#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_Mutation_Status	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
COMMD1	150684	broad.mit.edu	37	2	62132935	62132935	+	Missense_Mutation	SNP	C	C	A			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	6f4ff365-ee63-40d0-8f71-ed062f755d22	g.chr2:62132935C>A	ENST00000311832.5	+	1	154	c.122C>A	c.(121-123)cCa>cAa	p.P41Q	COMMD1_ENST00000538736.1_Missense_Mutation_p.P41Q|COMMD1_ENST00000472729.1_Intron	NM_152516.2	NP_689729.1	Q8N668	COMD1_HUMAN	copper metabolism (Murr1) domain containing 1	41					copper ion homeostasis (GO:0055070)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of protein ubiquitination (GO:0031398)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			large_intestine(1)|liver(2)|lung(5)|ovary(1)	9	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)			CAGCTATATCCAGAGGTGCCA	0.597																																						uc002sbp.3																			0				large_intestine(1)|liver(2)|lung(5)|ovary(1)	9						c.(121-123)cCa>cAa		Homo sapiens copper metabolism (Murr1) domain containing 1 (COMMD1), mRNA.							45.0	46.0	46.0					2																	62132935		2203	4300	6503	SO:0001583	missense	150684				copper ion homeostasis|negative regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|regulation of proteasomal ubiquitin-dependent protein catabolic process	Cul2-RING ubiquitin ligase complex|cell junction|cytoplasm|nucleolus	copper ion binding|protein homodimerization activity	g.chr2:62132935C>A	BC022046	CCDS1869.1	2p15	2004-03-02	2004-02-13	2004-02-18	ENSG00000173163	ENSG00000173163			23024	protein-coding gene	gene with protein product	"""copper metabolism gene MURR1"""	607238	"""chromosome 2 open reading frame 5 (MURR1)"""	C2orf5		9001233, 11809725	Standard	NM_152516		Approved	MURR1, MGC27155	uc002sbp.3	Q8N668	OTTHUMG00000129445	ENST00000311832.5:c.122C>A	2.37:g.62132935C>A	ENSP00000308236:p.Pro41Gln		Somatic					p.P41Q	NM_152516	NP_689729	WXS	Illumina GAIIx	Phase_I	Q8N668	COMD1_HUMAN	LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)		0	133	+	Lung NSC(7;0.035)|all_lung(7;0.0691)		41					B4DFQ4|Q96GS0	Missense_Mutation	SNP	ENST00000311832.5	37	c.122C>A	CCDS1869.1	.	.	.	.	.	.	.	.	.	.	C	15.64	2.893634	0.52121	.	.	ENSG00000173163	ENST00000311832;ENST00000538736	T;T	0.09630	2.96;2.96	5.6	4.72	0.59763	.	0.052645	0.85682	D	0.000000	T	0.28732	0.0712	M	0.74258	2.255	0.45662	D	0.998588	D	0.69078	0.997	D	0.64144	0.922	T	0.02226	-1.1192	10	0.87932	D	0	.	10.4553	0.44546	0.0:0.9107:0.0:0.0893	.	41	Q8N668	COMD1_HUMAN	Q	41	ENSP00000308236:P41Q;ENSP00000438961:P41Q	ENSP00000308236:P41Q	P	+	2	0	COMMD1	61986439	0.992000	0.36948	0.759000	0.31340	0.307000	0.27823	4.186000	0.58337	1.377000	0.46286	0.655000	0.94253	CCA		0.597	COMMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251607.2	NM_152516		3	49	0	0	0	1	0	3	49				
NEIL3	55247	broad.mit.edu	37	4	178283471	178283471	+	Missense_Mutation	SNP	A	A	G			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	6f4ff365-ee63-40d0-8f71-ed062f755d22	g.chr4:178283471A>G	ENST00000264596.3	+	10	1782	c.1664A>G	c.(1663-1665)aAc>aGc	p.N555S		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	555					base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		CCATTCTGCAACCATGGCAAG	0.388								Base excision repair (BER), DNA glycosylases																														uc003iut.2																			0				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						c.(1663-1665)aAc>aGc	Base excision repair (BER), DNA glycosylases	Homo sapiens nei endonuclease VIII-like 3 (E. coli) (NEIL3), mRNA.							92.0	93.0	93.0					4																	178283471		2203	4300	6503	SO:0001583	missense	55247				base-excision repair|nucleotide-excision repair	nucleus	DNA N-glycosylase activity|DNA-(apurinic or apyrimidinic site) lyase activity|bubble DNA binding|damaged DNA binding|double-stranded DNA binding|single-stranded DNA binding|zinc ion binding	g.chr4:178283471A>G	AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 3"""	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.1664A>G	4.37:g.178283471A>G	ENSP00000264596:p.Asn555Ser		Somatic					p.N555S	NM_018248	NP_060718	WXS	Illumina GAIIx	Phase_I	Q8TAT5	NEIL3_HUMAN		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)	9	1781	+		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)	555					Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	37	c.1664A>G	CCDS3828.1	.	.	.	.	.	.	.	.	.	.	A	10.79	1.449111	0.26074	.	.	ENSG00000109674	ENST00000264596	T	0.23348	1.91	4.63	0.95	0.19572	Zinc finger, GRF-type (1);	0.471433	0.22895	N	0.054335	T	0.14399	0.0348	N	0.17082	0.46	0.25080	N	0.990939	B	0.20368	0.044	B	0.23150	0.044	T	0.18903	-1.0322	10	0.52906	T	0.07	-2.0469	8.175	0.31276	0.768:0.0:0.232:0.0	.	555	Q8TAT5	NEIL3_HUMAN	S	555	ENSP00000264596:N555S	ENSP00000264596:N555S	N	+	2	0	NEIL3	178520465	1.000000	0.71417	0.991000	0.47740	0.736000	0.42039	1.495000	0.35627	0.095000	0.17434	-0.415000	0.06103	AAC		0.388	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248		15	73	0	0	0	1	0	15	73				
