616acdf	g.chr1:16360144T>C	ENST00000331433.4	+	20	2074	c.2055T>C	c.(2053-2055)gcT>gcC	p.A685A	CLCNKA_ENST00000375692.1_Silent_p.A684A|CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000420078.1_Silent_p.A684A|CLCNKA_ENST00000439316.2_Silent_p.A642A			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	685					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	ATCCGCCAGCTCCAAAGTGAG	0.582																																						dbGAP											0													82.0	81.0	82.0					1																	16360144		2202	4300	6502	-	-	-	SO:0001819	synonymous_variant	0				CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"""Ion channels / Chloride channels : Voltage-sensitive"""	2026	protein-coding gene	gene with protein product		602024	"""chloride channel Ka"""			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.2055T>C	1.37:g.16360144T>C			B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Silent	SNP	pfam_Cl-channel_volt-gated,pfam_Cysta_beta_synth_core,superfamily_Cl-channel_core,smart_Cysta_beta_synth_core,prints_Cl-channel_volt-gated,prints_Cl_channel-K	p.A685	ENST00000331433.4	37	c.2055	CCDS167.1	1																																																																																			CLCNKA	-	NULL	ENSG00000186510		0.582	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CLCNKA	HGNC	protein_coding	OTTHUMT00000026326.1	51	0.00	0	T			16360144	16360144	+1	no_errors	ENST00000331433	ensembl	human	known	69_37n	silent	34	10.53	4	SNP	0.903	C
HIST1H1A	3024	genome.wustl.edu	37	6	26017768	26017768	+	Missense_Mutation	SNP	G	G	T	rs145757054	byFrequency	TCGA-OL-A5RY-01A-21D-A28B-09	TCGA-OL-A5RY-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	476465ea-63a7-49d0-8b85-25e02d69b78d	90710e07-11e4-4116-a955-3a58f616acdf	g.chr6:26017768G>T	ENST00000244573.3	-	1	272	c.193C>A	c.(193-195)Ctt>Att	p.L65I	HIST1H3A_ENST00000357647.3_5'Flank	NM_005325.3	NP_005316.1	Q02539	H11_HUMAN	histone cluster 1, H1a	65	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|spermatogenesis (GO:0007283)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|ovary(3)|prostate(1)	13						GCCTTTTTAAGAGCTGCCAAC	0.572																																						dbGAP											0													50.0	52.0	51.0					6																	26017768		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF531299	CCDS4569.1	6p22.1	2012-11-16	2006-10-11	2003-02-21	ENSG00000124610	ENSG00000124610		"""Histones / Replication-dependent"""	4715	protein-coding gene	gene with protein product		142709	"""H1 histone family, member 1"", ""histone 1, H1a"""	H1F1		2759094, 12408966	Standard	NM_005325		Approved	H1.1, H1a	uc003nfo.3	Q02539	OTTHUMG00000016413	ENST00000244573.3:c.193C>A	6.37:g.26017768G>T	ENSP00000244573:p.Leu65Ile		Q3MJ34	Missense_Mutation	SNP	pfam_Histone_H1/H5,smart_Histone_H1/H5,prints_Histone_H5	p.L65I	ENST00000244573.3	37	c.193	CCDS4569.1	6	.	.	.	.	.	.	.	.	.	.	N	16.15	3.042126	0.55003	.	.	ENSG00000124610	ENST00000244573	T	0.15017	2.46	4.2	4.2	0.49525	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.144353	0.47093	D	0.000258	T	0.10078	0.0247	N	0.16602	0.42	0.58432	D	0.999998	P	0.50617	0.937	P	0.51806	0.68	T	0.21827	-1.0234	10	0.27082	T	0.32	-3.9005	16.4244	0.83809	0.0:0.0:1.0:0.0	.	65	Q02539	H11_HUMAN	I	65	ENSP00000244573:L65I	ENSP00000244573:L65I	L	-	1	0	HIST1H1A	26125747	1.000000	0.71417	0.939000	0.37840	0.029000	0.11900	3.311000	0.51919	2.260000	0.74910	0.609000	0.83330	CTT	HIST1H1A	-	pfam_Histone_H1/H5,smart_Histone_H1/H5,prints_Histone_H5	ENSG00000124610		0.572	HIST1H1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	HIST1H1A	HGNC	protein_coding	OTTHUMT00000043884.1	94	0.00	0	G	NM_005325		26017768	26017768	-1	no_errors	ENST00000244573	ensembl	human	known	69_37n	missense	63	10.00	7	SNP	1.000	T
