#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_EVS_AA	i_EVS_All	i_EVS_EA	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
APBA2	321	genome.wustl.edu	37	15	29346952	29346952	+	Missense_Mutation	SNP	G	G	A			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr15:29346952G>A	ENST00000558402.1	+	5	1464	c.865G>A	c.(865-867)Gag>Aag	p.E289K	APBA2_ENST00000411764.1_Missense_Mutation_p.E289K|APBA2_ENST00000561069.1_Missense_Mutation_p.E289K|APBA2_ENST00000558259.1_Missense_Mutation_p.E289K|APBA2_ENST00000558330.1_Missense_Mutation_p.E289K			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	289					in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CCTCCTTCCCGAGGCCAAGCA	0.667																																						dbGAP											0													19.0	23.0	22.0					15																	29346952		2202	4295	6497	-	-	-	SO:0001583	missense	0			AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"""X11-like"", ""amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"""	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.865G>A	15.37:g.29346952G>A	ENSP00000453293:p.Glu289Lys		E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	pfam_PTyr_interaction_dom,pfam_PDZ,superfamily_PDZ,smart_PTyr_interaction_dom,smart_PDZ,pfscan_PDZ,pfscan_PTyr_interaction_dom	p.E289K	ENST00000558402.1	37	c.865	CCDS10022.1	15	.	.	.	.	.	.	.	.	.	.	G	15.70	2.909895	0.52439	.	.	ENSG00000034053	ENST00000411764;ENST00000219865	T	0.26223	1.75	4.96	4.04	0.47022	.	0.285984	0.33235	N	0.005124	T	0.18087	0.0434	L	0.51422	1.61	0.27803	N	0.942427	B;B;B	0.34313	0.448;0.271;0.448	B;B;B	0.25140	0.058;0.042;0.037	T	0.14811	-1.0459	10	0.07325	T	0.83	.	12.691	0.56974	0.0812:0.0:0.9188:0.0	.	289;289;289	Q5XKC0;E9PGI4;Q99767	.;.;APBA2_HUMAN	K	289	ENSP00000409312:E289K	ENSP00000219865:E289K	E	+	1	0	APBA2	27134244	0.995000	0.38212	0.853000	0.33588	0.893000	0.52053	2.281000	0.43452	2.280000	0.76307	0.650000	0.86243	GAG	APBA2	-	NULL	ENSG00000034053		0.667	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	APBA2	HGNC	protein_coding	OTTHUMT00000251362.3	91	0.00	0	G	NM_005503		29346952	29346952	+1	no_errors	ENST00000558259	ensembl	human	known	69_37n	missense	76	32.74	37	SNP	0.991	A
CARNS1	57571	genome.wustl.edu	37	11	67184989	67184989	+	5'UTR	SNP	C	C	T			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr11:67184989C>T	ENST00000307823.3	+	0	198				CARNS1_ENST00000531040.1_Missense_Mutation_p.P39S|CARNS1_ENST00000445895.2_Missense_Mutation_p.P39S|CARNS1_ENST00000423745.2_5'UTR	NM_020811.1	NP_065862.1	A5YM72	CRNS1_HUMAN	carnosine synthase 1						ATP catabolic process (GO:0006200)|carnosine biosynthetic process (GO:0035499)		ATP binding (GO:0005524)|ATPase activity (GO:0016887)|carnosine synthase activity (GO:0047730)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)	11						AGGCTGCTTCCCTGGCTCCTG	0.697																																						dbGAP											0													5.0	10.0	9.0					11																	67184989		652	1536	2188	-	-	-	SO:0001623	5_prime_UTR_variant	0				CCDS44658.1, CCDS53667.1	11q13.1	2010-03-25	2010-03-25	2010-03-25	ENSG00000172508	ENSG00000172508			29268	protein-coding gene	gene with protein product		613368	"""ATP-grasp domain containing 1"""	ATPGD1		20097752	Standard	NM_020811		Approved	KIAA1394	uc010rpr.2	A5YM72		ENST00000307823.3:c.-255C>T	11.37:g.67184989C>T			A8K1M3|B4DFC6|E9PK38|F5H427|Q8N467|Q9P2F3	Missense_Mutation	SNP	superfamily_PreATP-grasp_fold,superfamily_TIL_dom,pfscan_ATP-grasp	p.P39S	ENST00000307823.3	37	c.115	CCDS44658.1	11	.	.	.	.	.	.	.	.	.	.	C	6.154	0.396666	0.11638	.	.	ENSG00000172508	ENST00000531040;ENST00000542831;ENST00000539452;ENST00000445895	T;T	0.33216	1.42;1.46	4.77	0.567	0.17325	.	.	.	.	.	T	0.15955	0.0384	N	0.19112	0.55	0.80722	D	1	B;B	0.14012	0.009;0.009	B;B	0.18561	0.015;0.022	T	0.08576	-1.0715	9	0.26408	T	0.33	.	5.3598	0.16081	0.0:0.5924:0.1555:0.2522	.	39;55	F5H427;A5YM72-3	.;.	S	39;39;55;39	ENSP00000431670:P39S;ENSP00000389009:P39S	ENSP00000389009:P39S	P	+	1	0	CARNS1	66941565	0.001000	0.12720	0.995000	0.50966	0.410000	0.31052	0.076000	0.14712	0.405000	0.25532	0.563000	0.77884	CCT	CARNS1	-	superfamily_TIL_dom	ENSG00000172508		0.697	CARNS1-001	KNOWN	basic|CCDS	protein_coding	CARNS1	HGNC	protein_coding	OTTHUMT00000395501.1	79	0.00	0	C	NM_020811		67184989	67184989	+1	no_errors	ENST00000445895	ensembl	human	known	69_37n	missense	45	34.78	24	SNP	0.932	T
C11orf53	341032	genome.wustl.edu	37	11	111156557	111156557	+	Silent	SNP	G	G	A			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr11:111156557G>A	ENST00000280325.4	+	4	636	c.489G>A	c.(487-489)tcG>tcA	p.S163S		NM_198498.1	NP_940900.1	Q8IXP5	CK053_HUMAN	chromosome 11 open reading frame 53	163										endometrium(1)|large_intestine(2)|lung(3)|skin(2)	8		all_cancers(61;2.05e-09)|Melanoma(852;4.04e-05)|all_epithelial(67;6.15e-05)|all_hematologic(158;0.000826)|Acute lymphoblastic leukemia(157;0.000966)|all_neural(223;0.0332)|Medulloblastoma(222;0.0425)|Breast(348;0.147)		Epithelial(105;1.7e-06)|BRCA - Breast invasive adenocarcinoma(274;3.16e-06)|all cancers(92;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0507)		AGTCATACTCGCTGCATGCTC	0.622																																						dbGAP											0													100.0	95.0	97.0					11																	111156557		2201	4297	6498	-	-	-	SO:0001819	synonymous_variant	0			BC039669	CCDS31674.1	11q23.1	2012-05-31			ENSG00000150750	ENSG00000150750			30527	protein-coding gene	gene with protein product						12477932	Standard	NM_198498		Approved	MGC50104	uc001plc.3	Q8IXP5	OTTHUMG00000166656	ENST00000280325.4:c.489G>A	11.37:g.111156557G>A				Silent	SNP	NULL	p.S163	ENST00000280325.4	37	c.489	CCDS31674.1	11																																																																																			C11orf53	-	NULL	ENSG00000150750		0.622	C11orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C11orf53	HGNC	protein_coding	OTTHUMT00000390989.1	40	0.00	0	G	NM_198498		111156557	111156557	+1	no_errors	ENST00000280325	ensembl	human	known	69_37n	silent	8	68.00	17	SNP	0.054	A
CDH7	1005	genome.wustl.edu	37	18	63529956	63529956	+	Nonsense_Mutation	SNP	C	C	A			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr18:63529956C>A	ENST00000397968.2	+	11	2093	c.1667C>A	c.(1666-1668)tCa>tAa	p.S556*	CDH7_ENST00000536984.2_Nonsense_Mutation_p.S556*|RP11-389J22.1_ENST00000581987.1_RNA|CDH7_ENST00000323011.3_Nonsense_Mutation_p.S556*	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	556	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				CAGGAACAATCAGTTTACTAT	0.473																																						dbGAP											0													146.0	121.0	129.0					18																	63529956		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"""Cadherins / Major cadherins"""	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.1667C>A	18.37:g.63529956C>A	ENSP00000381058:p.Ser556*		Q9H157	Nonsense_Mutation	SNP	pfam_Cadherin,pfam_Cadherin_cytoplasmic-dom,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.S556*	ENST00000397968.2	37	c.1667	CCDS11993.1	18	.	.	.	.	.	.	.	.	.	.	C	40	8.044221	0.98627	.	.	ENSG00000081138	ENST00000323011;ENST00000536984;ENST00000397966;ENST00000397968	.	.	.	5.37	5.37	0.77165	.	0.118424	0.64402	D	0.000016	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.0909	0.93227	0.0:1.0:0.0:0.0	.	.	.	.	X	556	.	ENSP00000319166:S556X	S	+	2	0	CDH7	61680936	0.043000	0.20138	0.064000	0.19789	0.383000	0.30230	3.223000	0.51231	2.528000	0.85240	0.591000	0.81541	TCA	CDH7	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin	ENSG00000081138		0.473	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDH7	HGNC	protein_coding	OTTHUMT00000256217.2	66	0.00	0	C	NM_033646		63529956	63529956	+1	no_errors	ENST00000323011	ensembl	human	known	69_37n	nonsense	41	39.71	27	SNP	0.988	A