CDK5RAP1	51654	broad.mit.edu	37	20	31981850	31981850	+	Missense_Mutation	SNP	G	G	A			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	6f4ff365-ee63-40d0-8f71-ed062f755d22	g.chr20:31981850G>A	ENST00000357886.4	-	4	584	c.431C>T	c.(430-432)aCa>aTa	p.T144I	CDK5RAP1_ENST00000544843.1_Missense_Mutation_p.T144I|CDK5RAP1_ENST00000477105.1_5'UTR|CDK5RAP1_ENST00000346416.2_Missense_Mutation_p.T144I|CDK5RAP1_ENST00000473997.1_Missense_Mutation_p.T54I|CDK5RAP1_ENST00000339269.5_Missense_Mutation_p.T144I			Q96SZ6	CK5P1_HUMAN	CDK5 regulatory subunit associated protein 1	144	CDK5 activation inhibition.|MTTase N-terminal.				brain development (GO:0007420)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|regulation of neuron differentiation (GO:0045664)|tRNA modification (GO:0006400)	cytoplasm (GO:0005737)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|transferase activity (GO:0016740)			endometrium(2)|kidney(2)|large_intestine(3)|lung(12)|ovary(3)|skin(3)|urinary_tract(1)	26						GATAGAGCATGTGACAAGGAG	0.403																																						uc010gek.3																			0				endometrium(2)|kidney(2)|large_intestine(3)|lung(12)|ovary(3)|skin(3)|urinary_tract(1)	26						c.(430-432)aCa>aTa		Homo sapiens CDK5 regulatory subunit associated protein 1 (CDK5RAP1), transcript variant 1, mRNA.							105.0	97.0	100.0					20																	31981850		2203	4300	6503	SO:0001583	missense	51654				brain development|negative regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation|tRNA modification	cytoplasm	4 iron, 4 sulfur cluster binding|metal ion binding|neuronal Cdc2-like kinase binding|transferase activity	g.chr20:31981850G>A	AF152097	CCDS13219.1, CCDS63255.1	20q11.21	2012-09-20	2002-07-22	2002-07-26	ENSG00000101391	ENSG00000101391			15880	protein-coding gene	gene with protein product		608200	"""chromosome 20 open reading frame 34"""	C20orf34		10721722, 11882646, 15329498	Standard	NM_016408		Approved	CGI-05, HSPC167, C42	uc002wyy.4	Q96SZ6	OTTHUMG00000032256	ENST00000357886.4:c.431C>T	20.37:g.31981850G>A	ENSP00000350558:p.Thr144Ile		Somatic				CDK5RAP1_uc002wyy.3_Missense_Mutation_p.T54I|CDK5RAP1_uc002wyz.3_Missense_Mutation_p.T144I|CDK5RAP1_uc002wza.3_Missense_Mutation_p.T144I|CDK5RAP1_uc010gel.3_Missense_Mutation_p.T54I|CDK5RAP1_uc010gem.3_Missense_Mutation_p.T144I|CDK5RAP1_uc002wzc.1_Missense_Mutation_p.T144I|CDK5RAP1_uc010gen.3_Missense_Mutation_p.T144I	p.T144I	NM_016408	NP_057492	WXS	Illumina GAIIx	Phase_I	Q96SZ6	CK5P1_HUMAN			3	555	-			144			CDK5 activation inhibition.|MTTase N-terminal.		A8K7R0|Q5QP46|Q5QP47|Q5QP48|Q675N4|Q675N5|Q9BVG6|Q9BWZ5|Q9H859|Q9NZZ9|Q9Y3F0	Missense_Mutation	SNP	ENST00000357886.4	37	c.431C>T		.	.	.	.	.	.	.	.	.	.	G	18.02	3.529834	0.64860	.	.	ENSG00000101391	ENST00000346416;ENST00000357886;ENST00000339269;ENST00000452723;ENST00000375351;ENST00000544843	.	.	.	4.48	4.48	0.54585	Methylthiotransferase, N-terminal (2);	0.000000	0.85682	D	0.000000	D	0.91205	0.7229	H	0.99770	4.765	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.997;1.0;1.0;1.0;1.0;1.0	D	0.94720	0.7900	9	0.87932	D	0	-11.5027	15.0177	0.71600	0.0:0.0:1.0:0.0	.	144;144;144;144;144;144;54	Q675N4;Q96SZ6-4;Q96SZ6;Q675N5;Q53H36;Q96SZ6-3;Q96SZ6-2	.;.;CK5P1_HUMAN;.;.;.;.	I	144;144;144;54;34;144	.	ENSP00000341840:T144I	T	-	2	0	CDK5RAP1	31445511	1.000000	0.71417	0.977000	0.42913	0.483000	0.33249	8.770000	0.91746	2.481000	0.83766	0.313000	0.20887	ACA		0.403	CDK5RAP1-011	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000078697.1	NM_016408		5	87	0	0	0	1	0	5	87				
POLR1A	25885	broad.mit.edu	37	2	86297188	86297188	+	Missense_Mutation	SNP	C	C	T			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	6f4ff365-ee63-40d0-8f71-ed062f755d22	g.chr2:86297188C>T	ENST00000263857.6	-	13	2197	c.1819G>A	c.(1819-1821)Gag>Aag	p.E607K	POLR1A_ENST00000409681.1_Missense_Mutation_p.E607K			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	607					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						ACGTAGGCCTCGGCCCGGCCC	0.572																																						uc002sqs.3																			0				NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						c.