MB21D2	151963	genome.wustl.edu	37	3	192517061	192517061	+	Missense_Mutation	SNP	G	G	A	rs191773261		TCGA-OL-A5RY-01A-21D-A28B-09	TCGA-OL-A5RY-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	476465ea-63a7-49d0-8b85-25e02d69b78d	90710e07-11e4-4116-a955-3a58f616acdf	g.chr3:192517061G>A	ENST00000392452.2	-	2	910	c.590C>T	c.(589-591)tCa>tTa	p.S197L		NM_178496.3	NP_848591.2	Q8IYB1	M21D2_HUMAN	Mab-21 domain containing 2	197							protein complex binding (GO:0032403)			endometrium(3)|kidney(1)|large_intestine(4)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	31						CTGTATTTCTGATAGGACAAT	0.463													G|||	1	0.000199681	0.0008	0.0	5008	,	,		21656	0.0		0.0	False		,,,				2504	0.0					dbGAP											0													115.0	115.0	115.0					3																	192517061		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK056276	CCDS3302.2	3q28-q29	2011-02-23	2011-02-23	2011-02-23	ENSG00000180611	ENSG00000180611			30438	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 59"""	C3orf59		12477932	Standard	NM_178496		Approved		uc011bsp.2	Q8IYB1	OTTHUMG00000155768	ENST00000392452.2:c.590C>T	3.37:g.192517061G>A	ENSP00000376246:p.Ser197Leu		Q86VD8	Missense_Mutation	SNP	pfam_Mab-21_dom	p.S197L	ENST00000392452.2	37	c.590	CCDS3302.2	3	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	9.865	1.197494	0.22037	.	.	ENSG00000180611	ENST00000392452	T	0.09073	3.02	5.63	5.63	0.86233	.	0.246855	0.38720	N	0.001598	T	0.04588	0.0125	N	0.02011	-0.69	0.39956	D	0.9746	B	0.02656	0.0	B	0.01281	0.0	T	0.50825	-0.8782	10	0.37606	T	0.19	.	18.6977	0.91607	0.0:0.0:1.0:0.0	.	197	Q8IYB1	M21D2_HUMAN	L	197	ENSP00000376246:S197L	ENSP00000376246:S197L	S	-	2	0	MB21D2	193999755	1.000000	0.71417	0.055000	0.19348	0.637000	0.38172	6.314000	0.72848	2.652000	0.90054	0.655000	0.94253	TCA	MB21D2	-	NULL	ENSG00000180611		0.463	MB21D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MB21D2	HGNC	protein_coding	OTTHUMT00000341543.1	87	0.00	0	G	NM_178496		192517061	192517061	-1	no_errors	ENST00000392452	ensembl	human	known	69_37n	missense	57	12.31	8	SNP	0.637	A
OXCT1	5019	genome.wustl.edu	37	5	41731834	41731834	+	Missense_Mutation	SNP	A	A	C			TCGA-OL-A5RY-01A-21D-A28B-09	TCGA-OL-A5RY-10A-01D-A28E-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	476465ea-63a7-49d0-8b85-25e02d69b78d	90710e07-11e4-4116-a955-3a58f616acdf	g.chr5:41731834A>C	ENST00000196371.5	-	17	1720	c.1560T>G	c.(1558-1560)aaT>aaG	p.N520K	OXCT1_ENST00000512084.1_Missense_Mutation_p.N123K|OXCT1_ENST00000509987.1_Missense_Mutation_p.N334K|OXCT1_ENST00000510634.1_Missense_Mutation_p.N123K	NM_000436.3	NP_000427.1	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1	520					adipose tissue development (GO:0060612)|brain development (GO:0007420)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular response to acid chemical (GO:0071229)|cellular response to glucose stimulus (GO:0071333)|heart development (GO:0007507)|ketone body catabolic process (GO:0046952)|ketone catabolic process (GO:0042182)|positive regulation of insulin secretion (GO:0032024)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hormone (GO:0009725)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-oxoacid CoA-transferase activity (GO:0008260)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(2)	28					Succinic acid(DB00139)	CCATATTTCAATTTGCGATCT	0.313																																						dbGAP											0													52.0	50.0	51.0					5																	41731834		2203	4299	6502	-	-	-	SO:0001583	missense	0			U62961	CCDS3937.1	5p13	2008-02-05		2004-05-12	ENSG00000083720	ENSG00000083720			8527	protein-coding gene	gene with protein product		601424	"""3-oxoacid CoA transferase"""	OXCT		8751852	Standard	NM_000436		Approved	SCOT	uc003jmn.3	P55809	OTTHUMG00000094783	ENST00000196371.5:c.1560T>G	5.37:g.41731834A>C	ENSP00000196371:p.Asn520Lys		B2R5V2|B7Z528	Missense_Mutation	SNP	pfam_CoA_trans_fam_I,smart_CoA_trans_fam_I,pirsf_3-oxoacid_CoA-transferase,tigrfam_3-oxoacid_CoA-transf_B,tigrfam_3-oxoacid_CoA-transf_A	p.N520K	ENST00000196371.5	37	c.1560	CCDS3937.1	5	.	.	.	.	.	.	.	.	.	.	A	11.48	1.650093	0.29336	.	.	ENSG00000083720	ENST00000196371;ENST00000512084;ENST00000510634;ENST00000509987	D;D;D;D	0.89875	-1.9;-2.58;-2.58;-2.11	5.66	3.22	0.36961	.	0.495155	0.18396	N	0.142485	T	0.74839	0.3769	N	0.08118	0	0.24081	N	0.995941	B	0.13145	0.007	B	0.11329	0.006	T	0.62959	-0.6743	10	0.44086	T	0.13	.	5.692	0.17835	0.7028:0.1451:0.1521:0.0	.	520	P55809	SCOT1_HUMAN	K	520;123;123;334	ENSP00000196371:N520K;ENSP00000421143:N123K;ENSP00000423144:N123K;ENSP00000425348:N334K	ENSP00000196371:N520K	N	-	3	2	OXCT1	41767591	0.994000	0.37717	0.964000	0.40570	0.273000	0.26683	0.429000	0.21412	0.405000	0.25532	-0.256000	0.11100	AAT	OXCT1	-	pirsf_3-oxoacid_CoA-transferase	ENSG00000083720		0.313	OXCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OXCT1	HGNC	protein_coding	OTTHUMT00000211594.2	39	0.00	0	A	NM_000436		41731834	41731834	-1	no_errors	ENST00000196371	ensembl	human	known	69_37n	missense	27	12.90	4	SNP	0.997	C
PGS1	9489	genome.wustl.edu	37	17	76395617	76395617	+	Splice_Site	SNP	G	G	T			TCGA-OL-A5RY-01A-21D-A28B-09	TCGA-OL-A5RY-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	476465ea-63a7-49d0-8b85-25e02d69b78d	90710e07-11e4-4116-a955-3a58f616acdf	g.chr17:76395617G>T	ENST00000262764.6	+	5	726	c.700G>T	c.(700-702)Ggt>Tgt	p.G234C	SNORA30_ENST00000363193.1_RNA|PGS1_ENST00000329897.7_Splice_Site_p.G99C|PGS1_ENST00000588281.1_3'UTR	NM_024419.3	NP_077733.3	Q32NB8	PGPS1_HUMAN	phosphatidylglycerophosphate synthase 1	234	PLD phosphodiesterase 1. {ECO:0000255|PROSITE-ProRule:PRU00153}.				cardiolipin biosynthetic process (GO:0032049)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity (GO:0008444)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	10			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)			CATCTTGAGCGGGTGAGTGCT	0.587																																					Esophageal Squamous(45;182 1126 10685 43198)	dbGAP											0													82.0	83.0	83.0					17																	76395617		2127	4239	6366	-	-	-	SO:0001630	splice_region_variant	0				CCDS42391.1	17q25.3	2006-02-09							30029	protein-coding gene	gene with protein product		614942				9880566	Standard	XR_243691		Approved	DKFZP762M186	uc002jvm.3	Q32NB8		ENST00000262764.6:c.701+1G>T	17.37:g.76395617G>T			B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Missense_Mutation	SNP	pirsf_PLipase-D_PtdSer-synthase-type,pfscan_PLipase_D/transphosphatidylase	p.G234C	ENST00000262764.6	37	c.700	CCDS42391.1	17	.	