CSTF2	1478	genome.wustl.edu	37	X	100093207	100093207	+	Intron	DEL	T	T	-			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chrX:100093207delT	ENST00000372972.2	+	13	1627				CSTF2_ENST00000415585.2_Intron	NM_001325.2	NP_001316.1	P33240	CSTF2_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa						gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cleavage body (GO:0071920)|mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|skin(2)|stomach(1)	13						ACTCACTACCTTTTTTTTTTC	0.418																																						dbGAP											0													66.0	66.0	66.0					X																	100093207		2201	4300	6501	-	-	-	SO:0001627	intron_variant	0			BC017712	CCDS14473.1	Xq22.1	2013-02-12	2002-08-29		ENSG00000101811	ENSG00000101811		"""RNA binding motif (RRM) containing"""	2484	protein-coding gene	gene with protein product		300907	"""cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kD"""			1741396	Standard	XM_006724622		Approved		uc004egh.3	P33240	OTTHUMG00000022709	ENST00000372972.2:c.1612-21T>-	X.37:g.100093207delT			Q5H951|Q6LA74|Q8N502	RNA	DEL	-	NULL	ENST00000372972.2	37	NULL	CCDS14473.1	X																																																																																			CSTF2	-	-	ENSG00000101811		0.418	CSTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CSTF2	HGNC	protein_coding	OTTHUMT00000058926.1	16	0.00	0	T	NM_001325		100093207	100093207	+1	no_errors	ENST00000486615	ensembl	human	known	69_37n	rna	8	27.27	3	DEL	0.003	-
CUL2	8453	genome.wustl.edu	37	10	35314087	35314087	+	Missense_Mutation	SNP	G	G	T			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr10:35314087G>T	ENST00000374748.1	-	18	1970	c.1657C>A	c.(1657-1659)Ctt>Att	p.L553I	CUL2_ENST00000374746.1_Missense_Mutation_p.L553I|CUL2_ENST00000602371.1_Missense_Mutation_p.L496I|CUL2_ENST00000374751.3_Missense_Mutation_p.L553I|CUL2_ENST00000374742.1_Missense_Mutation_p.L553I|CUL2_ENST00000537177.1_Missense_Mutation_p.L572I|CUL2_ENST00000374749.3_Missense_Mutation_p.L553I			Q13617	CUL2_HUMAN	cullin 2	553					cell cycle arrest (GO:0007050)|cellular response to hypoxia (GO:0071456)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|VCB complex (GO:0030891)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|prostate(2)|skin(1)|urinary_tract(2)	31						AACCATGTAAGTTTCCTTCCA	0.254																																						dbGAP											0													44.0	45.0	45.0					10																	35314087		2199	4293	6492	-	-	-	SO:0001583	missense	0			U83410	CCDS7179.1, CCDS73086.1	10p11.2	2011-05-24			ENSG00000108094	ENSG00000108094			2552	protein-coding gene	gene with protein product		603135				8681378	Standard	NM_003591		Approved		uc021ppa.1	Q13617	OTTHUMG00000017950	ENST00000374748.1:c.1657C>A	10.37:g.35314087G>T	ENSP00000363880:p.Leu553Ile		B3KT95|B7Z6K8|D3DRY6|G3V1S2|O00200|Q5T2B6|Q9UNF9	Missense_Mutation	SNP	pfam_Cullin_N,pfam_Cullin_neddylation_domain,superfamily_Cullin_repeat-like_dom,superfamily_Cullin_homology,smart_Cullin_homology,smart_Cullin_neddylation_domain,pfscan_Cullin_homology	p.L572I	ENST00000374748.1	37	c.1714	CCDS7179.1	10	.	.	.	.	.	.	.	.	.	.	G	23.1	4.380903	0.82792	.	.	ENSG00000108094	ENST00000374751;ENST00000374748;ENST00000374746;ENST00000374749;ENST00000374754;ENST00000374742;ENST00000537177	D;D;D;D;D;D	0.88975	-2.45;-2.45;-2.45;-2.45;-2.45;-2.45	5.85	5.85	0.93711	Cullin, N-terminal (1);Cullin homology (3);	0.000000	0.85682	D	0.000000	D	0.94739	0.8302	M	0.81497	2.545	0.80722	D	1	D;D;D	0.69078	0.997;0.994;0.995	D;D;D	0.67382	0.936;0.919;0.951	D	0.94685	0.7869	10	0.87932	D	0	-20.1788	20.1731	0.98165	0.0:0.0:1.0:0.0	.	553;572;553	Q5T2B5;G3V1S2;Q13617	.;.;CUL2_HUMAN	I	553;553;553;553;496;553;572	ENSP00000363883:L553I;ENSP00000363880:L553I;ENSP00000363878:L553I;ENSP00000363881:L553I;ENSP00000363874:L553I;ENSP00000444856:L572I	ENSP00000363874:L553I	L	-	1	0	CUL2	35354093	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.046000	0.71029	2.768000	0.95171	0.655000	0.94253	CTT	CUL2	-	pfam_Cullin_N,superfamily_Cullin_homology,smart_Cullin_homology,pfscan_Cullin_homology	ENSG00000108094		0.254	CUL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	CUL2	HGNC	protein_coding	OTTHUMT00000047538.1	52	0.00	0	G	NM_003591		35314087	35314087	-1	no_errors	ENST00000537177	ensembl	human	known	69_37n	missense	32	40.74	22	SNP	1.000	T
DMD	1756	genome.wustl.edu	37	X	31198556	31198556	+	Missense_Mutation	SNP	G	G	T			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chrX:31198556G>T	ENST00000357033.4	-	69	10223	c.10017C>A	c.(10015-10017)agC>agA	p.S3339R	DMD_ENST00000378723.3_Missense_Mutation_p.S271R|DMD_ENST00000378680.2_Missense_Mutation_p.S271R|DMD_ENST00000359836.1_Missense_Mutation_p.S879R|DMD_ENST00000343523.2_Missense_Mutation_p.S879R|DMD_ENST00000361471.4_Missense_Mutation_p.S271R|DMD_ENST00000378707.3_Missense_Mutation_p.S879R|DMD_ENST00000378677.2_Missense_Mutation_p.S3335R|DMD_ENST00000474231.1_Missense_Mutation_p.S879R|DMD_ENST00000541735.1_Missense_Mutation_p.S879R|DMD_ENST00000378702.4_Missense_Mutation_p.S271R	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	3339	Interaction with SYNM. {ECO:0000250}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				AAAAAAAGCAGCTTTGGCAGA	0.408																																						dbGAP											0													123.0	106.0	112.0					X																	31198556		2202	4300	6502	-	-	-	SO:0001583	missense	0			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.10017C>A	X.37:g.31198556G>T	ENSP00000354923:p.Ser3339Arg		E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	pfam_Spectrin_repeat,pfam_EF-hand_dom_typ1,pfam_EF-hand_dom_typ2,pfam_CH-domain,pfam_Znf_ZZ,pfam_WW_Rsp5_WWP,pfam_CAMSAP_CH,superfamily_CH-domain,superfamily_WW_Rsp5_WWP,smart_CH-domain,smart_Spectrin/alpha-actinin,smart_WW_Rsp5_WWP,smart_Znf_ZZ,pirsf_Dystrophin/utrophin,pfscan_CH-domain,pfscan_WW_Rsp5_WWP,pfscan_Znf_ZZ	p.S3339R	ENST00000357033.4	37	c.10017	CCDS14233.1	X	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.73|18.73	3.686211|3.686211	0.68157|0.68157	.|.	.|.	ENSG00000198947|ENSG00000198947	ENST00000465285|ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378723;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000378702;ENST00000474231;ENST00000361471;ENST00000378680;ENST00000378705	.|D;D;D;D;D;D;D;D;D;D;D;D;D	.|0.91945	.|-2.94;-2.94;-2.94;-2.94;-2.94;-2.94;-2.94;-2.94;-2.94;-2.94;-2.94;-2.94;-2.94	5.24|5.24	1.0|1.0	0.19881|0.19881	.|Zinc finger, ZZ-type (4);	.|0.000000	.|0.41001	.|U	.|0.000973	D|D	0.94215|0.94215	0.8143|0.8143	M|M	0.69358|0.69358	2.11|2.11	0.58432|0.58432	D|D	0.999998|0.999998	.|D;D;D;D;D;D;P;D;D;D;D;D;D;D;B;D	.|0.89917	.|0.996;0.98;0.999;1.0;0.999;0.999;0.746;0.999;0.999;1.0;1.0;0.998;0.994;1.0;0.36;0.999	.|D;P;D;D;D;D;P;D;D;D;D;D;D;D;B;D	.|0.91635	.