#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_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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
AMELX	265	genome.wustl.edu	37	X	11316986	11316986	+	Nonsense_Mutation	SNP	C	C	T			TCGA-BH-A0C3-01A-21D-A12Q-09	TCGA-BH-A0C3-11A-23D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	ec57ee0f-949e-4eee-91c2-dd129d657065	128e802b-64d9-42d9-8a22-59c8ce061eb4	g.chrX:11316986C>T	ENST00000380714.3	+	5	531	c.463C>T	c.(463-465)Cag>Tag	p.Q155*	ARHGAP6_ENST00000380736.1_Intron|ARHGAP6_ENST00000380732.3_Intron|ARHGAP6_ENST00000380718.1_Intron|ARHGAP6_ENST00000337414.4_Intron|AMELX_ENST00000380712.3_Nonsense_Mutation_p.Q169*|AMELX_ENST00000348912.4_Nonsense_Mutation_p.Q139*|ARHGAP6_ENST00000413512.3_Intron	NM_001142.2	NP_001133.1	Q99217	AMELX_HUMAN	amelogenin, X-linked	155					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|enamel mineralization (GO:0070166)|epithelial to mesenchymal transition (GO:0001837)|ion homeostasis (GO:0050801)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of tooth mineralization (GO:0070172)|signal transduction (GO:0007165)|tooth mineralization (GO:0034505)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|hydroxyapatite binding (GO:0046848)|identical protein binding (GO:0042802)|structural constituent of tooth enamel (GO:0030345)			endometrium(3)|kidney(2)|large_intestine(1)|lung(9)	15						CCTGCCGCCACAGCCACCTCT	0.657																																						dbGAP											0													46.0	39.0	42.0					X																	11316986		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0				CCDS14144.1, CCDS14145.1, CCDS14146.1	Xp22.31-p22.1	2010-04-20	2010-04-20		ENSG00000125363	ENSG00000125363			461	protein-coding gene	gene with protein product	"""amelogenesis imperfecta 1"""	300391	"""amelogenin (X chromosome, amelogenesis imperfecta 1)"""	AMG, AIH1		1734713	Standard	NM_182680		Approved		uc004cus.3	Q99217	OTTHUMG00000021130	ENST00000380714.3:c.463C>T	X.37:g.11316986C>T	ENSP00000370090:p.Gln155*	Somatic		WXS	Illumina GAIIx	Phase_IV	Q96NW6|Q9UCA7	Nonsense_Mutation	SNP	pfam_Amelogenin,smart_Amelogenin,prints_Amelogenin	p.Q169*	ENST00000380714.3	37	c.505	CCDS14144.1	X	.	.	.	.	.	.	.	.	.	.	C	24.8	4.566190	0.86439	.	.	ENSG00000125363	ENST00000380714;ENST00000380712;ENST00000348912	.	.	.	4.85	4.85	0.62838	.	0.191229	0.36519	N	0.002545	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-4.6642	12.1263	0.53919	0.0:0.8308:0.1691:0.0	.	.	.	.	X	155;169;139	.	ENSP00000335312:Q139X	Q	+	1	0	AMELX	11226907	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.429000	0.34903	2.168000	0.68352	0.415000	0.27848	CAG	AMELX	-	pfam_Amelogenin,smart_Amelogenin	ENSG00000125363		0.657	AMELX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AMELX	HGNC	protein_coding	OTTHUMT00000055746.1	137	0.00	0	C	NM_001142		11316986	11316986	+1	no_errors	ENST00000380712	ensembl	human	known	69_37n	nonsense	171	20.09	43	SNP	1.000	T
EPG5	57724	genome.wustl.edu	37	18	43534880	43534880	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0C3-01A-21D-A12Q-09	TCGA-BH-A0C3-11A-23D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	ec57ee0f-949e-4eee-91c2-dd129d657065	128e802b-64d9-42d9-8a22-59c8ce061eb4	g.chr18:43534880G>A	ENST00000282041.5	-	2	522	c.488C>T	c.(487-489)aCt>aTt	p.T163I		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	163					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						TGCTGGCTGAGTATAAGAAAA	0.408																																						dbGAP											0													75.0	71.0	72.0					18																	43534880		1859	4091	5950	-	-	-	SO:0001583	missense	0			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.488C>T	18.37:g.43534880G>A	ENSP00000282041:p.Thr163Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	A2BDF3|Q9H8C8	Missense_Mutation	SNP	NULL	p.T163I	ENST00000282041.5	37	c.488	CCDS11926.2	18	.	.	.	.	.	.	.	.	.	.	G	4.012	-0.000327	0.07819	.	.	ENSG00000152223	ENST00000282041	T	0.09723	2.95	5.16	-2.63	0.06133	.	2.169740	0.01402	N	0.013623	T	0.07458	0.0188	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.34750	-0.9816	10	0.36615	T	0.2	2.6838	5.8066	0.18444	0.2752:0.3823:0.3425:0.0	.	163;163	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	I	163	ENSP00000282041:T163I	ENSP00000282041:T163I	T	-	2	0	EPG5	41788878	0.000000	0.05858	0.016000	0.15963	0.046000	0.14306	-0.494000	0.06451	-0.352000	0.08237	0.563000	0.77884	ACT	EPG5	-	NULL	ENSG00000152223		0.408	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EPG5	HGNC	protein_coding	OTTHUMT00000445081.1	168	0.00	0	G	NM_020964		43534880	43534880	-1	no_errors	ENST00000282041	ensembl	human	known	69_37n	missense	168	18.84	39	SNP	0.011	A