.	.	.	.	.	.	.	.	.	G	29.7	5.031057	0.93575	.	.	ENSG00000087157	ENST00000262764;ENST00000329897;ENST00000335081	T;T	0.73363	-0.74;-0.74	5.56	5.56	0.83823	Phospholipase D/Transphosphatidylase (1);	0.105281	0.64402	D	0.000005	D	0.90539	0.7035	H	0.94542	3.55	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.92752	0.6217	10	0.87932	D	0	-16.0688	19.5245	0.95199	0.0:0.0:1.0:0.0	.	234	Q32NB8	PGPS1_HUMAN	C	234;99;99	ENSP00000262764:G234C;ENSP00000330039:G99C	ENSP00000262764:G234C	G	+	1	0	PGS1	73907212	1.000000	0.71417	0.997000	0.53966	0.925000	0.55904	9.197000	0.94985	2.608000	0.88229	0.655000	0.94253	GGT	PGS1	-	pirsf_PLipase-D_PtdSer-synthase-type,pfscan_PLipase_D/transphosphatidylase	ENSG00000087157		0.587	PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PGS1	HGNC	protein_coding	OTTHUMT00000437301.1	45	0.00	0	G	NM_024419	Missense_Mutation	76395617	76395617	+1	no_errors	ENST00000262764	ensembl	human	known	69_37n	missense	35	10.26	4	SNP	1.000	T
PHC2	1912	genome.wustl.edu	37	1	33789638	33789638	+	3'UTR	SNP	C	C	T	rs10914683	byFrequency	TCGA-OL-A5RY-01A-21D-A28B-09	TCGA-OL-A5RY-10A-01D-A28E-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	476465ea-63a7-49d0-8b85-25e02d69b78d	90710e07-11e4-4116-a955-3a58f616acdf	g.chr1:33789638C>T	ENST00000257118.5	-	0	3458				RP11-415J8.3_ENST00000588828.1_RNA|PHC2_ENST00000373418.3_3'UTR|A3GALT2_ENST00000442999.3_5'Flank|RP11-415J8.3_ENST00000457957.2_RNA|PHC2_ENST00000485928.1_5'UTR|RP11-415J8.3_ENST00000587696.1_RNA|PHC2_ENST00000373422.3_3'UTR|PHC2_ENST00000431992.1_3'UTR	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)						multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				TCTTTGTGAACCAGGAGGGCG	0.607													C|||	84	0.0167732	0.0522	0.0144	5008	,	,		18285	0.0		0.0	False		,,,				2504	0.0051					dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0			AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"""Sterile alpha motif (SAM) domain containing"""	3183	protein-coding gene	gene with protein product		602979	"""early development regulator 2 (homolog of polyhomeotic 2)"", ""polyhomeotic-like 2 (Drosophila)"""	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.*828G>A	1.37:g.33789638C>T			A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	RNA	SNP	-	NULL	ENST00000257118.5	37	NULL	CCDS378.1	1																																																																																			PHC2	-	-	ENSG00000134686		0.607	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	PHC2	HGNC	protein_coding	OTTHUMT00000011895.1	8	0.00	0	C	NM_198040		33789638	33789638	-1	no_errors	ENST00000485928	ensembl	human	known	69_37n	rna	4	60.00	6	SNP	0.632	T