(1819-1821)Gag>Aag		Homo sapiens polymerase (RNA) I polypeptide A, 194kDa (POLR1A), mRNA.							40.0	42.0	41.0					2																	86297188		2028	4167	6195	SO:0001583	missense	25885				termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding	g.chr2:86297188C>T	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"""RNA polymerase subunits"""	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.1819G>A	2.37:g.86297188C>T	ENSP00000263857:p.Glu607Lys		Somatic					p.E607K	NM_015425	NP_056240	WXS	Illumina GAIIx	Phase_I	O95602	RPA1_HUMAN			12	2198	-			607					B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	37	c.1819G>A	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.709521	0.89018	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	D;D	0.95238	-3.65;-3.65	5.3	5.3	0.74995	RNA polymerase, alpha subunit (1);RNA polymerase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98554	0.9517	H	0.98351	4.21	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99787	1.1030	10	0.87932	D	0	-30.4857	18.5668	0.91119	0.0:1.0:0.0:0.0	.	607	O95602	RPA1_HUMAN	K	607	ENSP00000263857:E607K;ENSP00000386300:E607K	ENSP00000263857:E607K	E	-	1	0	POLR1A	86150699	1.000000	0.71417	0.945000	0.38365	0.949000	0.60115	7.466000	0.80914	2.479000	0.83701	0.655000	0.94253	GAG		0.572	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		19	15	0	0	0	1	0	19	15				
TP53BP1	7158	broad.mit.edu	37	15	43738684	43738684	+	Missense_Mutation	SNP	C	C	A			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	6f4ff365-ee63-40d0-8f71-ed062f755d22	g.chr15:43738684C>A	ENST00000263801.3	-	14	3178	c.2926G>T	c.(2926-2928)Ggg>Tgg	p.G976W	TP53BP1_ENST00000450115.2_Missense_Mutation_p.G981W|TP53BP1_ENST00000382039.3_Missense_Mutation_p.G981W|TP53BP1_ENST00000382044.4_Missense_Mutation_p.G981W|TP53BP1_ENST00000605155.1_5'Flank	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	976					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		GGGGCAGCCCCAGAATCCCCT	0.473								Other conserved DNA damage response genes																														uc001zrr.4																			0				breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72						c.(2941-2943)Ggg>Tgg	Other conserved DNA damage response genes	Homo sapiens tumor protein p53 binding protein 1 (TP53BP1), transcript variant 1, mRNA.							101.0	101.0	101.0					15																	43738684		2201	4298	6499	SO:0001583	missense	7158				double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter	condensed chromosome kinetochore|cytoplasm|nucleoplasm	RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity|p53 binding	g.chr15:43738684C>A	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"""tumor protein p53-binding protein, 1"""			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.2926G>T	15.37:g.43738684C>A	ENSP00000263801:p.Gly976Trp		Somatic				TP53BP1_uc010udp.2_Missense_Mutation_p.G976W|TP53BP1_uc001zrq.4_Missense_Mutation_p.G981W|TP53BP1_uc001zrs.3_Missense_Mutation_p.G976W|TP53BP1_uc010udq.1_Missense_Mutation_p.G981W	p.G981W	NM_001141980	NP_005648	WXS	Illumina GAIIx	Phase_I	Q12888	TP53B_HUMAN		GBM - Glioblastoma multiforme(94;1.59e-06)	13	3054	-		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)	976					F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	37	c.2941G>T	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	C	18.75	3.691599	0.68271	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115;ENST00000413546	T;T;T;T;T	0.10005	3.71;3.71;3.71;3.71;2.92	5.47	4.54	0.55810	.	0.636189	0.16408	N	0.215760	T	0.27384	0.0672	M	0.65975	2.015	0.24486	N	0.994329	D;D;D;D	0.69078	0.991;0.994;0.997;0.997	P;P;D;D	0.65140	0.88;0.858;0.932;0.932	T	0.02610	-1.1134	10	0.72032	D	0.01	-2.455	10.7683	0.46308	0.1332:0.7931:0.0:0.0737	.	981;976;981;981	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	W	976;981;981;981;941	ENSP00000263801:G976W;ENSP00000371475:G981W;ENSP00000371470:G981W;ENSP00000393497:G981W;ENSP00000388028:G941W	ENSP00000263801:G976W	G	-	1	0	TP53BP1	41525976	0.483000	0.25956	1.000000	0.80357	0.990000	0.78478	0.860000	0.27871	2.729000	0.93468	0.655000	0.94253	GGG		0.473	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			84	87	0	0	0	1	0	84	87				