GOLGA8A	23015	genome.wustl.edu	37	15	34677517	34677517	+	Missense_Mutation	SNP	G	G	A	rs3179271	byFrequency	TCGA-BH-A0C3-01A-21D-A12Q-09	TCGA-BH-A0C3-11A-23D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	ec57ee0f-949e-4eee-91c2-dd129d657065	128e802b-64d9-42d9-8a22-59c8ce061eb4	g.chr15:34677517G>A	ENST00000359187.4	-	6	459	c.395C>T	c.(394-396)aCa>aTa	p.T132I	GOLGA8A_ENST00000360553.3_Missense_Mutation_p.T132I|GOLGA8A_ENST00000432566.2_Missense_Mutation_p.T162I|GOLGA8A_ENST00000543376.1_5'UTR	NM_181077.3	NP_851422.1	A7E2F4	GOG8A_HUMAN	golgin A8 family, member A	160						Golgi apparatus (GO:0005794)|membrane (GO:0016020)							all_lung(180;2.78e-08)		all cancers(64;8.27e-19)|GBM - Glioblastoma multiforme(113;6.98e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		CTTTTTCTCTGTGTTCAATCT	0.443													g|||	1236	0.246805	0.205	0.3473	5008	,	,		19221	0.1677		0.2594	False		,,,				2504	0.3006					dbGAP											0													1.0	1.0	1.0					15																	34677517		70	330	400	-	-	-	SO:0001583	missense	0			BX648160	CCDS10038.1	15q14	2011-10-25	2010-02-12		ENSG00000175265	ENSG00000175265			31972	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 8A"""			10660574, 10677249	Standard	NM_181077		Approved	GM88, GOLGIN-67	uc001zii.3	A7E2F4	OTTHUMG00000129447	ENST00000359187.4:c.395C>T	15.37:g.34677517G>A	ENSP00000352111:p.Thr132Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	A7MCY9|B7ZMK5|O94937|Q52M46|Q68DK6|Q9NZG8|Q9NZW0|Q9NZW3	Missense_Mutation	SNP	NULL	p.T162I	ENST00000359187.4	37	c.485	CCDS10038.1	15	.	.	.	.	.	.	.	.	.	.	g	0.003	-2.523871	0.00149	.	.	ENSG00000175265	ENST00000359187;ENST00000360553;ENST00000432566	T;T;T	0.12255	2.7;2.7;2.7	0.379	0.379	0.16213	.	.	.	.	.	T	0.03136	0.0092	N	0.00823	-1.155	0.09310	N	0.999999	B	0.06786	0.001	B	0.06405	0.002	T	0.41124	-0.9526	8	0.22109	T	0.4	.	.	.	.	.	132	A7E2F4-3	.	I	132;132;162	ENSP00000352111:T132I;ENSP00000353755:T132I;ENSP00000402791:T162I	ENSP00000352111:T132I	T	-	2	0	GOLGA8A	32464809	0.063000	0.20901	0.001000	0.08648	0.020000	0.10135	-0.265000	0.08644	-0.886000	0.03966	-1.451000	0.01035	ACA	GOLGA8A	-	NULL	ENSG00000175265		0.443	GOLGA8A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GOLGA8A	HGNC	protein_coding	OTTHUMT00000251830.2	8	0.00	0	G	NM_181076		34677517	34677517	-1	no_errors	ENST00000432566	ensembl	human	known	69_37n	missense	5	44.44	4	SNP	0.001	A
HNRNPR	10236	genome.wustl.edu	37	1	23650213	23650213	+	Missense_Mutation	SNP	T	T	G			TCGA-BH-A0C3-01A-21D-A12Q-09	TCGA-BH-A0C3-11A-23D-A12Q-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	ec57ee0f-949e-4eee-91c2-dd129d657065	128e802b-64d9-42d9-8a22-59c8ce061eb4	g.chr1:23650213T>G	ENST00000374612.1	-	6	634	c.511A>C	c.(511-513)Aaa>Caa	p.K171Q	HNRNPR_ENST00000606561.1_Missense_Mutation_p.K32Q|HNRNPR_ENST00000426846.2_Intron|HNRNPR_ENST00000302271.6_Missense_Mutation_p.K171Q|HNRNPR_ENST00000478691.1_Missense_Mutation_p.K70Q|HNRNPR_ENST00000374616.3_Missense_Mutation_p.K171Q|HNRNPR_ENST00000427764.2_Missense_Mutation_p.K133Q	NM_001102398.1|NM_005826.3	NP_001095868.1|NP_005817.1	O43390	HNRPR_HUMAN	heterogeneous nuclear ribonucleoprotein R	171	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00394)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;6.83e-27)|Colorectal(126;6.01e-08)|COAD - Colon adenocarcinoma(152;3.32e-06)|GBM - Glioblastoma multiforme(114;6.69e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00357)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0875)|LUSC - Lung squamous cell carcinoma(448;0.19)		CTTGGTATTTTGCCTACAAAT	0.408																																						dbGAP											0													73.0	78.0	76.0					1																	23650213		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF000364	CCDS232.1, CCDS44085.1, CCDS60020.1, CCDS72726.1, CCDS72727.1	1p36.12	2013-02-12		2007-08-16	ENSG00000125944	ENSG00000125944		"""RNA binding motif (RRM) containing"""	5047	protein-coding gene	gene with protein product		607201		HNRPR		9421497	Standard	XM_005245711		Approved	hnRNP-R	uc001bgp.4	O43390	OTTHUMG00000003224	ENST00000374612.1:c.511A>C	1.37:g.23650213T>G	ENSP00000363741:p.Lys171Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	Q2L7G6|Q5TEH1|Q9BV64|S4R3J4	Missense_Mutation	SNP	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom,tigrfam_HnRNP_R/Q_splicing_fac	p.K171Q	ENST00000374612.1	37	c.511	CCDS232.1	1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.666667	0.88251	.	.	ENSG00000125944	ENST00000374616;ENST00000374612;ENST00000302271;ENST00000427764	T;T;T;T	0.41758	0.99;0.99;0.99;1.31	5.14	5.14	0.70334	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.53514	0.1801	L	0.35414	1.06	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.998;1.0;0.988;1.0	D;D;D;D;D	0.91635	0.999;0.988;0.995;0.947;0.991	T	0.57464	-0.7807	10	0.87932	D	0	-5.7234	14.0871	0.64964	0.0:0.0:0.0:1.0	.	133;32;148;171;171	Q2L7G6;B4DT28;Q6MZS5;O43390;O43390-2	.;.;.;HNRPR_HUMAN;.	Q	171;171;171;133	ENSP00000363745:K171Q;ENSP00000363741:K171Q;ENSP00000304405:K171Q;ENSP00000392799:K133Q	ENSP00000304405:K171Q	K	-	1	0	HNRNPR	23522800	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.902000	0.87389	2.076000	0.62316	0.459000	0.35465	AAA	HNRNPR	-	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom,tigrfam_HnRNP_R/Q_splicing_fac	ENSG00000125944		0.408	HNRNPR-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	HNRNPR	HGNC	protein_coding	OTTHUMT00000008889.1	165	0.00	0	T	NM_005826		23650213	23650213	-1	no_errors	ENST00000374616	ensembl	human	known	69_37n	missense	145	16.18	28	SNP	1.000	G