PTPRZ1	5803	genome.wustl.edu	37	7	121513368	121513369	+	5'UTR	DEL	TG	TG	-			TCGA-OL-A5RY-01A-21D-A28B-09	TCGA-OL-A5RY-10A-01D-A28E-09	TG	TG					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	476465ea-63a7-49d0-8b85-25e02d69b78d	90710e07-11e4-4116-a955-3a58f616acdf	g.chr7:121513368_121513369delTG	ENST00000393386.2	+	0	226_227				PTPRZ1_ENST00000449182.1_5'Flank	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1						axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						tctctgtctctgtctctctctc	0.525																																						dbGAP											0																																										-	-	-	SO:0001623	5_prime_UTR_variant	0			M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.-185TG>-	7.37:g.121513368_121513369delTG			A4D0W5|C9JFM0|O76043|Q9UDR6	RNA	DEL	-	NULL	ENST00000393386.2	37	NULL	CCDS34740.1	7																																																																																			PTPRZ1	-	-	ENSG00000106278		0.525	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PTPRZ1	HGNC	protein_coding	OTTHUMT00000347288.1	14	0.00	0	TG	NM_002851		121513368	121513369	+1	no_errors	ENST00000471837	ensembl	human	known	69_37n	rna	3	40.00	2	DEL	0.000:0.000	-
TCHH	7062	genome.wustl.edu	37	1	152083754	152083754	+	Missense_Mutation	SNP	G	G	C			TCGA-OL-A5RY-01A-21D-A28B-09	TCGA-OL-A5RY-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	476465ea-63a7-49d0-8b85-25e02d69b78d	90710e07-11e4-4116-a955-3a58f616acdf	g.chr1:152083754G>C	ENST00000368804.1	-	2	1938	c.1939C>G	c.(1939-1941)Cta>Gta	p.L647V		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	647	9 X 28 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCGCGCCTTAGTTGCTGCTGG	0.672																																						dbGAP											0													48.0	56.0	53.0					1																	152083754		2012	4172	6184	-	-	-	SO:0001583	missense	0			L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1939C>G	1.37:g.152083754G>C	ENSP00000357794:p.Leu647Val		Q5VUI3	Missense_Mutation	SNP	pfam_S100_Ca-bd_sub,pfscan_EF_HAND_2	p.L647V	ENST00000368804.1	37	c.1939	CCDS41396.1	1	.	.	.	.	.	.	.	.	.	.	g	6.091	0.385112	0.11524	.	.	ENSG00000159450	ENST00000368804	T	0.06933	3.24	3.02	-2.65	0.06095	.	.	.	.	.	T	0.01765	0.0056	L	0.27053	0.805	0.09310	N	1	B	0.25486	0.127	B	0.22601	0.04	T	0.43261	-0.9402	9	0.22706	T	0.39	.	12.447	0.55657	0.0:0.7157:0.2843:0.0	.	647	Q07283	TRHY_HUMAN	V	647	ENSP00000357794:L647V	ENSP00000357794:L647V	L	-	1	2	TCHH	150350378	0.067000	0.21026	0.000000	0.03702	0.016000	0.09150	2.030000	0.41108	-0.183000	0.10585	0.388000	0.25769	CTA	TCHH	-	NULL	ENSG00000159450		0.672	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TCHH	HGNC	protein_coding	OTTHUMT00000036671.2	128	0.00	0	G	NM_007113		152083754	152083754	-1	no_errors	ENST00000368804	ensembl	human	known	69_37n	missense	113	11.02	14	SNP	0.000	C
TIAM1	7074	genome.wustl.edu	37	21	32624173	32624173	+	Silent	SNP	G	G	A			TCGA-OL-A5RY-01A-21D-A28B-09	TCGA-OL-A5RY-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	476465ea-63a7-49d0-8b85-25e02d69b78d	90710e07-11e4-4116-a955-3a58f616acdf	g.chr21:32624173G>A	ENST00000286827.3	-	6	1767	c.1296C>T	c.(1294-1296)ggC>ggT	p.G432G	TIAM1_ENST00000541036.1_Silent_p.G432G|TIAM1_ENST00000469412.1_5'UTR	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	432					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						TGCGCACCGTGCCCTGTGCGG	0.657																																						dbGAP											0													64.0	67.0	66.0					21																	32624173		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.1296C>T	21.37:g.32624173G>A			B7ZLR6|F5GZ53|Q17RT7	Silent	SNP	pfam_DH-domain,pfam_Pleckstrin_homology,pfam_Raf-like_ras-bd,pfam_PDZ,superfamily_DH-domain,superfamily_PDZ,smart_Pleckstrin_homology,smart_Raf-like_ras-bd,smart_PDZ,smart_DH-domain,pfscan_PDZ,pfscan_Pleckstrin_homology,pfscan_Raf-like_ras-bd,pfscan_DH-domain	p.G432	ENST00000286827.3	37	c.1296	CCDS13609.1	21																																																																																			TIAM1	-	NULL	ENSG00000156299		0.657	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TIAM1	HGNC	protein_coding	OTTHUMT00000192552.1	62	0.00	0	G	NM_003253		32624173	32624173	-1	no_errors	ENST00000286827	ensembl	human	known	69_37n	silent	48	11.11	6	SNP	0.995	A