SLC25A22	79751	broad.mit.edu	37	11	799816	799816	+	5'Flank	SNP	G	G	A			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	6f4ff365-ee63-40d0-8f71-ed062f755d22	g.chr11:799816G>A	ENST00000531214.1	-	0	0				PIDD_ENST00000347755.5_Splice_Site_p.R825W|PIDD_ENST00000411829.2_Splice_Site_p.R808W	NM_001191060.1	NP_001177989.1	Q9H936	GHC1_HUMAN	solute carrier family 25 (mitochondrial carrier: glutamate), member 22						L-glutamate transport (GO:0015813)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			endometrium(1)|kidney(1)|lung(2)|urinary_tract(1)	5		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;6.27e-26)|Epithelial(43;4.84e-25)|OV - Ovarian serous cystadenocarcinoma(40;2.72e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GAGCCTCACCGGAACTCGTGC	0.687																																					Colon(93;848 1468 3270 23355 49636)	uc001lro.2																			0											c.e15+1		Homo sapiens p53-induced death domain protein (PIDD), transcript variant 1, mRNA.							12.0	15.0	14.0					11																	799816		2170	4272	6442	SO:0001631	upstream_gene_variant	55367				apoptosis|signal transduction	cytoplasm|nucleus	death receptor binding	g.chr11:799816G>A	AJ428202	CCDS7715.1	11p15.5	2013-05-22			ENSG00000177542	ENSG00000177542		"""Solute carriers"""	19954	protein-coding gene	gene with protein product		609302				11897791	Standard	NM_024698		Approved	GC1, FLJ13044, NET44, EIEE3	uc001lrj.3	Q9H936	OTTHUMG00000133310		11.37:g.799816G>A	Exception_encountered		Somatic				SLC25A22_uc009yci.3_5'Flank|SLC25A22_uc001lrj.3_5'Flank|PIDD_uc009yck.1_Splice_Site|PIDD_uc001lrl.1_Splice_Site_p.R668_splice|PIDD_uc001lrm.1_Splice_Site_p.R512_splice|PIDD_uc001lrn.2_Splice_Site_p.R668_splice|PIDD_uc001lrk.2_Splice_Site_p.R808_splice|PIDD_uc001lrp.2_3'UTR	p.R825_splice	NM_145886	NP_665893	WXS	Illumina GAIIx	Phase_I	Q9HB75	PIDD_HUMAN			15	2621	-			825			Death.		A8K366|C9J1H6|E9PJD3|E9PKB2|E9PL68|E9PN26|E9PNQ3|E9PP01|E9PR97|Q8TBU8	Splice_Site	SNP	ENST00000531214.1	37	c.2474_splice	CCDS7715.1	.	.	.	.	.	.	.	.	.	.	G	16.85	3.236950	0.58886	.	.	ENSG00000177595	ENST00000411829;ENST00000347755	D;D	0.86164	-2.08;-2.08	4.1	0.546	0.17196	Death (3);DEATH-like (2);	0.064498	0.64402	D	0.000014	D	0.90177	0.6930	L	0.55990	1.75	0.46954	D	0.999266	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.89009	0.3427	10	0.66056	D	0.02	.	11.9657	0.53033	0.0:0.0:0.2603:0.7397	.	825;668;808	Q9HB75;Q9HB75-3;Q9HB75-2	PIDD_HUMAN;.;.	W	808;825	ENSP00000416801:R808W;ENSP00000337797:R825W	ENSP00000337797:R825W	R	-	1	2	PIDD	789816	1.000000	0.71417	0.993000	0.49108	0.415000	0.31203	1.535000	0.36061	0.306000	0.22856	0.462000	0.41574	CGG		0.687	SLC25A22-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384124.1			2	0	0	0	0	1	0	2	0				
COMMD1	150684	broad.mit.edu	37	2	62132935	62132935	+	Missense_Mutation	SNP	C	C	A			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr2:62132935C>A	ENST00000311832.5	+	1	154	c.122C>A	c.(121-123)cCa>cAa	p.P41Q	COMMD1_ENST00000538736.1_Missense_Mutation_p.P41Q|COMMD1_ENST00000472729.1_Intron	NM_152516.2	NP_689729.1	Q8N668	COMD1_HUMAN	copper metabolism (Murr1) domain containing 1	41					copper ion homeostasis (GO:0055070)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of protein ubiquitination (GO:0031398)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			large_intestine(1)|liver(2)|lung(5)|ovary(1)	9	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)			CAGCTATATCCAGAGGTGCCA	0.597																																						uc002sbp.3																			0				large_intestine(1)|liver(2)|lung(5)|ovary(1)	9						c.(121-123)cCa>cAa		Homo sapiens copper metabolism (Murr1) domain containing 1 (COMMD1), mRNA.							45.0	46.0	46.0					2																	62132935		2203	4300	6503	SO:0001583	missense	150684				copper ion homeostasis|negative regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|regulation of proteasomal ubiquitin-dependent protein catabolic process	Cul2-RING ubiquitin ligase complex|cell junction|cytoplasm|nucleolus	copper ion binding|protein homodimerization activity	g.chr2:62132935C>A	BC022046	CCDS1869.1	2p15	2004-03-02	2004-02-13	2004-02-18	ENSG00000173163	ENSG00000173163			23024	protein-coding gene	gene with protein product	"""copper metabolism gene MURR1"""	607238	"""chromosome 2 open reading frame 5 (MURR1)"""	C2orf5		9001233, 11809725	Standard	NM_152516		Approved	MURR1, MGC27155	uc002sbp.3	Q8N668	OTTHUMG00000129445	ENST00000311832.5:c.122C>A	2.37:g.62132935C>A	ENSP00000308236:p.Pro41Gln		Somatic					p.P41Q	NM_152516	NP_689729	WXS	Illumina GAIIx	Phase_I	Q8N668	COMD1_HUMAN	LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)		0	133	+	Lung NSC(7;0.035)|all_lung(7;0.0691)		41					B4DFQ4|Q96GS0	Missense_Mutation	SNP	ENST00000311832.5	37	c.122C>A	CCDS1869.1	.	.	.	.	.	.	.	.	.	.	C	15.64	2.893634	0.52121	.	.	ENSG00000173163	ENST00000311832;ENST00000538736	T;T	0.09630	2.96;2.96	5.6	4.72	0.59763	.	0.052645	0.85682	D	0.000000	T	0.28732	0.0712	M	0.74258	2.255	0.45662	D	0.998588	D	0.69078	0.997	D	0.64144	0.922	T	0.02226	-1.1192	10	0.87932	D	0	.	10.4553	0.44546	0.0:0.9107:0.0:0.0893	.	41	Q8N668	COMD1_HUMAN	Q	41	ENSP00000308236:P41Q;ENSP00000438961:P41Q	ENSP00000308236:P41Q	P	+	2	0	COMMD1	61986439	0.992000	0.36948	0.759000	0.31340	0.307000	0.27823	4.186000	0.58337	1.377000	0.46286	0.655000	0.94253	CCA		0.597	COMMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251607.2	NM_152516		3	49	0	0	0	1	0	3	49				