|0.985;0.903;0.996;0.999;0.996;0.996;0.535;0.986;0.993;0.998;0.997;0.991;0.983;0.995;0.414;0.996	D|D	0.92599|0.92599	0.6089|0.6089	5|10	.|0.72032	.|D	.|0.01	.|.	10.1455|10.1455	0.42760|0.42760	0.4013:0.0:0.5987:0.0|0.4013:0.0:0.5987:0.0	.|.	.|271;3331;3339;3335;1998;1995;879;879;879;879;879;3216;271;271;271;271	.|B4DSV7;P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6;F8VX32;E7ESB2;E7EQS5;E7EQR9;F5GZY3;F5GZT3;P11532-5;Q8N754;Q6NSJ9;E9PDN1	.|.;.;DMD_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.	M|R	1068|3331;1998;1995;271;1035;3335;3339;879;879;3339;3216;879;879;271;879;271;271;129	.|ENSP00000367997:S271R;ENSP00000350765:S1035R;ENSP00000367948:S3335R;ENSP00000354923:S3339R;ENSP00000352894:S879R;ENSP00000340057:S879R;ENSP00000367979:S879R;ENSP00000444119:S879R;ENSP00000367974:S271R;ENSP00000417123:S879R;ENSP00000354464:S271R;ENSP00000367951:S271R;ENSP00000367977:S129R	.|ENSP00000340057:S879R	L|S	-|-	1|3	2|2	DMD|DMD	31108477|31108477	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.207000|2.207000	0.42788|0.42788	0.123000|0.123000	0.18342|0.18342	0.544000|0.544000	0.68410|0.68410	CTG|AGC	DMD	-	pfam_Znf_ZZ,smart_Znf_ZZ,pirsf_Dystrophin/utrophin,pfscan_Znf_ZZ	ENSG00000198947		0.408	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DMD	HGNC	protein_coding	OTTHUMT00000056182.2	40	0.00	0	G	NM_004006		31198556	31198556	-1	no_errors	ENST00000357033	ensembl	human	known	69_37n	missense	21	38.24	13	SNP	1.000	T
EHD3	30845	genome.wustl.edu	37	2	31483605	31483605	+	Silent	SNP	G	G	A			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr2:31483605G>A	ENST00000322054.5	+	4	1017	c.732G>A	c.(730-732)gtG>gtA	p.V244V	EHD3_ENST00000541626.1_Intron	NM_014600.2	NP_055415.1	Q9NZN3	EHD3_HUMAN	EH-domain containing 3	244	Dynamin-type G.				blood coagulation (GO:0007596)|endocytic recycling (GO:0032456)|protein homooligomerization (GO:0051260)|protein targeting to plasma membrane (GO:0072661)|regulation of cardiac muscle cell membrane potential (GO:0086036)	cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|skin(3)	33	Acute lymphoblastic leukemia(172;0.155)					GGAAGATCGTGAACACCCCAG	0.592																																						dbGAP											0													103.0	95.0	98.0					2																	31483605		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF181264	CCDS1774.1	2p21	2013-01-10			ENSG00000013016	ENSG00000013016		"""EF-hand domain containing"""	3244	protein-coding gene	gene with protein product		605891		PAST3		10673336	Standard	NM_014600		Approved		uc002rnu.3	Q9NZN3	OTTHUMG00000099365	ENST00000322054.5:c.732G>A	2.37:g.31483605G>A			B4DFR5|D6W574|Q8N514|Q9NZB3	Silent	SNP	pfam_Dynamin_GTPase,smart_EPS15_homology,pfscan_EF_HAND_2,pfscan_EPS15_homology	p.V244	ENST00000322054.5	37	c.732	CCDS1774.1	2																																																																																			EHD3	-	NULL	ENSG00000013016		0.592	EHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EHD3	HGNC	protein_coding	OTTHUMT00000216810.1	51	0.00	0	G	NM_014600		31483605	31483605	+1	no_errors	ENST00000322054	ensembl	human	known	69_37n	silent	61	50.81	63	SNP	1.000	A
EHD3	30845	genome.wustl.edu	37	2	31489433	31489433	+	Missense_Mutation	SNP	G	G	A			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr2:31489433G>A	ENST00000322054.5	+	6	1756	c.1471G>A	c.(1471-1473)Gac>Aac	p.D491N	EHD3_ENST00000541626.1_3'UTR	NM_014600.2	NP_055415.1	Q9NZN3	EHD3_HUMAN	EH-domain containing 3	491	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.|EH. {ECO:0000255|PROSITE- ProRule:PRU00077}.				blood coagulation (GO:0007596)|endocytic recycling (GO:0032456)|protein homooligomerization (GO:0051260)|protein targeting to plasma membrane (GO:0072661)|regulation of cardiac muscle cell membrane potential (GO:0086036)	cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|skin(3)	33	Acute lymphoblastic leukemia(172;0.155)					GGCCGACATTGACAAGGATGG	0.587																																						dbGAP											0													116.0	100.0	105.0					2																	31489433		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF181264	CCDS1774.1	2p21	2013-01-10			ENSG00000013016	ENSG00000013016		"""EF-hand domain containing"""	3244	protein-coding gene	gene with protein product		605891		PAST3		10673336	Standard	NM_014600		Approved		uc002rnu.3	Q9NZN3	OTTHUMG00000099365	ENST00000322054.5:c.1471G>A	2.37:g.31489433G>A	ENSP00000327116:p.Asp491Asn		B4DFR5|D6W574|Q8N514|Q9NZB3	Missense_Mutation	SNP	pfam_Dynamin_GTPase,smart_EPS15_homology,pfscan_EF_HAND_2,pfscan_EPS15_homology	p.D491N	ENST00000322054.5	37	c.1471	CCDS1774.1	2	.	.	.	.	.	.	.	.	.	.	G	24.6	4.551253	0.86127	.	.	ENSG00000013016	ENST00000322054	T	0.36520	1.25	5.55	5.55	0.83447	EPS15 homology (EH) (2);EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.48003	0.1476	L	0.54908	1.71	0.80722	D	1	P	0.44627	0.839	P	0.49012	0.598	T	0.42085	-0.9472	10	0.54805	T	0.06	-39.5034	19.4915	0.95052	0.0:0.0:1.0:0.0	.	491	Q9NZN3	EHD3_HUMAN	N	491	ENSP00000327116:D491N	ENSP00000327116:D491N	D	+	1	0	EHD3	31342937	1.000000	0.71417	0.985000	0.45067	0.969000	0.65631	9.869000	0.99810	2.619000	0.88677	0.462000	0.41574	GAC	EHD3	-	smart_EPS15_homology,pfscan_EF_HAND_2,pfscan_EPS15_homology	ENSG00000013016		0.587	EHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EHD3	HGNC	protein_coding	OTTHUMT00000216810.1	51	0.00	0	G	NM_014600		31489433	31489433	+1	no_errors	ENST00000322054	ensembl	human	known	69_37n	missense	43	54.26	51	SNP	1.000	A
FMNL3	91010	genome.wustl.edu	37	12	50055828	50055828	+	Missense_Mutation	SNP	C	C	G			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr12:50055828C>G	ENST00000293590.5	-	5	606	c.373G>C	c.(373-375)Gtg>Ctg	p.V125L	FMNL3_ENST00000352151.5_Missense_Mutation_p.V125L|FMNL3_ENST00000335154.5_Missense_Mutation_p.V125L|FMNL3_ENST00000550488.1_Missense_Mutation_p.V125L			Q8IVF7	FMNL3_HUMAN	formin-like 3	125	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)	GTPase activating protein binding (GO:0032794)			breast(4)|endometrium(7)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|stomach(1)	39						AATTCCCGCACCCACCTGCAG	0.537																																						dbGAP											0													80.0	81.0	81.0					12																	50055828		1923	4136	6059	-	-	-	SO:0001583	missense	0			AK128195	CCDS41780.1, CCDS44874.1	12q13.12	2006-04-10							23698	protein-coding gene	gene with protein product						12684686	Standard	NM_198900		Approved	DKFZp762B245, MGC45819, WBP3	uc001ruv.1	Q8IVF7	OTTHUMG00000169651	ENST00000293590.5:c.373G>C	12.37:g.50055828C>G	ENSP00000293590:p.Val125Leu		B0JZA7|Q6ZRJ1	Missense_Mutation	SNP	pfam_FH2_actin-bd,pfam_Drf_FH3,pfam_Drf_GTPase-bd,superfamily_FH2_actin-bd,superfamily_ARM-type_fold,smart_Actin-bd_FH2/DRF_autoreg	p.V125L	ENST00000293590.5	37	c.373		12	.	.	.	.	.	.	.	.	.	.	C	25.4	4.637822	0.87760	.	.	ENSG00000161791	ENST00000335154;ENST00000550488;ENST00000352151;ENST00000293590	D;D;D;D	0.92299	-3.01;-3.01;-3.01;-3.01	4.41	4.41	0.53225	.	0.068014	0.56097	D	0.000023	D	0.95787	0.8629	M	0.81614	2.55	0.80722	D	1	D;P	0.61697	0.99;0.75	D;B	0.70935	0.971;0.24	D	0.95998	0.8991	10	0.59425	D	0.04	.	16.2917	0.82756	0.0:1.0:0.0:0.0	.	125;125	Q8IVF7-2;Q8IVF7-3	.;.	L	125	ENSP00000335655:V125L;ENSP00000447479:V125L;ENSP00000344311:V125L;ENSP00000293590:V125L	ENSP00000293590:V125L	V	-	1	0	FMNL3	48342095	1.000000	0.71417	0.998000	0.56505	0.810000	0.45777	7.587000	0.82613	2.460000	0.83146	0.462000	0.41574	GTG	FMNL3	-	pfam_Drf_GTPase-bd,superfamily_ARM-type_fold	ENSG00000161791		0.537	FMNL3-201	KNOWN	basic	protein_coding	FMNL3	HGNC	protein_coding		48	0.00	0	C	NM_175736		50055828	50055828	-1	no_errors	ENST00000293590	ensembl	human	known	69_37n	missense	26	39.53	17	SNP	1.000	G