TP53	7157	genome.wustl.edu	37	17	7578393	7578393	+	Missense_Mutation	SNP	A	A	T			TCGA-OL-A5RY-01A-21D-A28B-09	TCGA-OL-A5RY-10A-01D-A28E-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	476465ea-63a7-49d0-8b85-25e02d69b78d	90710e07-11e4-4116-a955-3a58f616acdf	g.chr17:7578393A>T	ENST00000269305.4	-	5	726	c.537T>A	c.(535-537)caT>caA	p.H179Q	TP53_ENST00000455263.2_Missense_Mutation_p.H179Q|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000445888.2_Missense_Mutation_p.H179Q|TP53_ENST00000359597.4_Missense_Mutation_p.H179Q|TP53_ENST00000420246.2_Missense_Mutation_p.H179Q|TP53_ENST00000413465.2_Missense_Mutation_p.H179Q	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	179	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		H -> D (in sporadic cancers; somatic mutation).|H -> L (in sporadic cancers; somatic mutation).|H -> N (in sporadic cancers; somatic mutation).|H -> P (in sporadic cancers; somatic mutation).|H -> Q (in sporadic cancers; somatic mutation).|H -> R (in sporadic cancers; somatic mutation).|H -> Y (in LFS; germline mutation and in sporadic cancers; somatic mutation).|HH -> QS (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.H179Q(23)|p.P177_C182delPHHERC(8)|p.0?(8)|p.C176_R181delCPHHER(3)|p.R174fs*24(3)|p.H178_S183delHHERCS(3)|p.R175_E180delRCPHHE(3)|p.H179H(2)|p.P177fs*3(2)|p.V173fs*59(2)|p.H86Q(2)|p.H47Q(2)|p.C176fs*65(1)|p.P177_H179delPHH(1)|p.V173fs*23(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.H46_S51delHHERCS(1)|p.H178fs*6(1)|p.P177_E180delPHHE(1)|p.R42fs*24(1)|p.H85_S90delHHERCS(1)|p.R174fs*3(1)|p.E171fs*61(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)	AGCAGCGCTCATGGTGGGGGC	0.642		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"""	76	Substitution - Missense(27)|Deletion - In frame(24)|Deletion - Frameshift(14)|Whole gene deletion(8)|Substitution - coding silent(2)|Complex - deletion inframe(1)	large_intestine(18)|breast(10)|upper_aerodigestive_tract(8)|lung(7)|liver(7)|haematopoietic_and_lymphoid_tissue(5)|ovary(5)|bone(5)|central_nervous_system(4)|stomach(2)|oesophagus(2)|pancreas(2)|endometrium(1)											47.0	47.0	47.0					17																	7578393		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.537T>A	17.37:g.7578393A>T	ENSP00000269305:p.His179Gln		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.H179Q	ENST00000269305.4	37	c.537	CCDS11118.1	17	.	.	.	.	.	.	.	.	.	.	A	23.0	4.360270	0.82353	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99909	-7.87;-7.87;-7.87;-7.87;-7.87;-7.87;-7.87;-7.87	5.47	-9.19	0.00685	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.048592	0.85682	N	0.000000	D	0.99878	0.9942	M	0.92507	3.315	0.58432	D	0.999998	D;D;D;D;D;D;D	0.89917	0.989;1.0;0.995;1.0;0.996;1.0;0.999	D;D;D;D;D;D;D	0.97110	0.952;0.997;0.939;1.0;0.985;0.995;0.971	D	0.99861	1.1083	10	0.87932	D	0	-15.4889	14.291	0.66278	0.2679:0.1015:0.6306:0.0	.	