NEIL3	55247	broad.mit.edu	37	4	178283471	178283471	+	Missense_Mutation	SNP	A	A	G			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr4:178283471A>G	ENST00000264596.3	+	10	1782	c.1664A>G	c.(1663-1665)aAc>aGc	p.N555S		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	555					base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		CCATTCTGCAACCATGGCAAG	0.388								Base excision repair (BER), DNA glycosylases																														uc003iut.2																			0				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						c.(1663-1665)aAc>aGc	Base excision repair (BER), DNA glycosylases	Homo sapiens nei endonuclease VIII-like 3 (E. coli) (NEIL3), mRNA.							92.0	93.0	93.0					4																	178283471		2203	4300	6503	SO:0001583	missense	55247				base-excision repair|nucleotide-excision repair	nucleus	DNA N-glycosylase activity|DNA-(apurinic or apyrimidinic site) lyase activity|bubble DNA binding|damaged DNA binding|double-stranded DNA binding|single-stranded DNA binding|zinc ion binding	g.chr4:178283471A>G	AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 3"""	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.1664A>G	4.37:g.178283471A>G	ENSP00000264596:p.Asn555Ser		Somatic					p.N555S	NM_018248	NP_060718	WXS	Illumina GAIIx	Phase_I	Q8TAT5	NEIL3_HUMAN		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)	9	1781	+		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)	555					Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	37	c.1664A>G	CCDS3828.1	.	.	.	.	.	.	.	.	.	.	A	10.79	1.449111	0.26074	.	.	ENSG00000109674	ENST00000264596	T	0.23348	1.91	4.63	0.95	0.19572	Zinc finger, GRF-type (1);	0.471433	0.22895	N	0.054335	T	0.14399	0.0348	N	0.17082	0.46	0.25080	N	0.990939	B	0.20368	0.044	B	0.23150	0.044	T	0.18903	-1.0322	10	0.52906	T	0.07	-2.0469	8.175	0.31276	0.768:0.0:0.232:0.0	.	555	Q8TAT5	NEIL3_HUMAN	S	555	ENSP00000264596:N555S	ENSP00000264596:N555S	N	+	2	0	NEIL3	178520465	1.000000	0.71417	0.991000	0.47740	0.736000	0.42039	1.495000	0.35627	0.095000	0.17434	-0.415000	0.06103	AAC		0.388	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248		15	73	0	0	0	1	0	15	73				
CDK5RAP1	51654	broad.mit.edu	37	20	31981850	31981850	+	Missense_Mutation	SNP	G	G	A			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr20:31981850G>A	ENST00000357886.4	-	4	584	c.431C>T	c.(430-432)aCa>aTa	p.T144I	CDK5RAP1_ENST00000544843.1_Missense_Mutation_p.T144I|CDK5RAP1_ENST00000477105.1_5'UTR|CDK5RAP1_ENST00000346416.2_Missense_Mutation_p.T144I|CDK5RAP1_ENST00000473997.1_Missense_Mutation_p.T54I|CDK5RAP1_ENST00000339269.5_Missense_Mutation_p.T144I			Q96SZ6	CK5P1_HUMAN	CDK5 regulatory subunit associated protein 1	144	CDK5 activation inhibition.|MTTase N-terminal.				brain development (GO:0007420)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|regulation of neuron differentiation (GO:0045664)|tRNA modification (GO:0006400)	cytoplasm (GO:0005737)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|transferase activity (GO:0016740)			endometrium(2)|kidney(2)|large_intestine(3)|lung(12)|ovary(3)|skin(3)|urinary_tract(1)	26						GATAGAGCATGTGACAAGGAG	0.403																																						uc010gek.3																			0				endometrium(2)|kidney(2)|large_intestine(3)|lung(12)|ovary(3)|skin(3)|urinary_tract(1)	26						c.(430-432)aCa>aTa		Homo sapiens CDK5 regulatory subunit associated protein 1 (CDK5RAP1), transcript variant 1, mRNA.							105.0	97.0	100.0					20																	31981850		2203	4300	6503	SO:0001583	missense	51654				brain development|negative regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation|tRNA modification	cytoplasm	4 iron, 4 sulfur cluster binding|metal ion binding|neuronal Cdc2-like kinase binding|transferase activity	g.chr20:31981850G>A	AF152097	CCDS13219.1, CCDS63255.1	20q11.21	2012-09-20	2002-07-22	2002-07-26	ENSG00000101391	ENSG00000101391			15880	protein-coding gene	gene with protein product		608200	"""chromosome 20 open reading frame 34"""	C20orf34		10721722, 11882646, 15329498	Standard	NM_016408		Approved	CGI-05, HSPC167, C42	uc002wyy.4	Q96SZ6	OTTHUMG00000032256	ENST00000357886.4:c.431C>T	20.37:g.31981850G>A	ENSP00000350558:p.Thr144Ile		Somatic				CDK5RAP1_uc002wyy.3_Missense_Mutation_p.T54I|CDK5RAP1_uc002wyz.3_Missense_Mutation_p.T144I|CDK5RAP1_uc002wza.3_Missense_Mutation_p.T144I|CDK5RAP1_uc010gel.3_Missense_Mutation_p.T54I|CDK5RAP1_uc010gem.3_Missense_Mutation_p.T144I|CDK5RAP1_uc002wzc.1_Missense_Mutation_p.T144I|CDK5RAP1_uc010gen.3_Missense_Mutation_p.T144I	p.T144I	NM_016408	NP_057492	WXS	Illumina GAIIx	Phase_I	Q96SZ6	CK5P1_HUMAN			3	555	-			144			CDK5 activation inhibition.