GATA3	2625	genome.wustl.edu	37	10	8106093	8106094	+	Frame_Shift_Ins	INS	-	-	G			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr10:8106093_8106094insG	ENST00000346208.3	+	4	1368_1369	c.913_914insG	c.(913-915)cgafs	p.R305fs	GATA3_ENST00000461472.1_Intron|GATA3_ENST00000379328.3_Frame_Shift_Ins_p.R306fs			P23771	GATA3_HUMAN	GATA binding protein 3	305	Flexible linker.				anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cardiac right ventricle morphogenesis (GO:0003215)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|cellular response to interferon-alpha (GO:0035457)|cellular response to interleukin-4 (GO:0071353)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|developmental growth (GO:0048589)|ear development (GO:0043583)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|interferon-gamma secretion (GO:0072643)|interleukin-4 secretion (GO:0072602)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lymphocyte migration (GO:0072676)|male gonad development (GO:0008584)|mast cell differentiation (GO:0060374)|mesenchymal to epithelial transition (GO:0060231)|mesonephros development (GO:0001823)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell motility (GO:2000146)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in mesonephros development (GO:2000607)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation (GO:2000703)|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation (GO:2000734)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|nephric duct morphogenesis (GO:0072178)|neuron migration (GO:0001764)|norepinephrine biosynthetic process (GO:0042421)|otic vesicle development (GO:0071599)|parathyroid gland development (GO:0060017)|parathyroid hormone secretion (GO:0035898)|pharyngeal system development (GO:0060037)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of signal transduction (GO:0009967)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureteric bud formation (GO:0072107)|post-embryonic development (GO:0009791)|pro-T cell differentiation (GO:0002572)|regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043370)|regulation of cellular response to X-ray (GO:2000683)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of establishment of cell polarity (GO:2000114)|regulation of histone H3-K27 methylation (GO:0061085)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to virus (GO:0009615)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|T cell receptor signaling pathway (GO:0050852)|T-helper 2 cell differentiation (GO:0045064)|thymic T cell selection (GO:0045061)|thymus development (GO:0048538)|TOR signaling (GO:0031929)|transcription from RNA polymerase II promoter (GO:0006366)|type IV hypersensitivity (GO:0001806)|ureter maturation (GO:0035799)|ureteric bud formation (GO:0060676)|uterus development (GO:0060065)|ventricular septum development (GO:0003281)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer sequence-specific DNA binding (GO:0001158)|HMG box domain binding (GO:0071837)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			NS(1)|breast(44)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(24)|ovary(3)|skin(2)	87						TAAGCCCAAGCGAAGGCTGGTA	0.55			"""F, N, S"""		breast		"""HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"""																															dbGAP		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	0																																										-	-	-	SO:0001589	frameshift_variant	0			X55122	CCDS7083.1, CCDS31143.1	10p15	2013-01-25	2001-11-28		ENSG00000107485	ENSG00000107485		"""GATA zinc finger domain containing"""	4172	protein-coding gene	gene with protein product		131320	"""GATA-binding protein 3"""			2050118, 15087456	Standard	NM_002051		Approved	HDR	uc001ijz.3	P23771	OTTHUMG00000017640	ENST00000346208.3:c.914dupG	10.37:g.8106094_8106094dupG	ENSP00000341619:p.Arg305fs		Q5VWG7|Q5VWG8|Q96J16	Frame_Shift_Ins	INS	pfam_Znf_GATA,smart_Znf_GATA,pirsf_TF_GATA-1/2/3,pfscan_Znf_GATA,prints_Znf_GATA	p.R307fs	ENST00000346208.3	37	c.916_917	CCDS7083.1	10																																																																																			GATA3	-	smart_Znf_GATA,pirsf_TF_GATA-1/2/3,pfscan_Znf_GATA	ENSG00000107485		0.550	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	GATA3	HGNC	protein_coding	OTTHUMT00000046719.1	50	0.00	0	-	NM_001002295		8106093	8106094	+1	no_errors	ENST00000379328	ensembl	human	known	69_37n	frame_shift_ins	36	29.41	15	INS	1.000:1.000	G
HDAC6	10013	genome.wustl.edu	37	X	48681345	48681345	+	Missense_Mutation	SNP	T	T	A			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chrX:48681345T>A	ENST00000334136.5	+	25	2714	c.2536T>A	c.(2536-2538)Tcc>Acc	p.S846T	HDAC6_ENST00000444343.2_Missense_Mutation_p.S860T|HDAC6_ENST00000376619.2_Missense_Mutation_p.S846T			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	846					aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	AGAAGGACCCTCCAGTTCTAA	0.552																																					Pancreas(112;205 1675 2305 8976 15959)	dbGAP											0													57.0	47.0	50.0					X																	48681345		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 90"""	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.2536T>A	X.37:g.48681345T>A	ENSP00000334061:p.Ser846Thr		O94975|Q6NT75|Q7L3E5|Q96CY0	Missense_Mutation	SNP	pfam_His_deacetylse_dom,pfam_Znf_UBP,smart_Znf_UBP,pfscan_Znf_UBP,prints_His_deacetylse	p.S860T	ENST00000334136.5	37	c.2578	CCDS14306.1	X	.	.	.	.	.	.	.	.	.	.	T	10.84	1.462793	0.26248	.	.	ENSG00000094631	ENST00000444343;ENST00000334136;ENST00000376619	T;T;T	0.59906	0.23;0.23;0.23	5.05	3.91	0.45181	.	1.650830	0.03334	N	0.193763	T	0.49012	0.1532	L	0.52364	1.645	0.09310	N	1	B;B;P;B	0.34815	0.272;0.323;0.47;0.41	B;B;B;B	0.31390	0.073;0.059;0.129;0.049	T	0.41070	-0.9529	10	0.22109	T	0.4	-1.1559	4.0035	0.09590	0.0:0.108:0.2136:0.6784	.	836;209;494;846	B4DZN1;B3KY98;B3KVK5;Q9UBN7	.;.;.;HDAC6_HUMAN	T	860;846;846	ENSP00000398566:S860T;ENSP00000334061:S846T;ENSP00000365804:S846T	ENSP00000334061:S846T	S	+	1	0	HDAC6	48566289	0.002000	0.14202	0.003000	0.11579	0.091000	0.18340	1.299000	0.33424	1.973000	0.57446	0.486000	0.48141	TCC	HDAC6	-	NULL	ENSG00000094631		0.552	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	HDAC6	HGNC	protein_coding	OTTHUMT00000083394.2	24	0.00	0	T	NM_006044		48681345	48681345	+1	no_errors	ENST00000444343	ensembl	human	known	69_37n	missense	13	43.48	10	SNP	0.000	A