140;179;179;86;179;179;179	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	Q	179;179;179;179;179;179;168;86;47;86;47	ENSP00000410739:H179Q;ENSP00000352610:H179Q;ENSP00000269305:H179Q;ENSP00000398846:H179Q;ENSP00000391127:H179Q;ENSP00000391478:H179Q;ENSP00000425104:H47Q;ENSP00000423862:H86Q	ENSP00000269305:H179Q	H	-	3	2	TP53	7519118	0.081000	0.21417	0.351000	0.25721	0.844000	0.47949	-0.635000	0.05471	-2.028000	0.00931	-0.376000	0.06991	CAT	TP53	-	pfam_p53_DNA-bd,superfamily_p53-like_TF_DNA-bd,prints_p53_tumour_suppressor	ENSG00000141510		0.642	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TP53	HGNC	protein_coding	OTTHUMT00000367397.1	33	0.00	0	A	NM_000546		7578393	7578393	-1	no_errors	ENST00000269305	ensembl	human	known	69_37n	missense	14	17.65	3	SNP	0.699	T
TSPYL1	7259	genome.wustl.edu	37	6	116600681	116600681	+	Missense_Mutation	SNP	C	C	T			TCGA-OL-A5RY-01A-21D-A28B-09	TCGA-OL-A5RY-10A-01D-A28E-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	476465ea-63a7-49d0-8b85-25e02d69b78d	90710e07-11e4-4116-a955-3a58f616acdf	g.chr6:116600681C>T	ENST00000368608.3	-	1	385	c.313G>A	c.(313-315)Gcc>Acc	p.A105T	RP1-93H18.1_ENST00000449314.1_lincRNA|DSE_ENST00000452085.3_5'Flank|DSE_ENST00000540275.1_Intron	NM_003309.3	NP_003300.1	Q9H0U9	TSYL1_HUMAN	TSPY-like 1	105					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)	enzyme binding (GO:0019899)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(3)|urinary_tract(1)	11		all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234)		all cancers(137;0.0235)|OV - Ovarian serous cystadenocarcinoma(136;0.0469)|GBM - Glioblastoma multiforme(226;0.0503)|Epithelial(106;0.094)		AGGCCTTCGGCGGGAGGCTGG	0.662																																						dbGAP											0													27.0	32.0	31.0					6																	116600681		2201	4290	6491	-	-	-	SO:0001583	missense	0			AF042181	CCDS34518.1	6q22.1	2014-09-17	2004-04-05	2004-04-07	ENSG00000189241	ENSG00000189241			12382	protein-coding gene	gene with protein product		604714	"""TSPY-like"""	TSPYL		9730615	Standard	NM_003309		Approved		uc003pwp.4	Q9H0U9	OTTHUMG00000015427	ENST00000368608.3:c.313G>A	6.37:g.116600681C>T	ENSP00000357597:p.Ala105Thr		O75885|Q5TFE6	Missense_Mutation	SNP	pfam_NAP_family	p.A105T	ENST00000368608.3	37	c.313	CCDS34518.1	6	.	.	.	.	.	.	.	.	.	.	C	1.724	-0.495958	0.04291	.	.	ENSG00000189241	ENST00000368608;ENST00000545830	T	0.21734	1.99	4.19	-8.38	0.00973	.	2.785180	0.01507	N	0.017775	T	0.01353	0.0044	N	0.11064	0.09	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.29882	-0.9997	10	0.06099	T	0.92	4.2835	0.9256	0.01324	0.2822:0.4208:0.1745:0.1225	.	105	Q9H0U9	TSYL1_HUMAN	T	105	ENSP00000357597:A105T	ENSP00000357597:A105T	A	-	1	0	TSPYL1	116707374	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.569000	0.00915	-2.892000	0.00315	-0.367000	0.07326	GCC	TSPYL1	-	NULL	ENSG00000189241		0.662	TSPYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TSPYL1	HGNC	protein_coding	OTTHUMT00000041929.1	59	0.00	0	C			116600681	116600681	-1	no_errors	ENST00000368608	ensembl	human	known	69_37n	missense	36	12.20	5	SNP	0.000	T