|MTTase N-terminal.		A8K7R0|Q5QP46|Q5QP47|Q5QP48|Q675N4|Q675N5|Q9BVG6|Q9BWZ5|Q9H859|Q9NZZ9|Q9Y3F0	Missense_Mutation	SNP	ENST00000357886.4	37	c.431C>T		.	.	.	.	.	.	.	.	.	.	G	18.02	3.529834	0.64860	.	.	ENSG00000101391	ENST00000346416;ENST00000357886;ENST00000339269;ENST00000452723;ENST00000375351;ENST00000544843	.	.	.	4.48	4.48	0.54585	Methylthiotransferase, N-terminal (2);	0.000000	0.85682	D	0.000000	D	0.91205	0.7229	H	0.99770	4.765	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.997;1.0;1.0;1.0;1.0;1.0	D	0.94720	0.7900	9	0.87932	D	0	-11.5027	15.0177	0.71600	0.0:0.0:1.0:0.0	.	144;144;144;144;144;144;54	Q675N4;Q96SZ6-4;Q96SZ6;Q675N5;Q53H36;Q96SZ6-3;Q96SZ6-2	.;.;CK5P1_HUMAN;.;.;.;.	I	144;144;144;54;34;144	.	ENSP00000341840:T144I	T	-	2	0	CDK5RAP1	31445511	1.000000	0.71417	0.977000	0.42913	0.483000	0.33249	8.770000	0.91746	2.481000	0.83766	0.313000	0.20887	ACA		0.403	CDK5RAP1-011	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000078697.1	NM_016408		5	87	0	0	0	1	0	5	87				
POLR1A	25885	broad.mit.edu	37	2	86297188	86297188	+	Missense_Mutation	SNP	C	C	T			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr2:86297188C>T	ENST00000263857.6	-	13	2197	c.1819G>A	c.(1819-1821)Gag>Aag	p.E607K	POLR1A_ENST00000409681.1_Missense_Mutation_p.E607K			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	607					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						ACGTAGGCCTCGGCCCGGCCC	0.572																																						uc002sqs.3																			0				NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						c.(1819-1821)Gag>Aag		Homo sapiens polymerase (RNA) I polypeptide A, 194kDa (POLR1A), mRNA.							40.0	42.0	41.0					2																	86297188		2028	4167	6195	SO:0001583	missense	25885				termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding	g.chr2:86297188C>T	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"""RNA polymerase subunits"""	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.1819G>A	2.37:g.86297188C>T	ENSP00000263857:p.Glu607Lys		Somatic					p.E607K	NM_015425	NP_056240	WXS	Illumina GAIIx	Phase_I	O95602	RPA1_HUMAN			12	2198	-			607					B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	37	c.1819G>A	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.709521	0.89018	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	D;D	0.95238	-3.65;-3.65	5.3	5.3	0.74995	RNA polymerase, alpha subunit (1);RNA polymerase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98554	0.9517	H	0.98351	4.21	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99787	1.1030	10	0.87932	D	0	-30.4857	18.5668	0.91119	0.0:1.0:0.0:0.0	.	607	O95602	RPA1_HUMAN	K	607	ENSP00000263857:E607K;ENSP00000386300:E607K	ENSP00000263857:E607K	E	-	1	0	POLR1A	86150699	1.000000	0.71417	0.945000	0.38365	0.949000	0.60115	7.466000	0.80914	2.479000	0.83701	0.655000	0.94253	GAG		0.572	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		19	15	0	0	0	1	0	19	15				
TP53BP1	7158	broad.mit.edu	37	15	43738684	43738684	+	Missense_Mutation	SNP	C	C	A			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr15:43738684C>A	ENST00000263801.3	-	14	3178	c.2926G>T	c.(2926-2928)Ggg>Tgg	p.G976W	TP53BP1_ENST00000450115.2_Missense_Mutation_p.G981W|TP53BP1_ENST00000382039.3_Missense_Mutation_p.G981W|TP53BP1_ENST00000382044.4_Missense_Mutation_p.G981W|TP53BP1_ENST00000605155.1_5'Flank	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	976					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		GGGGCAGCCCCAGAATCCCCT	0.473								Other conserved DNA damage response genes																														uc001zrr.4																			0				breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72						c.(2941-2943)Ggg>Tgg	Other conserved DNA damage response genes	Homo sapiens tumor protein p53 binding protein 1 (TP53BP1), transcript variant 1, mRNA.							101.0	101.0	101.0					15																	43738684		2201	4298	6499	SO:0001583	missense	7158				double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter	condensed chromosome kinetochore|cytoplasm|nucleoplasm	RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity|p53 binding	g.chr15:43738684C>A	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"""tumor protein p53-binding protein, 1"""			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.2926G>T	15.37:g.43738684C>A	ENSP00000263801:p.Gly976Trp		Somatic				TP53BP1_uc010udp.2_Missense_Mutation_p.G976W|TP53BP1_uc001zrq.4_Missense_Mutation_p.G981W|TP53BP1_uc001zrs.3_Missense_Mutation_p.G976W|TP53BP1_uc010udq.1_Missense_Mutation_p.G981W	p.G981W	NM_001141980	NP_005648	WXS	Illumina GAIIx	Phase_I	Q12888	TP53B_HUMAN		GBM - Glioblastoma multiforme(94;1.59e-06)	13	3054	-		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)	976					F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	37	c.2941G>T	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	C	18.75	3.691599	0.68271	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115;ENST00000413546	T;T;T;T;T	0.10005	3.71;3.71;3.71;3.71;2.92	5.47	4.54	0.55810	.	