IGF1R	3480	genome.wustl.edu	37	15	99456511	99456511	+	Splice_Site	SNP	G	G	A			TCGA-BH-A0C3-01A-21D-A12Q-09	TCGA-BH-A0C3-11A-23D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	ec57ee0f-949e-4eee-91c2-dd129d657065	128e802b-64d9-42d9-8a22-59c8ce061eb4	g.chr15:99456511G>A	ENST00000268035.6	+	8	2439	c.1828G>A	c.(1828-1830)Gtt>Att	p.V610I	IGF1R_ENST00000558762.1_Splice_Site_p.V610I	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	610	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""""""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	CAATGCTTCAGGTATCCATGC	0.532																																						dbGAP											0													153.0	105.0	122.0					15																	99456511		2197	4297	6494	-	-	-	SO:0001630	splice_region_variant	0			M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"""CD molecules"", ""Fibronectin type III domain containing"""	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.1828+1G>A	15.37:g.99456511G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	pirsf_Tyr_kinase_insulin-like_rcpt,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_EGF_rcpt_L,pfam_Prot_kinase_cat_dom,pfam_Furin-like_Cys-rich_dom,pfam_Fibronectin_type3,superfamily_Kinase-like_dom,superfamily_Growth_fac_rcpt,superfamily_Fibronectin_type3,smart_Furin_repeat,smart_Fibronectin_type3,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Fibronectin_type3,pfscan_Prot_kinase_cat_dom	p.V610I	ENST00000268035.6	37	c.1828	CCDS10378.1	15	.	.	.	.	.	.	.	.	.	.	G	16.29	3.082105	0.55861	.	.	ENSG00000140443	ENST00000268035	T	0.71817	-0.6	4.59	4.59	0.56863	Fibronectin, type III (1);	0.000000	0.51477	D	0.000094	T	0.64294	0.2585	L	0.49571	1.57	0.49798	D	0.99982	P;B	0.36990	0.577;0.006	B;B	0.31442	0.13;0.009	T	0.66945	-0.5795	10	0.38643	T	0.18	.	17.9418	0.89027	0.0:0.0:1.0:0.0	.	610;610	C9J5X1;P08069	.;IGF1R_HUMAN	I	610	ENSP00000268035:V610I	ENSP00000268035:V610I	V	+	1	0	IGF1R	97274034	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	4.878000	0.63093	2.527000	0.85204	0.563000	0.77884	GTT	IGF1R	-	pirsf_Tyr_kinase_insulin-like_rcpt,superfamily_Fibronectin_type3	ENSG00000140443		0.532	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	IGF1R	HGNC	protein_coding	OTTHUMT00000313537.2	36	0.00	0	G	NM_000875	Missense_Mutation	99456511	99456511	+1	no_errors	ENST00000268035	ensembl	human	known	69_37n	missense	47	16.07	9	SNP	1.000	A
ITPR1	3708	genome.wustl.edu	37	3	4856841	4856841	+	Silent	SNP	T	T	C			TCGA-BH-A0C3-01A-21D-A12Q-09	TCGA-BH-A0C3-11A-23D-A12Q-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	ec57ee0f-949e-4eee-91c2-dd129d657065	128e802b-64d9-42d9-8a22-59c8ce061eb4	g.chr3:4856841T>C	ENST00000443694.2	+	56	7761	c.7761T>C	c.(7759-7761)gcT>gcC	p.A2587A	ITPR1_ENST00000423119.2_Silent_p.A2554A|ITPR1_ENST00000544951.1_Silent_p.A565A|ITPR1_ENST00000302640.8_Silent_p.A2587A|ITPR1_ENST00000354582.6_Silent_p.A2587A|ITPR1_ENST00000357086.4_Silent_p.A2554A|ITPR1_ENST00000456211.2_Silent_p.A2539A|AC018816.3_ENST00000489771.1_Intron|ITPR1_ENST00000463980.1_3'UTR|AC018816.3_ENST00000449914.1_Intron|AC018816.3_ENST00000441894.1_Intron			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2602					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	ACACTTTTGCTGACCTGAGGA	0.463																																						dbGAP											0													140.0	138.0	138.0					3																	4856841		2128	4271	6399	-	-	-	SO:0001819	synonymous_variant	0			D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"""Ion channels / Inositol triphosphate receptors"""	6180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 94"""	147265	"""spinocerebellar ataxia 15"", ""spinocerebellar ataxia 16"", ""spinocerebellar ataxia 29"""	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.7761T>C	3.37:g.4856841T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	E7EPX7|E9PDE9|Q14660|Q99897	Silent	SNP	pfam_Ca-rel_channel,pfam_Ins145_P3_rcpt,pfam_MIR,pfam_RIH_assoc-dom,pfam_Ion_trans_dom,superfamily_MIR,smart_MIR_motif,prints_InsP3_rcpt-bd,pfscan_MIR_motif	p.A2587	ENST00000443694.2	37	c.7761	CCDS54551.1	3																																																																																			ITPR1	-	NULL	ENSG00000150995		0.463	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	ITPR1	HGNC	protein_coding	OTTHUMT00000337982.3	307	0.00	0	T	NM_002222		4856841	4856841	+1	no_errors	ENST00000302640	ensembl	human	known	69_37n	silent	282	19.89	70	SNP	0.047	C