WHSC1L1	54904	genome.wustl.edu	37	8	38174774	38174774	+	Intron	SNP	G	G	T			TCGA-OL-A5RY-01A-21D-A28B-09	TCGA-OL-A5RY-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	476465ea-63a7-49d0-8b85-25e02d69b78d	90710e07-11e4-4116-a955-3a58f616acdf	g.chr8:38174774G>T	ENST00000317025.8	-	10	2373				WHSC1L1_ENST00000527502.1_Intron|WHSC1L1_ENST00000316985.3_3'UTR|WHSC1L1_ENST00000525081.1_5'UTR|WHSC1L1_ENST00000433384.2_Intron	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1						histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			TTCACTGAATGTTTCCTGACA	0.438			T	NUP98	AML																																	dbGAP		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	0																																										-	-	-	SO:0001627	intron_variant	0			AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548			12767	protein-coding gene	gene with protein product		607083				10802047, 23269674	Standard	NM_023034		Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.1856-1214C>A	8.37:g.38174774G>T			B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	RNA	SNP	-	NULL	ENST00000317025.8	37	NULL	CCDS43729.1	8																																																																																			WHSC1L1	-	-	ENSG00000147548		0.438	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WHSC1L1	HGNC	protein_coding	OTTHUMT00000381924.3	32	0.00	0	G	NM_023034		38174774	38174774	-1	no_errors	ENST00000525081	ensembl	human	known	69_37n	rna	18	14.29	3	SNP	1.000	T
ZDHHC11	79844	genome.wustl.edu	37	5	833915	833915	+	Missense_Mutation	SNP	G	G	T	rs605088	byFrequency	TCGA-OL-A5RY-01A-21D-A28B-09	TCGA-OL-A5RY-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	476465ea-63a7-49d0-8b85-25e02d69b78d	90710e07-11e4-4116-a955-3a58f616acdf	g.chr5:833915G>T	ENST00000283441.8	-	7	1291	c.908C>A	c.(907-909)gCt>gAt	p.A303D	ZDHHC11_ENST00000503758.2_5'UTR|ZDHHC11_ENST00000424784.2_Missense_Mutation_p.A303D	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	303						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.A303D(10)		haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			CAGGGCGCCAGCTCCTTGCTG	0.438																																						dbGAP											10	Substitution - Missense(10)	prostate(8)|liver(2)											8.0	8.0	8.0					5																	833915		2154	4191	6345	-	-	-	SO:0001583	missense	0			AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"""Zinc fingers, DHHC-type"""	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.908C>A	5.37:g.833915G>T	ENSP00000283441:p.Ala303Asp		Q6UWR9	Missense_Mutation	SNP	pfam_Znf_DHHC_palmitoyltrfase,pfscan_Znf_DHHC_palmitoyltrfase	p.A303D	ENST00000283441.8	37	c.908	CCDS3857.1	5	515	0.2358058608058608	134	0.27235772357723576	83	0.2292817679558011	145	0.2534965034965035	153	0.20184696569920843	t	0.056	-1.237364	0.01493	.	.	ENSG00000188818	ENST00000424784;ENST00000283441	T;T	0.32023	1.47;1.47	1.32	-2.64	0.06114	.	159.412000	0.01375	U	0.012736	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.24333	-1.0163	9	0.30854	T	0.27	.	0.5085	0.00591	0.2028:0.3259:0.2042:0.267	rs605088;rs4045358;rs59272565	303	Q9H8X9	ZDH11_HUMAN	D	303	ENSP00000397719:A303D;ENSP00000283441:A303D	ENSP00000283441:A303D	A	-	2	0	ZDHHC11	886915	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-2.877000	0.00717	-2.317000	0.00644	-1.448000	0.01049	GCT	ZDHHC11	-	NULL	ENSG00000188818		0.438	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZDHHC11	HGNC	protein_coding	OTTHUMT00000206681.3	34	0.00	0	G	NM_024786		833915	833915	-1	no_errors	ENST00000283441	ensembl	human	known	69_37n	missense	20	28.57	8	SNP	0.000	T