HEATR5A	25938	genome.wustl.edu	37	14	31844038	31844038	+	Silent	SNP	T	T	C			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr14:31844038T>C	ENST00000389961.3	-	11	1826	c.1827A>G	c.(1825-1827)cgA>cgG	p.R609R	HEATR5A_ENST00000404677.3_Silent_p.R615R|HEATR5A_ENST00000439348.1_Silent_p.R609R|HEATR5A_ENST00000543095.2_Silent_p.R615R|HEATR5A_ENST00000439727.1_Silent_p.R322R			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	609										breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)	26	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		GTGCACCAGCTCGTCCTTCCA	0.438																																						dbGAP											0													60.0	63.0	62.0					14																	31844038		1977	4161	6138	-	-	-	SO:0001819	synonymous_variant	0			AB037737		14q12	2012-04-19	2007-01-02	2007-01-02	ENSG00000129493	ENSG00000129493			20276	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 125"""	C14orf125			Standard	NM_015473		Approved	DKFZP434I1735	uc001wrf.4	Q86XA9	OTTHUMG00000169043	ENST00000389961.3:c.1827A>G	14.37:g.31844038T>C			Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Missense_Mutation	SNP	superfamily_ARM-type_fold	p.E243G	ENST00000389961.3	37	c.728		14	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.51|10.51	1.371407|1.371407	0.24771|0.24771	.|.	.|.	ENSG00000129493|ENSG00000129493	ENST00000538864|ENST00000550366	.|.	.|.	.|.	5.75|5.75	0.804|0.804	0.18697|0.18697	.|.	.|.	.|.	.|.	.|.	T|T	0.41627|0.41627	0.1167|0.1167	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.32877|0.32877	-0.9890|-0.9890	4|4	.|.	.|.	.|.	.|.	1.6455|1.6455	0.02761|0.02761	0.377:0.0884:0.114:0.4206|0.377:0.0884:0.114:0.4206	.|.	.|.	.|.	.|.	G|G	243|258	.|.	.|.	E|S	-|-	2|1	0|0	HEATR5A|HEATR5A	30913789|30913789	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	0.486000|0.486000	0.22340|0.22340	0.973000|0.973000	0.38340|0.38340	0.528000|0.528000	0.53228|0.53228	GAG|AGC	HEATR5A	-	superfamily_ARM-type_fold	ENSG00000129493		0.438	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	HEATR5A	HGNC	protein_coding		26	0.00	0	T	NM_015473		31844038	31844038	-1	pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000538864	ensembl	human	novel	69_37n	missense	21	16.00	4	SNP	1.000	C
HMCN1	83872	genome.wustl.edu	37	1	186086186	186086186	+	Nonsense_Mutation	SNP	T	T	A			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr1:186086186T>A	ENST00000271588.4	+	76	11851	c.11622T>A	c.(11620-11622)taT>taA	p.Y3874*	HMCN1_ENST00000367492.2_Nonsense_Mutation_p.Y3874*	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3874	Ig-like C2-type 37.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CTGCAACCTATGAATGTACTG	0.403																																						dbGAP											0													163.0	150.0	154.0					1																	186086186		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.11622T>A	1.37:g.186086186T>A	ENSP00000271588:p.Tyr3874*		A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Nonsense_Mutation	SNP	pfam_Ig_I-set,pfam_Immunoglobulin,pfam_Ig_V-set,pfam_G2_nidogen/fibulin_G2F,pfam_EGF-like_Ca-bd,pfam_Thrombospondin_1_rpt,superfamily_Green_fluorescent_prot-like,superfamily_Thrombospondin_1_rpt,superfamily_Growth_fac_rcpt,superfamily_Cadherin-like,smart_Ig_sub,smart_Ig_sub2,smart_Ig_V-set_subgr,smart_Thrombospondin_1_rpt,smart_G2_nidogen/fibulin_G2F,smart_EGF-like_Ca-bd,smart_EGF-like,pfscan_EG-like_dom,pfscan_G2_nidogen/fibulin_G2F,pfscan_Thrombospondin_1_rpt,pfscan_Ig-like	p.Y3874*	ENST00000271588.4	37	c.11622	CCDS30956.1	1	.	.	.	.	.	.	.	.	.	.	T	54	22.182055	0.99946	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	.	.	.	5.35	3.05	0.35203	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.8303	0.35080	0.0:0.1552:0.0:0.8448	.	.	.	.	X	3874	.	ENSP00000271588:Y3874X	Y	+	3	2	HMCN1	184352809	0.997000	0.39634	1.000000	0.80357	0.955000	0.61496	0.278000	0.18753	0.982000	0.38575	0.533000	0.62120	TAT	HMCN1	-	pfam_Ig_I-set,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like	ENSG00000143341		0.403	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HMCN1	HGNC	protein_coding	OTTHUMT00000131848.1	62	0.00	0	T	NM_031935		186086186	186086186	+1	no_errors	ENST00000271588	ensembl	human	known	69_37n	nonsense	47	29.85	20	SNP	1.000	A
HNRNPLL	92906	genome.wustl.edu	37	2	38818727	38818728	+	Frame_Shift_Del	DEL	CA	CA	-			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	CA	CA					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr2:38818727_38818728delCA	ENST00000449105.3	-	2	591_592	c.252_253delTG	c.(250-255)tgtgaafs	p.CE84fs	HNRNPLL_ENST00000378915.3_Frame_Shift_Del_p.CE84fs|HNRNPLL_ENST00000409636.1_Frame_Shift_Del_p.CE79fs|HNRNPLL_ENST00000608859.1_Frame_Shift_Del_p.CE84fs|HNRNPLL_ENST00000358367.4_Frame_Shift_Del_p.CE84fs|HNRNPLL_ENST00000409328.1_Frame_Shift_Del_p.CE84fs|HNRNPLL_ENST00000410076.1_Frame_Shift_Del_p.CE79fs|HNRNPLL_ENST00000498516.1_5'UTR			Q8WVV9	HNRLL_HUMAN	heterogeneous nuclear ribonucleoprotein L-like	84	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|positive regulation of RNA splicing (GO:0033120)	membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)										ACCACAGATTCACAGAGTCCTC	0.406																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			BC008217	CCDS46261.1, CCDS1796.2	2p22	2014-02-10		2013-06-12	ENSG00000143889	ENSG00000143889		"""RNA binding motif (RRM) containing"""	25127	protein-coding gene	gene with protein product		611208		HNRPLL		18669861	Standard	NM_138394		Approved		uc021vgc.1	Q8WVV9	OTTHUMG00000102075	ENST00000449105.3:c.252_253delTG	2.37:g.38818729_38818730delCA	ENSP00000390625:p.Cys84fs		Q53T80|Q5JB51|Q5JB52|Q659B9|Q8IVH5|Q8IVH6|Q96HR5	Frame_Shift_Del	DEL	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom,tigrfam_HnRNP-L_PTB	p.C84fs	ENST00000449105.3	37	c.253_252		2																																																																																			HNRPLL	-	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom,tigrfam_HnRNP-L_PTB	ENSG00000143889		0.406	HNRNPLL-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	HNRPLL	HGNC	protein_coding	OTTHUMT00000219887.2	16	0.00	0	CA	NM_138394		38818727	38818728	-1	no_errors	ENST00000449105	ensembl	human	known	69_37n	frame_shift_del	21	22.22	6	DEL	1.000:1.000	-
IRX3	79191	genome.wustl.edu	37	16	54319430	54319431	+	Frame_Shift_Del	DEL	GC	GC	-			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	GC	GC					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr16:54319430_54319431delGC	ENST00000329734.3	-	2	1074_1075	c.362_363delGC	c.(361-363)ggcfs	p.G121fs		NM_024336.2	NP_077312.2	P78415	IRX3_HUMAN	iroquois homeobox 3	121					mesoderm development (GO:0007498)|metanephros development (GO:0001656)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of neuron differentiation (GO:0045666)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)|transcription, DNA-templated (GO:0006351)	axon (GO:0030424)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|soft_tissue(1)|urinary_tract(1)	14						ACTGGTACTGGCCATACGGGTA	0.678																																					GBM(143;1830 1866 4487 4646 37383)	dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			U90308	CCDS10750.1	16q12.2	2011-06-20	2007-07-13		ENSG00000177508	ENSG00000177508		"""Homeoboxes / TALE class"""	14360	protein-coding gene	gene with protein product		612985					Standard	NM_024336		Approved	IRX-1	uc002eht.1	P78415	OTTHUMG00000133200	ENST00000329734.3:c.362_363delGC	16.37:g.54319430_54319431delGC	ENSP00000331608:p.Gly121fs		Q7Z4A4|Q7Z4A5|Q8IVC6	Frame_Shift_Del	DEL	pfam_Homeodomain,superfamily_Homeodomain-like,smart_Homeodomain,smart_Iroquois_homeo,pfscan_Homeodomain	p.G121fs	ENST00000329734.3	37	c.363_362	CCDS10750.1	16																																																																																			IRX3	-	superfamily_Homeodomain-like	ENSG00000177508		0.678	IRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IRX3	HGNC	protein_coding	OTTHUMT00000256910.2	46	0.00	0	GC			54319430	54319431	-1	no_errors	ENST00000329734	ensembl	human	known	69_37n	frame_shift_del	11	67.57	25	DEL	1.000:1.000	-