KIRREL	55243	genome.wustl.edu	37	1	158059318	158059318	+	Silent	SNP	G	G	T			TCGA-BH-A0C3-01A-21D-A12Q-09	TCGA-BH-A0C3-11A-23D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	ec57ee0f-949e-4eee-91c2-dd129d657065	128e802b-64d9-42d9-8a22-59c8ce061eb4	g.chr1:158059318G>T	ENST00000359209.6	+	9	1138	c.1071G>T	c.(1069-1071)ctG>ctT	p.L357L	KIRREL_ENST00000368172.1_Silent_p.L171L|KIRREL_ENST00000416935.2_Silent_p.L257L|KIRREL_ENST00000392272.2_Silent_p.L254L|KIRREL_ENST00000360089.4_Silent_p.L193L|KIRREL_ENST00000368173.3_Silent_p.L373L			Q96J84	KIRR1_HUMAN	kin of IRRE like (Drosophila)	357	Ig-like C2-type 4.				excretion (GO:0007588)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of actin filament polymerization (GO:0030838)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|dendritic shaft (GO:0043198)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	myosin binding (GO:0017022)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(5)|skin(3)|stomach(1)	38	all_hematologic(112;0.0378)					ACCAGCTGCTGCTGAAGTCGG	0.657																																						dbGAP											0													36.0	39.0	38.0					1																	158059318		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AK001707	CCDS1172.2, CCDS72952.1	1q21-q25	2013-01-29			ENSG00000183853	ENSG00000183853		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15734	protein-coding gene	gene with protein product	"""nephrin-like protein 1"""	607428				12424224	Standard	NM_001286349		Approved	NEPH1	uc001frn.4	Q96J84	OTTHUMG00000022438	ENST00000359209.6:c.1071G>T	1.37:g.158059318G>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q5W0F8|Q5XKC6|Q7Z696|Q7Z7N8|Q8TB15|Q9H9N1|Q9NVA5	Silent	SNP	pfam_Ig_I-set,pfam_Ig_V-set,pfam_Immunoglobulin,pfam_CD80_C2-set,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like	p.L373	ENST00000359209.6	37	c.1119	CCDS1172.2	1																																																																																			KIRREL	-	pfam_Ig_I-set,pfam_Ig_V-set,pfam_Immunoglobulin,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like	ENSG00000183853		0.657	KIRREL-001	KNOWN	basic|CCDS	protein_coding	KIRREL	HGNC	protein_coding	OTTHUMT00000058342.3	25	0.00	0	G	NM_018240		158059318	158059318	+1	no_errors	ENST00000368173	ensembl	human	known	69_37n	silent	45	22.41	13	SNP	0.993	T
NHS	4810	genome.wustl.edu	37	X	17745442	17745443	+	Frame_Shift_Del	DEL	TA	TA	-			TCGA-BH-A0C3-01A-21D-A12Q-09	TCGA-BH-A0C3-11A-23D-A12Q-09	TA	TA					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	ec57ee0f-949e-4eee-91c2-dd129d657065	128e802b-64d9-42d9-8a22-59c8ce061eb4	g.chrX:17745442_17745443delTA	ENST00000380060.3	+	6	3491_3492	c.3153_3154delTA	c.(3151-3156)actatafs	p.I1052fs	NHS_ENST00000398097.3_Frame_Shift_Del_p.I896fs	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	1073					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					AAGATGGAACTATATCACTGAG	0.406																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0				CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.3153_3154delTA	X.37:g.17745444_17745445delTA	ENSP00000369400:p.Ile1052fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Frame_Shift_Del	DEL	NULL	p.S1053fs	ENST00000380060.3	37	c.3153_3154	CCDS14181.1	X																																																																																			NHS	-	NULL	ENSG00000188158		0.406	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NHS	HGNC	protein_coding	OTTHUMT00000059120.1	324	0.00	0	TA	NM_198270		17745442	17745443	+1	no_errors	ENST00000380060	ensembl	human	known	69_37n	frame_shift_del	378	16.52	75	DEL	0.007:0.000	-
POLI	11201	genome.wustl.edu	37	18	51795960	51795960	+	Missense_Mutation	SNP	A	A	G	rs78943519|rs10584411|rs3729509	byFrequency	TCGA-BH-A0C3-01A-21D-A12Q-09	TCGA-BH-A0C3-11A-23D-A12Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	ec57ee0f-949e-4eee-91c2-dd129d657065	128e802b-64d9-42d9-8a22-59c8ce061eb4	g.chr18:51795960A>G	ENST00000579534.1	+	1	187	c.44A>G	c.(43-45)gAc>gGc	p.D15G	POLI_ENST00000406285.3_Missense_Mutation_p.D15G|POLI_ENST00000217800.5_5'Flank|POLI_ENST00000579434.1_5'UTR	NM_007195.2	NP_009126.2	Q9UNA4	POLI_HUMAN	polymerase (DNA directed) iota	15				Missing (in Ref. 3; AAD50381, 4; CAB66605 and 6; AAF63383). {ECO:0000305}.	DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)	intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)	p.D17delD(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(5)|ovary(3)|urinary_tract(1)	26				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)		GGCGGCGGCGACGACGACGAG	0.731								DNA polymerases (catalytic subunits)																														dbGAP											1	Deletion - In frame(1)	large_intestine(1)											5.0	9.0	8.0					18																	51795960		1457	3272	4729	-	-	-	SO:0001583	missense	0				CCDS11954.2	18q21.1	2012-05-18			ENSG00000101751	ENSG00000101751		"""DNA polymerases"""	9182	protein-coding gene	gene with protein product		605252		RAD3OB, RAD30B		17609217	Standard	NM_007195		Approved		uc002lfj.4	Q9UNA4	OTTHUMG00000132704	ENST00000579534.1:c.44A>G	18.37:g.51795960A>G	ENSP00000462664:p.Asp15Gly	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8N590|Q9H0S1|Q9NYH6	Missense_Mutation	SNP	pfam_DNA_repair_prot_UmuC-like,pfam_DNA_pol_Y-fam_little_finger,superfamily_DNA_pol_Y-fam_little_finger,pfscan_DNA_repair_prot_UmuC-like_N	p.D15G	ENST00000579534.1	37	c.44	CCDS11954.2	18	.	.	.	.	.	.	.	.	.	.	A	8.165	0.790329	0.16258	.	.	ENSG00000101751	ENST00000406285;ENST00000217800	T	0.53857	0.6	4.54	-0.887	0.10587	.	.	.	.	.	T	0.29914	0.0748	N	0.19112	0.55	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.17077	-1.0381	9	0.21540	T	0.41	.	4.4239	0.11493	0.4916:0.3143:0.194:0.0	.	15	Q9UNA4	POLI_HUMAN	G	15	ENSP00000385196:D15G	ENSP00000217800:D15G	D	+	2	0	POLI	50049958	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.072000	0.11486	-0.303000	0.08856	-0.512000	0.04463	GAC	POLI	-	NULL	ENSG00000101751		0.731	POLI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	POLI	HGNC	protein_coding	OTTHUMT00000256002.3	9	0.00	0	A	NM_007195		51795960	51795960	+1	no_errors	ENST00000579534	ensembl	human	known	69_37n	missense	10	33.33	5	SNP	0.000	G
RPS6KA2	6196	genome.wustl.edu	37	6	166912078	166912078	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A0C3-01A-21D-A12Q-09	TCGA-BH-A0C3-11A-23D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	ec57ee0f-949e-4eee-91c2-dd129d657065	128e802b-64d9-42d9-8a22-59c8ce061eb4	g.chr6:166912078G>A	ENST00000265678.4	-	8	888	c.665C>T	c.(664-666)aCg>aTg	p.T222M	RPS6KA2_ENST00000405189.3_Missense_Mutation_p.T133M|RPS6KA2_ENST00000366863.2_Missense_Mutation_p.T68M|RPS6KA2_ENST00000481261.2_Missense_Mutation_p.T133M|RPS6KA2_ENST00000510118.1_Missense_Mutation_p.T247M|RPS6KA2_ENST00000503859.1_Missense_Mutation_p.T230M	NM_021135.4	NP_066958.2	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2	222	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|brain renin-angiotensin system (GO:0002035)|cardiac muscle cell apoptotic process (GO:0010659)|cellular response to carbohydrate stimulus (GO:0071322)|heart contraction (GO:0060047)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression (GO:0010628)|regulation of protein processing (GO:0070613)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		GTACTCGATCGTCCCGCAGAA	0.607																																						dbGAP											0													204.0	135.0	158.0					6																	166912078		2203	4300	6503	-	-	-	SO:0001583	missense	0			L07598	CCDS5294.1, CCDS34570.1	6q27	2011-04-05	2002-08-29		ENSG00000071242	ENSG00000071242			10431	protein-coding gene	gene with protein product		601685	"""ribosomal protein S6 kinase, 90kD, polypeptide 2"""			8141249	Standard	NM_001006932		Approved	RSK, RSK3, HU-2	uc003qvc.1	Q15349	OTTHUMG00000016007	ENST00000265678.4:c.665C>T	6.37:g.166912078G>A	ENSP00000265678:p.Thr222Met	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	Missense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Pkinase_C,pfam_LipoPS_kinase,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_AGC-kinase_C,pirsf_Ribosomal_S6_kinase_II,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	p.T247M	ENST00000265678.4	37	c.740	CCDS5294.1	6	.	.	.	.	.	.	.	.	.	.	G	28.2	4.899968	0.92035	.	.	ENSG00000071242	ENST00000265678;ENST00000510118;ENST00000503859;ENST00000481261;ENST00000405189;ENST00000366863	T;T;T;T;T;T	0.76839	0.79;0.79;0.79;0.79;0.79;-1.05	4.89	4.89	0.63831	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91707	0.7378	H	0.97240	3.965	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.985;0.975;0.995	D	0.94548	0.7751	10	0.87932	D	0	.	17.4164	0.87502	0.0:0.0:1.0:0.0	.	247;230;222	F2Z2J1;Q15349-3;Q15349	.;.;KS6A2_HUMAN	M	222;247;230;133;133;68	ENSP00000265678:T222M;ENSP00000422435:T247M;ENSP00000427015:T230M;ENSP00000422484:T133M;ENSP00000386050:T133M;ENSP00000355828:T68M	ENSP00000265678:T222M	T	-	2	0	RPS6KA2	166832068	1.000000	0.71417	0.709000	0.30452	0.903000	0.53119	9.057000	0.93889	2.403000	0.81681	0.655000	0.94253	ACG	RPS6KA2	-	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pirsf_Ribosomal_S6_kinase_II,pfscan_Prot_kinase_cat_dom	ENSG00000071242		0.607	RPS6KA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RPS6KA2	HGNC	protein_coding	OTTHUMT00000043075.3	45	0.00	0	G	NM_021135		166912078	166912078	-1	no_errors	ENST00000510118	ensembl	human	known	69_37n	missense	48	26.15	17	SNP	1.000	A