0.636189	0.16408	N	0.215760	T	0.27384	0.0672	M	0.65975	2.015	0.24486	N	0.994329	D;D;D;D	0.69078	0.991;0.994;0.997;0.997	P;P;D;D	0.65140	0.88;0.858;0.932;0.932	T	0.02610	-1.1134	10	0.72032	D	0.01	-2.455	10.7683	0.46308	0.1332:0.7931:0.0:0.0737	.	981;976;981;981	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	W	976;981;981;981;941	ENSP00000263801:G976W;ENSP00000371475:G981W;ENSP00000371470:G981W;ENSP00000393497:G981W;ENSP00000388028:G941W	ENSP00000263801:G976W	G	-	1	0	TP53BP1	41525976	0.483000	0.25956	1.000000	0.80357	0.990000	0.78478	0.860000	0.27871	2.729000	0.93468	0.655000	0.94253	GGG		0.473	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			84	87	0	0	0	1	0	84	87				
SLC25A22	79751	broad.mit.edu	37	11	799816	799816	+	5'Flank	SNP	G	G	A			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr11:799816G>A	ENST00000531214.1	-	0	0				PIDD_ENST00000347755.5_Splice_Site_p.R825W|PIDD_ENST00000411829.2_Splice_Site_p.R808W	NM_001191060.1	NP_001177989.1	Q9H936	GHC1_HUMAN	solute carrier family 25 (mitochondrial carrier: glutamate), member 22						L-glutamate transport (GO:0015813)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			endometrium(1)|kidney(1)|lung(2)|urinary_tract(1)	5		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;6.27e-26)|Epithelial(43;4.84e-25)|OV - Ovarian serous cystadenocarcinoma(40;2.72e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GAGCCTCACCGGAACTCGTGC	0.687																																					Colon(93;848 1468 3270 23355 49636)	uc001lro.2																			0											c.e15+1		Homo sapiens p53-induced death domain protein (PIDD), transcript variant 1, mRNA.							12.0	15.0	14.0					11																	799816		2170	4272	6442	SO:0001631	upstream_gene_variant	55367				apoptosis|signal transduction	cytoplasm|nucleus	death receptor binding	g.chr11:799816G>A	AJ428202	CCDS7715.1	11p15.5	2013-05-22			ENSG00000177542	ENSG00000177542		"""Solute carriers"""	19954	protein-coding gene	gene with protein product		609302				11897791	Standard	NM_024698		Approved	GC1, FLJ13044, NET44, EIEE3	uc001lrj.3	Q9H936	OTTHUMG00000133310		11.37:g.799816G>A	Exception_encountered		Somatic				SLC25A22_uc009yci.3_5'Flank|SLC25A22_uc001lrj.3_5'Flank|PIDD_uc009yck.1_Splice_Site|PIDD_uc001lrl.1_Splice_Site_p.R668_splice|PIDD_uc001lrm.1_Splice_Site_p.R512_splice|PIDD_uc001lrn.2_Splice_Site_p.R668_splice|PIDD_uc001lrk.2_Splice_Site_p.R808_splice|PIDD_uc001lrp.2_3'UTR	p.R825_splice	NM_145886	NP_665893	WXS	Illumina GAIIx	Phase_I	Q9HB75	PIDD_HUMAN			15	2621	-			825			Death.		A8K366|C9J1H6|E9PJD3|E9PKB2|E9PL68|E9PN26|E9PNQ3|E9PP01|E9PR97|Q8TBU8	Splice_Site	SNP	ENST00000531214.1	37	c.2474_splice	CCDS7715.1	.	.	.	.	.	.	.	.	.	.	G	16.85	3.236950	0.58886	.	.	ENSG00000177595	ENST00000411829;ENST00000347755	D;D	0.86164	-2.08;-2.08	4.1	0.546	0.17196	Death (3);DEATH-like (2);	0.064498	0.64402	D	0.000014	D	0.90177	0.6930	L	0.55990	1.75	0.46954	D	0.999266	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.89009	0.3427	10	0.66056	D	0.02	.	11.9657	0.53033	0.0:0.0:0.2603:0.7397	.	825;668;808	Q9HB75;Q9HB75-3;Q9HB75-2	PIDD_HUMAN;.;.	W	808;825	ENSP00000416801:R808W;ENSP00000337797:R825W	ENSP00000337797:R825W	R	-	1	2	PIDD	789816	1.000000	0.71417	0.993000	0.49108	0.415000	0.31203	1.535000	0.36061	0.306000	0.22856	0.462000	0.41574	CGG		0.687	SLC25A22-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384124.1			2	0	0	0	0	1	0	2	0				
EPG5	57724	broad.mit.edu	37	18	43487997	43487997	+	Missense_Mutation	SNP	C	C	T			TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr18:43487997C>T	ENST00000282041.5	-	24	4289	c.4255G>A	c.(4255-4257)Gga>Aga	p.G1419R	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1419					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						TAGGTATCTCCTTTTTGAAAA	0.313																																						uc002lbm.3																			0				NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						c.