KCNS3	3790	genome.wustl.edu	37	2	18112885	18112885	+	Missense_Mutation	SNP	G	G	T	rs144701569		TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr2:18112885G>T	ENST00000403915.1	+	3	1061	c.610G>T	c.(610-612)Gtt>Ttt	p.V204F	KCNS3_ENST00000465292.1_Intron|KCNS3_ENST00000304101.4_Missense_Mutation_p.V204F	NM_001282428.1	NP_001269357.1	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	204					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(5)|kidney(1)|large_intestine(7)|lung(11)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GGCCATGTGCGTTCACAGCAT	0.552																																						dbGAP											0													67.0	65.0	65.0					2																	18112885		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF043472	CCDS1692.1	2p24	2011-07-05			ENSG00000170745	ENSG00000170745		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6302	protein-coding gene	gene with protein product		603888				10484328, 16382104	Standard	NM_002252		Approved	Kv9.3	uc002rcw.3	Q9BQ31	OTTHUMG00000044150	ENST00000403915.1:c.610G>T	2.37:g.18112885G>T	ENSP00000385968:p.Val204Phe		D6W520|O43651|Q4ZFY1|Q96B56	Missense_Mutation	SNP	pfam_Ion_trans_dom,pfam_T1-type_BTB,pfam_Ion_trans_2,superfamily_BTB/POZ_fold,smart_BTB/POZ-like,prints_K_chnl,prints_K_chnl_volt-dep_Kv9,prints_K_chnl_volt-dep_Kv,prints_K_chnl_volt-dep_Kv6,prints_K_chnl_volt-dep_Kv3,prints_K_chnl_volt-dep_Kv2	p.V204F	ENST00000403915.1	37	c.610	CCDS1692.1	2	.	.	.	.	.	.	.	.	.	.	G	8.175	0.792466	0.16258	.	.	ENSG00000170745	ENST00000403915;ENST00000304101	D;D	0.97505	-4.41;-4.41	6.07	-2.27	0.06846	.	0.373102	0.28865	N	0.013885	D	0.93096	0.7802	L	0.37561	1.115	0.28811	N	0.898219	P	0.38167	0.621	B	0.36418	0.224	D	0.87527	0.2450	10	0.87932	D	0	.	13.6407	0.62249	0.75:0.0:0.25:0.0	.	204	Q9BQ31	KCNS3_HUMAN	F	204	ENSP00000385968:V204F;ENSP00000305824:V204F	ENSP00000305824:V204F	V	+	1	0	KCNS3	17976366	0.851000	0.29673	0.002000	0.10522	0.531000	0.34715	1.304000	0.33482	-0.533000	0.06323	-1.553000	0.00894	GTT	KCNS3	-	prints_K_chnl	ENSG00000170745		0.552	KCNS3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	KCNS3	HGNC	protein_coding	OTTHUMT00000323808.1	41	0.00	0	G	NM_002252		18112885	18112885	+1	no_errors	ENST00000304101	ensembl	human	known	69_37n	missense	63	21.25	17	SNP	0.164	T
MARC2	54996	genome.wustl.edu	37	1	220936309	220936309	+	Silent	SNP	T	T	C			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr1:220936309T>C	ENST00000366913.3	+	4	865	c.667T>C	c.(667-669)Ttg>Ctg	p.L223L	MARC2_ENST00000359316.2_Silent_p.L223L	NM_017898.3	NP_060368.2	Q969Z3	MARC2_HUMAN	mitochondrial amidoxime reducing component 2	223	MOSC. {ECO:0000255|PROSITE- ProRule:PRU00670}.				detoxification of nitrogen compound (GO:0051410)|nitrate metabolic process (GO:0042126)|oxidation-reduction process (GO:0055114)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|nitrate reductase activity (GO:0008940)|pyridoxal phosphate binding (GO:0030170)										CCTGGTAGATTTGAATACCAG	0.502																																						dbGAP											0													111.0	111.0	111.0					1																	220936309		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS1525.1	1q41	2011-11-02	2011-11-02	2011-11-02	ENSG00000117791	ENSG00000117791			26064	protein-coding gene	gene with protein product		614127	"""MOCO sulphurase C-terminal domain containing 2"""	MOSC2		11886751	Standard	NM_017898		Approved	FLJ20605	uc001hmq.3	Q969Z3	OTTHUMG00000037354	ENST00000366913.3:c.667T>C	1.37:g.220936309T>C			B2D0R5|D3DTB3|Q0JSK7|Q5VT67|Q5VXC7|Q7L317|Q9H066|Q9NWU0	Silent	SNP	pfam_MOSC_N,pfam_MoCF_Sase_C,superfamily_Pyrv_Knase-like_insert_dom	p.L223	ENST00000366913.3	37	c.667	CCDS1525.1	1																																																																																			MARC2	-	pfam_MoCF_Sase_C,superfamily_Pyrv_Knase-like_insert_dom	ENSG00000117791		0.502	MARC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MARC2	HGNC	protein_coding	OTTHUMT00000090911.1	65	0.00	0	T	NM_017898		220936309	220936309	+1	no_errors	ENST00000366913	ensembl	human	known	69_37n	silent	28	50.00	28	SNP	0.996	C
MTHFSD	64779	genome.wustl.edu	37	16	86585647	86585647	+	Missense_Mutation	SNP	C	C	T			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr16:86585647C>T	ENST00000360900.6	-	3	254	c.229G>A	c.(229-231)Gtg>Atg	p.V77M	MTHFSD_ENST00000543303.2_Intron|MTHFSD_ENST00000322911.6_Missense_Mutation_p.V76M|MTHFSD_ENST00000381214.5_Intron|MTHFSD_ENST00000546093.1_Intron|MTHFSD_ENST00000568037.1_Intron	NM_001159380.1	NP_001152852.1	Q2M296	MTHSD_HUMAN	methenyltetrahydrofolate synthetase domain containing	77							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(3)|lung(6)|skin(1)	11						ACCTGCAGCACCAGCAGCCGA	0.532																																						dbGAP											0													149.0	158.0	155.0					16																	86585647		1967	4147	6114	-	-	-	SO:0001583	missense	0			AK023060	CCDS54047.1, CCDS54048.1, CCDS58490.1	16q24.1	2013-02-12				ENSG00000103248		"""RNA binding motif (RRM) containing"""	25778	protein-coding gene	gene with protein product						12477932	Standard	NM_022764		Approved	FLJ12998	uc010vor.2	Q2M296		ENST00000360900.6:c.229G>A	16.37:g.86585647C>T	ENSP00000354152:p.Val77Met		A8MQ77|B7ZLC0|B7ZLC2|D3DUM9|E9PAM1|Q9H878|Q9H954	Nonsense_Mutation	SNP	pfam_FTHF_cligase	p.W70*	ENST00000360900.6	37	c.210	CCDS54047.1	16	.	.	.	.	.	.	.	.	.	.	C	18.43	3.622255	0.66787	.	.	ENSG00000103248	ENST00000543303;ENST00000360900;ENST00000322911	T;T	0.46451	0.87;0.87	5.93	4.99	0.66335	5-formyltetrahydrofolate cyclo-ligase-like domain (1);	0.485483	0.23524	N	0.047245	T	0.49372	0.1553	M	0.80183	2.485	0.28644	N	0.907011	B;B	0.20052	0.041;0.033	B;B	0.24701	0.055;0.033	T	0.52888	-0.8515	10	0.66056	D	0.02	-10.9333	14.3649	0.66799	0.0:0.9291:0.0:0.0709	.	77;76	Q2M296;Q2M296-2	MTHSD_HUMAN;.	M	75;77;76	ENSP00000354152:V77M;ENSP00000326777:V76M	ENSP00000326777:V76M	V	-	1	0	MTHFSD	85143148	0.990000	0.36364	0.972000	0.41901	0.926000	0.56050	4.296000	0.59055	1.513000	0.48852	0.655000	0.94253	GTG	MTHFSD	-	pfam_FTHF_cligase	ENSG00000103248		0.532	MTHFSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	MTHFSD	HGNC	protein_coding	OTTHUMT00000432182.1	74	0.00	0	C	NM_022764		86585647	86585647	-1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000566469	ensembl	human	putative	69_37n	nonsense	31	11.43	4	SNP	0.992	T