RUNX1	861	genome.wustl.edu	37	21	36231791	36231791	+	Missense_Mutation	SNP	T	T	C			TCGA-BH-A0C3-01A-21D-A12Q-09	TCGA-BH-A0C3-11A-23D-A12Q-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	ec57ee0f-949e-4eee-91c2-dd129d657065	128e802b-64d9-42d9-8a22-59c8ce061eb4	g.chr21:36231791T>C	ENST00000344691.4	-	3	2089	c.512A>G	c.(511-513)gAt>gGt	p.D171G	RUNX1_ENST00000325074.5_Missense_Mutation_p.D186G|RUNX1_ENST00000358356.5_Missense_Mutation_p.D171G|RUNX1_ENST00000300305.3_Missense_Mutation_p.D198G|RUNX1_ENST00000486278.2_Missense_Mutation_p.D174G|RUNX1_ENST00000437180.1_Missense_Mutation_p.D198G|RUNX1_ENST00000399240.1_Missense_Mutation_p.D171G	NM_001001890.2	NP_001001890.1	Q01196	RUNX1_HUMAN	runt-related transcription factor 1	171	Interaction with DNA.|Runt. {ECO:0000255|PROSITE- ProRule:PRU00399}.				behavioral response to pain (GO:0048266)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system development (GO:0007417)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|hair follicle morphogenesis (GO:0031069)|hematopoietic stem cell proliferation (GO:0071425)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|myeloid cell differentiation (GO:0030099)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of granulocyte differentiation (GO:0030853)|peripheral nervous system neuron development (GO:0048935)|positive regulation of angiogenesis (GO:0045766)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of progesterone secretion (GO:2000872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hair follicle cell proliferation (GO:0071336)|regulation of signal transduction (GO:0009966)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.D198G(6)|p.D198V(2)		breast(5)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(428)|large_intestine(3)|lung(6)|oesophagus(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	452						TCGGGGCCCATCCACTGTGAT	0.552			T	"""RPL22, MDS1, EVI1, CBFA2T3, CBFA2T1, ETV6, LAF4"""	"""AML, preB- ALL, T-ALL"""																																	dbGAP		Dom	yes		21	21q22.3	861	runt-related transcription factor 1  (AML1)		L	8	Substitution - Missense(8)	haematopoietic_and_lymphoid_tissue(8)											295.0	257.0	270.0					21																	36231791		2203	4300	6503	-	-	-	SO:0001583	missense	0			X79549	CCDS13639.1, CCDS42922.1, CCDS46646.1	21q22.3	2014-09-17	2008-07-29		ENSG00000159216	ENSG00000159216			10471	protein-coding gene	gene with protein product	"""aml1 oncogene"""	151385	"""acute myeloid leukemia 1"""	AML1, CBFA2		1427868, 7835892	Standard	NM_001001890		Approved	PEBP2A2, AMLCR1	uc010gmv.3	Q01196	OTTHUMG00000086299	ENST00000344691.4:c.512A>G	21.37:g.36231791T>C	ENSP00000340690:p.Asp171Gly	Somatic		WXS	Illumina GAIIx	Phase_IV	A8MV94|B2RMS4|D3DSG1|O60472|O60473|O76047|O76089|Q13081|Q13755|Q13756|Q13757|Q13758|Q13759|Q15341|Q15343|Q16122|Q16284|Q16285|Q16286|Q16346|Q16347|Q92479	Missense_Mutation	SNP	pfam_AML1/Runt_N,pfam_RunxI,superfamily_p53-like_TF_DNA-bd,pirsf_TF_Runt-rel_RUNX,pfscan_AML1/Runt_N,prints_AML1_Runt	p.D198G	ENST00000344691.4	37	c.593	CCDS42922.1	21	.	.	.	.	.	.	.	.	.	.	T	24.6	4.554490	0.86231	.	.	ENSG00000159216	ENST00000344691;ENST00000300305;ENST00000437180;ENST00000325074;ENST00000399240;ENST00000399245;ENST00000358356;ENST00000399237;ENST00000486278	D;D;D;D;D;D;D;D	0.99722	-6.53;-6.53;-6.53;-6.53;-6.53;-6.53;-6.53;-6.53	5.12	5.12	0.69794	Acute myeloid leukemia 1 (AML 1)/Runt (2);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99725	0.9893	M	0.91300	3.195	0.80722	D	1	D;D;D;P;P;D;D	0.89917	0.991;1.0;0.98;0.885;0.605;0.996;0.997	D;D;D;P;P;D;D	0.91635	0.944;0.999;0.983;0.869;0.597;0.964;0.998	D	0.97379	0.9981	10	0.87932	D	0	-14.8335	12.8933	0.58084	0.0:0.0:0.0:1.0	.	198;171;171;174;198;186;171	Q2TAM6;Q01196-5;Q01196-3;C9JK12;Q01196-8;Q01196-10;Q01196	.;.;.;.;.;.;RUNX1_HUMAN	G	171;198;198;186;171;174;171;186;174	ENSP00000340690:D171G;ENSP00000300305:D198G;ENSP00000409227:D198G;ENSP00000319459:D186G;ENSP00000382184:D171G;ENSP00000351123:D171G;ENSP00000382182:D186G;ENSP00000438019:D174G	ENSP00000300305:D198G	D	-	2	0	RUNX1	35153661	1.000000	0.71417	0.983000	0.44433	0.991000	0.79684	7.698000	0.84413	1.926000	0.55796	0.533000	0.62120	GAT	RUNX1	-	pfam_AML1/Runt_N,superfamily_p53-like_TF_DNA-bd,pirsf_TF_Runt-rel_RUNX,pfscan_AML1/Runt_N,prints_AML1_Runt	ENSG00000159216		0.552	RUNX1-001	KNOWN	basic|CCDS	protein_coding	RUNX1	HGNC	protein_coding	OTTHUMT00000194230.1	434	0.23	1	T			36231791	36231791	-1	no_errors	ENST00000300305	ensembl	human	known	69_37n	missense	485	19.27	116	SNP	1.000	C