(4255-4257)Gga>Aga		Homo sapiens ectopic P-granules autophagy protein 5 homolog (C. elegans) (EPG5), mRNA.							74.0	77.0	76.0					18																	43487997		1813	4068	5881	SO:0001583	missense	57724				autophagy			g.chr18:43487997C>T	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"""KIAA1632"""	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.4255G>A	18.37:g.43487997C>T	ENSP00000282041:p.Gly1419Arg		Somatic				EPG5_uc002lbo.1_Missense_Mutation_p.G1419R|EPG5_uc010xcr.1_Non-coding_Transcript|EPG5_uc010xcs.1_Non-coding_Transcript|EPG5_uc010xcq.1_5'UTR|EPG5_uc002lbn.2_Missense_Mutation_p.G294R	p.G1419R	NM_020964	NP_066015	WXS	Illumina GAIIx	Phase_I	Q9HCE0	EPG5_HUMAN			23	4355	-			1419					A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	c.4255G>A	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	C	23.1	4.379485	0.82682	.	.	ENSG00000152223	ENST00000282041;ENST00000308403	T	0.09723	2.95	5.91	5.91	0.95273	.	0.122547	0.56097	D	0.000028	T	0.30510	0.0767	L	0.53249	1.67	0.49130	D	0.99975	D;D	0.76494	0.999;0.999	D;D	0.67900	0.954;0.954	T	0.00072	-1.2128	10	0.51188	T	0.08	-18.9457	20.2983	0.98569	0.0:1.0:0.0:0.0	.	1419;1419	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	R	1419;294	ENSP00000282041:G1419R	ENSP00000282041:G1419R	G	-	1	0	EPG5	41741995	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.087000	0.57671	2.802000	0.96397	0.655000	0.94253	GGA		0.313	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		9	89	0	0	0	1	0	9	89				
PADI2	11240	broad.mit.edu	37	1	17411155	17411155	+	Frame_Shift_Del	DEL	G	G	-	rs149752241		TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-10A-01D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	6f4ff365-ee63-40d0-8f71-ed062f755d22	g.chr1:17411155delG	ENST00000375486.4	-	8	940	c.877delC	c.(877-879)cggfs	p.R293fs	PADI2_ENST00000444885.2_Intron|PADI2_ENST00000466151.1_5'Flank|PADI2_ENST00000375481.1_Frame_Shift_Del_p.R293fs	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	293					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	GGAGCAATCCGGAATATCACG	0.577																																						uc001baf.3																			0				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29						c.(877-879)cggfs		Homo sapiens peptidyl arginine deiminase, type II (PADI2), mRNA.	L-Citrulline(DB00155)						94.0	62.0	73.0					1																	17411155		2199	4294	6493	SO:0001589	frameshift_variant	11240				peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity	g.chr1:17411155delG	AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"""Peptidyl arginine deiminases"""	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.877delC	1.37:g.17411155delG	ENSP00000364635:p.Arg293fs		Somatic				PADI2_uc010ocm.2_Intron|PADI2_uc001bag.1_Frame_Shift_Del_p.R293fs	p.R293fs	NM_007365	NP_031391	WXS	Illumina GAIIx	Phase_I	Q9Y2J8	PADI2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	7	959	-		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)	293					Q96DA7|Q9UPN2	Frame_Shift_Del	DEL	ENST00000375486.4	37	c.877delC	CCDS177.1																																																																																				0.577	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1			2	4						2	4	---	---	---	---
PADI2	11240	broad.mit.edu	37	1	17411155	17411155	+	Frame_Shift_Del	DEL	G	G	-	rs149752241		TCGA-DO-A1JZ-01A-11D-A13W-08	TCGA-DO-A1JZ-11A-11D-A13W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7c622602-14bf-4377-bb3d-c6197a55a8cc	64f1b3b9-24c9-4715-b6ce-834b3443d46f	g.chr1:17411155delG	ENST00000375486.4	-	8	940	c.877delC	c.(877-879)cggfs	p.R293fs	PADI2_ENST00000444885.2_Intron|PADI2_ENST00000466151.1_5'Flank|PADI2_ENST00000375481.1_Frame_Shift_Del_p.R293fs	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	293					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	GGAGCAATCCGGAATATCACG	0.577																																						uc001baf.3																			0				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29						c.(877-879)cggfs		Homo sapiens peptidyl arginine deiminase, type II (PADI2), mRNA.	L-Citrulline(DB00155)						94.0	62.0	73.0					1																	17411155		2199	4294	6493	SO:0001589	frameshift_variant	11240				peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity	g.chr1:17411155delG	AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"""Peptidyl arginine deiminases"""	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.877delC	1.37:g.17411155delG	ENSP00000364635:p.Arg293fs		Somatic				PADI2_uc010ocm.2_Intron|PADI2_uc001bag.1_Frame_Shift_Del_p.R293fs	p.R293fs	NM_007365	NP_031391	WXS	Illumina GAIIx	Phase_I	Q9Y2J8	PADI2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	7	959	-		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)	293					Q96DA7|Q9UPN2	Frame_Shift_Del	DEL	ENST00000375486.4	37	c.877delC	CCDS177.1																																																																																				0.577	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1			2	4						2	4	---	---	---	---