NARS	4677	genome.wustl.edu	37	18	55274371	55274371	+	Silent	SNP	C	C	G			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr18:55274371C>G	ENST00000256854.5	-	9	1451	c.996G>C	c.(994-996)ctG>ctC	p.L332L	NARS_ENST00000423481.2_Silent_p.L83L	NM_004539.3	NP_004530.1	O43776	SYNC_HUMAN	asparaginyl-tRNA synthetase	332					asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(5)|large_intestine(5)|lung(8)|skin(1)	20		Colorectal(73;0.227)			L-Asparagine(DB00174)	CATACTCAGCCAGGTGCCTTC	0.393																																						dbGAP											0													87.0	95.0	92.0					18																	55274371		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			D84273	CCDS32837.1	18q21.31	2014-05-06			ENSG00000134440	ENSG00000134440	6.1.1.22	"""Aminoacyl tRNA synthetases / Class II"""	7643	protein-coding gene	gene with protein product	"""asparagine tRNA ligase 1, cytoplasmic"""	108410				6836455, 9421509	Standard	NM_004539		Approved	NARS1	uc002lgs.2	O43776	OTTHUMG00000180125	ENST00000256854.5:c.996G>C	18.37:g.55274371C>G			B4DG16|Q53GU6	Silent	SNP	pfam_aa-tRNA-synt_II,pfam_NA-bd_OB_tRNA-helicase,superfamily_NA-bd_OB-fold-like,pfscan_aa-tRNA-synth_II,prints_Asp/Asn-tRNA-synth_IIb,tigrfam_Asn-tRNA-synth_IIb	p.L332	ENST00000256854.5	37	c.996	CCDS32837.1	18																																																																																			NARS	-	pfam_aa-tRNA-synt_II,pfscan_aa-tRNA-synth_II,tigrfam_Asn-tRNA-synth_IIb	ENSG00000134440		0.393	NARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NARS	HGNC	protein_coding	OTTHUMT00000449872.2	59	0.00	0	C	NM_004539		55274371	55274371	-1	no_errors	ENST00000256854	ensembl	human	known	69_37n	silent	29	38.30	18	SNP	1.000	G
NCOA1	8648	genome.wustl.edu	37	2	24949504	24949504	+	Missense_Mutation	SNP	A	A	T			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr2:24949504A>T	ENST00000406961.1	+	15	3298	c.2646A>T	c.(2644-2646)caA>caT	p.Q882H	NCOA1_ENST00000395856.3_Missense_Mutation_p.Q882H|NCOA1_ENST00000538539.1_Missense_Mutation_p.Q882H|NCOA1_ENST00000405141.1_Missense_Mutation_p.Q882H|NCOA1_ENST00000348332.3_Missense_Mutation_p.Q882H|NCOA1_ENST00000288599.5_Missense_Mutation_p.Q882H|NCOA1_ENST00000407230.1_Missense_Mutation_p.Q731H			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	882	Interaction with CREBBP.				androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)		PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AATTTGGACAACCAGGAACAG	0.343			T	PAX3	alveolar rhadomyosarcoma																																	dbGAP		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	0													97.0	99.0	98.0					2																	24949504		2203	4299	6502	-	-	-	SO:0001583	missense	0			U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.2646A>T	2.37:g.24949504A>T	ENSP00000385216:p.Gln882His		O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Missense_Mutation	SNP	pfam_DUF1518,pfam_SRC-1,pfam_Nuc_rcpt_coact_Ncoa-typ,pfam_PAS_fold,superfamily_Nuc_rcpt_coact,superfamily_HLH_DNA-bd,smart_HLH_DNA-bd,smart_PAS,pirsf_Nuclear_rcpt_coactivator,pfscan_PAS,pfscan_HLH_DNA-bd	p.Q882H	ENST00000406961.1	37	c.2646	CCDS1712.1	2	.	.	.	.	.	.	.	.	.	.	A	19.50	3.839759	0.71488	.	.	ENSG00000084676	ENST00000406961;ENST00000405141;ENST00000407230;ENST00000538539;ENST00000348332;ENST00000288599;ENST00000395856	T;T;T;T;T;T;T	0.02787	4.25;4.25;4.16;4.25;4.25;4.25;4.22	5.31	-2.55	0.06288	.	0.386422	0.29335	N	0.012450	T	0.05868	0.0153	L	0.27053	0.805	0.26317	N	0.977739	D;D;D;D	0.61697	0.987;0.978;0.987;0.99	P;P;P;D	0.70487	0.775;0.601;0.838;0.969	T	0.07790	-1.0754	10	0.44086	T	0.13	.	12.997	0.58652	0.3164:0.0:0.6836:0.0	.	882;882;882;731	Q15788-3;Q15788;Q15788-2;B5MCN7	.;NCOA1_HUMAN;.;.	H	882;882;731;882;882;882;882	ENSP00000385216:Q882H;ENSP00000385097:Q882H;ENSP00000385195:Q731H;ENSP00000444039:Q882H;ENSP00000320940:Q882H;ENSP00000288599:Q882H;ENSP00000379197:Q882H	ENSP00000288599:Q882H	Q	+	3	2	NCOA1	24803008	0.970000	0.33590	0.990000	0.47175	0.998000	0.95712	-0.031000	0.12287	-0.377000	0.07930	0.524000	0.50904	CAA	NCOA1	-	pirsf_Nuclear_rcpt_coactivator	ENSG00000084676		0.343	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NCOA1	HGNC	protein_coding	OTTHUMT00000246852.3	65	0.00	0	A	NM_147223		24949504	24949504	+1	no_errors	ENST00000348332	ensembl	human	known	69_37n	missense	26	18.75	6	SNP	0.993	T
NCOR1	9611	genome.wustl.edu	37	17	15965426	15965426	+	Nonsense_Mutation	SNP	G	G	A			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr17:15965426G>A	ENST00000268712.3	-	36	5637	c.5380C>T	c.(5380-5382)Cga>Tga	p.R1794*	NCOR1_ENST00000395857.3_Nonsense_Mutation_p.R378*|NCOR1_ENST00000395851.1_Nonsense_Mutation_p.R1810*	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1794	Interaction with C1D. {ECO:0000250}.|Interaction with ETO.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		GACATGATTCGTAGCTGAGCA	0.378																																						dbGAP											0													152.0	133.0	139.0					17																	15965426		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"""thyroid hormone- and retinoic acid receptor-associated corepressor 1"", ""protein phosphatase 1, regulatory subunit 109"""	600849	"""nuclear receptor co-repressor 1"""			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.5380C>T	17.37:g.15965426G>A	ENSP00000268712:p.Arg1794*		B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Nonsense_Mutation	SNP	pfam_SANT/Myb,superfamily_Homeodomain-like,smart_SANT/Myb,pfscan_Myb-like_dom	p.R1794*	ENST00000268712.3	37	c.5380	CCDS11175.1	17	.	.	.	.	.	.	.	.	.	.	G	37	6.131882	0.97310	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395857	.	.	.	5.74	5.74	0.90152	.	0.136830	0.48767	D	0.000161	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.8779	18.9133	0.92494	0.0:0.0:1.0:0.0	.	.	.	.	X	1794;1810;1698;378	.	ENSP00000268712:R1794X	R	-	1	2	NCOR1	15906151	1.000000	0.71417	0.992000	0.48379	0.987000	0.75469	5.496000	0.66918	2.715000	0.92844	0.650000	0.86243	CGA	NCOR1	-	NULL	ENSG00000141027		0.378	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NCOR1	HGNC	protein_coding	OTTHUMT00000131751.5	57	0.00	0	G	NM_006311		15965426	15965426	-1	no_errors	ENST00000268712	ensembl	human	known	69_37n	nonsense	20	50.00	20	SNP	0.994	A
PLEKHB2	55041	genome.wustl.edu	37	2	132110828	132110828	+	Missense_Mutation	SNP	G	G	T	rs373666409	byFrequency	TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr2:132110828G>T	ENST00000404460.1	+	7	713	c.659G>T	c.(658-660)aGg>aTg	p.R220M	PLEKHB2_ENST00000303908.3_Missense_Mutation_p.R220M			Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B (evectins) member 2	85						endosome (GO:0005768)|membrane (GO:0016020)		p.R220M(1)		large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.0828)		GCAGGGAAGAGGGCGCCCAGC	0.652													.|||	3765	0.751797	0.5877	0.8876	5008	,	,		8416	0.7599		0.8827	False		,,,				2504	0.7342					dbGAP											1	Substitution - Missense(1)	pancreas(1)											3.0	2.0	2.0					2																	132110828		608	1074	1682	-	-	-	SO:0001583	missense	0				CCDS2166.1, CCDS46413.1, CCDS58729.1, CCDS58730.1, CCDS74576.1, CCDS74577.1	2q22.1	2013-01-10			ENSG00000115762	ENSG00000115762		"""Pleckstrin homology (PH) domain containing"""	19236	protein-coding gene	gene with protein product						10200314	Standard	NM_017958		Approved	EVT2, FLJ20783	uc031rpd.1	Q96CS7	OTTHUMG00000131656	ENST00000404460.1:c.659G>T	2.37:g.132110828G>T	ENSP00000385609:p.Arg220Met		B4DF08|B4DZ66|B8ZZN1|Q53FF1|Q53TH7|Q86W37|Q9BV75|Q9NWK1	Missense_Mutation	SNP	pfam_Pleckstrin_homology,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	p.R220M	ENST00000404460.1	37	c.659		2	.	.	.	.	.	.	.	.	.	.	.	1.804	-0.476272	0.04414	.	.	ENSG00000115762	ENST00000404460;ENST00000303908	.	.	.	0.0465	0.0465	0.14256	.	0.468674	0.22714	U	0.056539	T	0.18045	0.0433	.	.	.	0.09310	P	0.99999999756555	P	0.47034	0.889	B	0.28385	0.089	T	0.25745	-1.0123	6	0.72032	D	0.01	-33.5243	.	.	.	.	220	B7WPA5	.	M	220	.	ENSP00000306852:R220M	R	+	2	0	PLEKHB2	131827298	0.967000	0.33354	0.026000	0.17262	0.026000	0.11368	0.116000	0.15561	0.132000	0.18615	0.134000	0.15878	AGG	PLEKHB2	-	NULL	ENSG00000115762		0.652	PLEKHB2-002	KNOWN	basic	protein_coding	PLEKHB2	HGNC	protein_coding	OTTHUMT00000318943.2	31	0.00	0	G	NM_017958		132110828	132110828	+1	no_errors	ENST00000303908	ensembl	human	known	69_37n	missense	26	25.71	9	SNP	0.981	T