TNFRSF10C	8794	genome.wustl.edu	37	8	22973124	22973124	+	Silent	SNP	T	T	C			TCGA-BH-A0C3-01A-21D-A12Q-09	TCGA-BH-A0C3-11A-23D-A12Q-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	ec57ee0f-949e-4eee-91c2-dd129d657065	128e802b-64d9-42d9-8a22-59c8ce061eb4	g.chr8:22973124T>C	ENST00000356864.3	+	4	916	c.384T>C	c.(382-384)tgT>tgC	p.C128C	TNFRSF10C_ENST00000540813.1_Silent_p.C26C	NM_003841.3	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	128					apoptotic process (GO:0006915)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(6)|lung(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		GCCGGAAGTGTAGCAGGTGAG	0.522																																						dbGAP											0													78.0	72.0	74.0					8																	22973124		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF012536	CCDS6037.1	8p22-p21	2006-02-22			ENSG00000173535	ENSG00000173535		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11906	protein-coding gene	gene with protein product		603613				9314565, 9325248	Standard	NM_003841		Approved	DcR1, TRAILR3, LIT, TRID, CD263	uc003xcy.3	O14798	OTTHUMG00000097844	ENST00000356864.3:c.384T>C	8.37:g.22973124T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	O14755|Q08AS6|Q6FH98|Q6UXM5	Silent	SNP	pfam_TNFR/NGFR_Cys_rich_reg,smart_TNFR/NGFR_Cys_rich_reg,prints_TNFR_10,pfscan_TNFR/NGFR_Cys_rich_reg	p.C128	ENST00000356864.3	37	c.384	CCDS6037.1	8																																																																																			TNFRSF10C	-	pfam_TNFR/NGFR_Cys_rich_reg,smart_TNFR/NGFR_Cys_rich_reg,prints_TNFR_10,pfscan_TNFR/NGFR_Cys_rich_reg	ENSG00000173535		0.522	TNFRSF10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TNFRSF10C	HGNC	protein_coding	OTTHUMT00000215134.3	71	0.00	0	T			22973124	22973124	+1	no_errors	ENST00000356864	ensembl	human	known	69_37n	silent	106	15.87	20	SNP	0.000	C
TP53	7157	genome.wustl.edu	37	17	7578371	7578371	+	Splice_Site	SNP	C	C	T			TCGA-BH-A0C3-01A-21D-A12Q-09	TCGA-BH-A0C3-11A-23D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	ec57ee0f-949e-4eee-91c2-dd129d657065	128e802b-64d9-42d9-8a22-59c8ce061eb4	g.chr17:7578371C>T	ENST00000269305.4	-	5	748	c.559G>A	c.(559-561)Ggt>Agt	p.G187S	TP53_ENST00000413465.2_Splice_Site_p.G187S|TP53_ENST00000420246.2_Splice_Site_p.G187S|TP53_ENST00000445888.2_Splice_Site_p.G187S|TP53_ENST00000455263.2_Splice_Site_p.G187S|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000359597.4_Splice_Site_p.G187S	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	187	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		G -> C (in sporadic cancers; somatic mutation).|G -> D (in sporadic cancers; somatic mutation).|G -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|G -> R (in sporadic cancers; somatic mutation).|G -> S (in sporadic cancers; somatic mutation).|G -> V (in sporadic cancers; 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.G187S(14)|p.0?(8)|p.?(2)|p.V173fs*59(2)|p.G187fs*16(2)|p.G187C(2)|p.D186_P191delDGLAPP(1)|p.L188fs*19(1)|p.G187_L188delGL(1)|p.G187fs*60(1)|p.G187fs*22(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)	AGCTGCTCACCATCGCTATCT	0.637		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"""	35	Substitution - Missense(16)|Whole gene deletion(8)|Deletion - Frameshift(6)|Deletion - In frame(2)|Unknown(2)|Insertion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(6)|breast(5)|bone(4)|liver(4)|upper_aerodigestive_tract(3)|large_intestine(3)|lung(3)|central_nervous_system(2)|stomach(1)|urinary_tract(1)|skin(1)|oesophagus(1)|pancreas(1)											48.0	47.0	47.0					17																	7578371		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.559+1G>A	17.37:g.7578371C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	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.G187S	ENST00000269305.4	37	c.559	CCDS11118.1	17	.	.	.	.	.	.	.	.	.	.	C	12.78	2.041601	0.35989	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99751	-6.63;-6.63;-6.63;-6.63;-6.63;-6.63;-6.63;-6.63	4.7	4.7	0.59300	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.104625	0.64402	D	0.000005	D	0.98924	0.9635	L	0.28192	0.835	0.51012	D	0.999903	B;B;B;B;B;B;P	0.46656	0.099;0.012;0.031;0.065;0.014;0.143;0.882	B;B;B;B;B;B;P	0.46975	0.124;0.06;0.063;0.132;0.099;0.27;0.533	D	0.99577	1.0972	9	.	.	.	-7.9296	15.9577	0.79898	0.0:1.0:0.0:0.0	.	148;187;187;94;187;187;187	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	S	187;187;187;187;187;187;176;94;55;94;55	ENSP00000410739:G187S;ENSP00000352610:G187S;ENSP00000269305:G187S;ENSP00000398846:G187S;ENSP00000391127:G187S;ENSP00000391478:G187S;ENSP00000425104:G55S;ENSP00000423862:G94S	.	G	-	1	0	TP53	7519096	1.000000	0.71417	0.944000	0.38274	0.185000	0.23345	2.866000	0.48420	2.545000	0.85829	0.655000	0.94253	GGT	TP53	-	pfam_p53_DNA-bd,superfamily_p53-like_TF_DNA-bd	ENSG00000141510		0.637	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TP53	HGNC	protein_coding	OTTHUMT00000367397.1	63	0.00	0	C	NM_000546	Missense_Mutation	7578371	7578371	-1	no_errors	ENST00000269305	ensembl	human	known	69_37n	missense	57	24.00	18	SNP	1.000	T
UCK2	7371	genome.wustl.edu	37	1	165872480	165872480	+	Silent	SNP	G	G	C	rs372509507		TCGA-BH-A0C3-01A-21D-A12Q-09	TCGA-BH-A0C3-11A-23D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	ec57ee0f-949e-4eee-91c2-dd129d657065	128e802b-64d9-42d9-8a22-59c8ce061eb4	g.chr1:165872480G>C	ENST00000367879.4	+	5	864	c.561G>C	c.(559-561)acG>acC	p.T187T	RP11-525G13.2_ENST00000455257.2_RNA|UCK2_ENST00000462329.1_3'UTR|UCK2_ENST00000469256.2_Silent_p.T37T|UCK2_ENST00000372212.4_3'UTR|UCK2_ENST00000470820.1_Silent_p.T37T	NM_012474.4	NP_036606.2	Q9BZX2	UCK2_HUMAN	uridine-cytidine kinase 2	187					cellular response to oxygen levels (GO:0071453)|CTP salvage (GO:0044211)|feeding behavior (GO:0007631)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|response to axon injury (GO:0048678)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)|nucleoside kinase activity (GO:0019206)|uridine kinase activity (GO:0004849)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	10	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)					AGTACATTACGTTCGTCAAGC	0.378																																						dbGAP											0													255.0	217.0	229.0					1																	165872480		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF236637	CCDS1252.1	1p32	2012-10-02	2004-07-13	2004-07-14	ENSG00000143179	ENSG00000143179	2.7.1.48		12562	protein-coding gene	gene with protein product		609329	"""uridine monophosphate kinase"""	UMPK			Standard	NM_012474		Approved		uc001gdp.3	Q9BZX2	OTTHUMG00000040117	ENST00000367879.4:c.561G>C	1.37:g.165872480G>C		Somatic		WXS	Illumina GAIIx	Phase_IV	Q5VV91|Q7KZV3|Q92528|Q96KG5|Q9BU42	Silent	SNP	pfam_PRK/URK,pfam_Depp_CoAkinase,prints_Uridine_kinase,prints_PRK,tigrfam_Uridine_kinase	p.T187	ENST00000367879.4	37	c.561	CCDS1252.1	1																																																																																			UCK2	-	pfam_PRK/URK,tigrfam_Uridine_kinase	ENSG00000143179		0.378	UCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	UCK2	HGNC	protein_coding	OTTHUMT00000096753.1	389	0.26	1	G	NM_012474		165872480	165872480	+1	no_errors	ENST00000367879	ensembl	human	known	69_37n	silent	565	17.64	121	SNP	0.000	C
ZNF462	58499	genome.wustl.edu	37	9	109771874	109771874	+	Missense_Mutation	SNP	G	G	A	rs199563340		TCGA-BH-A0C3-01A-21D-A12Q-09	TCGA-BH-A0C3-11A-23D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	ec57ee0f-949e-4eee-91c2-dd129d657065	128e802b-64d9-42d9-8a22-59c8ce061eb4	g.chr9:109771874G>A	ENST00000277225.5	+	12	7527	c.7238G>A	c.(7237-7239)cGt>cAt	p.R2413H	ZNF462_ENST00000542028.1_Missense_Mutation_p.R370H|ZNF462_ENST00000441147.2_Missense_Mutation_p.R1319H|RP11-508N12.2_ENST00000439901.1_RNA|ZNF462_ENST00000457913.1_Missense_Mutation_p.R2473H			Q96JM2	ZN462_HUMAN	zinc finger protein 462	2413					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						ACTGAGAAGCGTTTTCCATGT	0.493																																						dbGAP											0													125.0	116.0	119.0					9																	109771874		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"""Zinc fingers, C2H2-type"""	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.7238G>A	9.37:g.109771874G>A	ENSP00000277225:p.Arg2413His	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5T0T4|Q8N408	Missense_Mutation	SNP	smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.R2473H	ENST00000277225.5	37	c.7418	CCDS35096.1	9	.	.	.	.	.	.	.	.	.	.	G	34	5.302765	0.95601	.	.	ENSG00000148143	ENST00000277225;ENST00000457913;ENST00000374686;ENST00000441147;ENST00000542028	T;T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45;-0.45	5.67	5.67	0.87782	Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.123268	0.56097	D	0.000032	T	0.79516	0.4459	L	0.52126	1.63	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.987	T	0.79429	-0.1807	10	0.59425	D	0.04	.	19.7664	0.96346	0.0:0.0:1.0:0.0	.	2473;2413	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	H	2413;2473;1356;1319;370	ENSP00000277225:R2413H;ENSP00000414570:R2473H;ENSP00000363818:R1356H;ENSP00000397306:R1319H;ENSP00000439771:R370H	ENSP00000277225:R2413H	R	+	2	0	ZNF462	108811695	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.164000	0.89661	2.671000	0.90904	0.557000	0.71058	CGT	ZNF462	-	NULL	ENSG00000148143		0.493	ZNF462-001	KNOWN	basic|CCDS	protein_coding	ZNF462	HGNC	protein_coding	OTTHUMT00000053532.2	289	0.00	0	G	NM_021224		109771874	109771874	+1	no_errors	ENST00000457913	ensembl	human	known	69_37n	missense	254	21.60	70	SNP	1.000	A