RNF113A	7737	genome.wustl.edu	37	X	119004944	119004944	+	Silent	SNP	G	G	A			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chrX:119004944G>A	ENST00000371442.2	-	1	847	c.633C>T	c.(631-633)tgC>tgT	p.C211C	NDUFA1_ENST00000371437.4_5'Flank	NM_006978.2	NP_008909.1	O15541	R113A_HUMAN	ring finger protein 113A	211							zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(6)	15						CTCCGAAGCCGCAGAAGCCAG	0.562																																						dbGAP											0													79.0	76.0	77.0					X																	119004944		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			X98253	CCDS14589.1	Xq24	2013-10-22	2005-03-22	2005-03-22	ENSG00000125352	ENSG00000125352		"""RING-type (C3HC4) zinc fingers"""	12974	protein-coding gene	gene with protein product			"""zinc finger protein 183 (RING finger, C3HC4 type)"""	ZNF183		9224902	Standard	NM_006978		Approved	RNF113, Cwc24	uc004esb.3	O15541	OTTHUMG00000022283	ENST00000371442.2:c.633C>T	X.37:g.119004944G>A			B2RBR7	Silent	SNP	pfam_Znf_CCCH,smart_Znf_CCCH,smart_Znf_RING,pfscan_Znf_RING	p.C211	ENST00000371442.2	37	c.633	CCDS14589.1	X																																																																																			RNF113A	-	pfam_Znf_CCCH,smart_Znf_CCCH	ENSG00000125352		0.562	RNF113A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RNF113A	HGNC	protein_coding	OTTHUMT00000058071.1	18	0.00	0	G	NM_006978		119004944	119004944	-1	no_errors	ENST00000371442	ensembl	human	known	69_37n	silent	16	38.46	10	SNP	1.000	A
RP1L1	94137	genome.wustl.edu	37	8	10468681	10468681	+	Missense_Mutation	SNP	G	G	A	rs200854148		TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr8:10468681G>A	ENST00000382483.3	-	4	3150	c.2927C>T	c.(2926-2928)gCg>gTg	p.A976V		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	976					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		GGTCTCGTCCGCCAACTCATA	0.632																																						dbGAP											0													53.0	57.0	56.0					8																	10468681		1950	4133	6083	-	-	-	SO:0001583	missense	0			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.2927C>T	8.37:g.10468681G>A	ENSP00000371923:p.Ala976Val		Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	pfam_Doublecortin_dom,superfamily_Doublecortin_dom,smart_Doublecortin_dom,pfscan_Doublecortin_dom	p.A976V	ENST00000382483.3	37	c.2927	CCDS43708.1	8	.	.	.	.	.	.	.	.	.	.	G	0.488	-0.876739	0.02550	.	.	ENSG00000183638	ENST00000382483	T	0.78364	-1.17	4.31	-8.62	0.00881	.	.	.	.	.	T	0.41351	0.1155	N	0.02916	-0.46	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36261	-0.9755	9	0.12103	T	0.63	-1.4533	2.3691	0.04326	0.2763:0.0928:0.3854:0.2455	.	976	A6NKC6	.	V	976	ENSP00000371923:A976V	ENSP00000371923:A976V	A	-	2	0	RP1L1	10506091	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.486000	0.06513	-2.138000	0.00808	-1.744000	0.00683	GCG	RP1L1	-	NULL	ENSG00000183638		0.632	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RP1L1	HGNC	protein_coding	OTTHUMT00000375673.1	20	0.00	0	G			10468681	10468681	-1	no_errors	ENST00000382483	ensembl	human	known	69_37n	missense	22	42.11	16	SNP	0.010	A
RPGRIP1	57096	genome.wustl.edu	37	14	21794169	21794169	+	Frame_Shift_Del	DEL	C	C	-			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr14:21794169delC	ENST00000400017.2	+	16	2547	c.2547delC	c.(2545-2547)gacfs	p.D849fs	RPGRIP1_ENST00000382933.4_Intron|RPGRIP1_ENST00000556336.1_Intron|RPGRIP1_ENST00000206660.6_Frame_Shift_Del_p.D849fs|RPGRIP1_ENST00000557771.1_Frame_Shift_Del_p.D811fs|RPGRIP1_ENST00000307974.4_Frame_Shift_Del_p.D208fs	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	849	C2.				eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)				breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		ACTTTAGAGACCAGGCTCGAT	0.488																																						dbGAP											0													91.0	91.0	91.0					14																	21794169		1997	4168	6165	-	-	-	SO:0001589	frameshift_variant	0			AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.2547delC	14.37:g.21794169delC	ENSP00000382895:p.Asp849fs		Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Frame_Shift_Del	DEL	pfam_DUF3250,superfamily_C2_Ca/lipid-bd_dom_CaLB	p.Q850fs	ENST00000400017.2	37	c.2547	CCDS45080.1	14																																																																																			RPGRIP1	-	superfamily_C2_Ca/lipid-bd_dom_CaLB	ENSG00000092200		0.488	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RPGRIP1	HGNC	protein_coding	OTTHUMT00000410258.1	103	0.00	0	C	NM_020366		21794169	21794169	+1	no_errors	ENST00000206660	ensembl	human	known	69_37n	frame_shift_del	66	32.65	32	DEL	0.987	-
RPL17	6139	genome.wustl.edu	37	18	47017223	47017223	+	Silent	SNP	A	A	C			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr18:47017223A>C	ENST00000418495.1	-	4	496	c.156T>G	c.(154-156)acT>acG	p.T52T	RPL17-C18orf32_ENST00000332968.6_Silent_p.T14T|RPL17_ENST00000579248.1_Silent_p.T52T|RPL17_ENST00000579408.1_Silent_p.T52T|SNORD58B_ENST00000607313.1_RNA|RPL17-C18orf32_ENST00000584895.1_Silent_p.T52T|RPL17_ENST00000581373.1_Silent_p.T14T|RPL17_ENST00000580210.1_Silent_p.T42T|SNORD58C_ENST00000365223.1_RNA|MIR1539_ENST00000581232.1_RNA|RPL17_ENST00000580261.1_Silent_p.T52T|RPL17_ENST00000581091.1_5'UTR|SNORD58A_ENST00000383875.1_RNA	NM_000985.4|NM_001199340.1	NP_000976.1|NP_001186269.1	P18621	RL17_HUMAN	ribosomal protein L17	52					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|lung(3)	5						GTTTCTGTAAAGTGACATCTT	0.413																																						dbGAP											0													108.0	101.0	103.0					18																	47017223		1873	4097	5970	-	-	-	SO:0001819	synonymous_variant	0			AB007174	CCDS45865.1, CCDS56070.1	18q21	2011-04-06				ENSG00000265681		"""L ribosomal proteins"""	10307	protein-coding gene	gene with protein product		603661				2402465, 9582194	Standard	NM_000985		Approved	rpL23, L17		P18621		ENST00000418495.1:c.156T>G	18.37:g.47017223A>C			B2R4H3|B4E3C2|B5ME31|J3QL51|Q3KQW2|Q6NZ54|Q7M4M5	Silent	SNP	pfam_Ribosomal_L22,superfamily_Ribosomal_L22,tigrfam_Ribosomal_L22/L17_euk/arc	p.T52	ENST00000418495.1	37	c.156	CCDS45865.1	18																																																																																			RP11-110H1.2	-	pfam_Ribosomal_L22,superfamily_Ribosomal_L22,tigrfam_Ribosomal_L22/L17_euk/arc	ENSG00000215472		0.413	RPL17-201	KNOWN	basic|appris_principal|CCDS	protein_coding	RPL17-C18ORF32	Clone_based_vega_gene	protein_coding	OTTHUMT00000447589.2	96	0.00	0	A	NM_000985		47017223	47017223	-1	no_errors	ENST00000418495	ensembl	human	known	69_37n	silent	84	26.96	31	SNP	0.931	C
SF3B4	10262	genome.wustl.edu	37	1	149898647	149898648	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	AG	AG					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr1:149898647_149898648delAG	ENST00000271628.8	-	3	910_911	c.326_327delCT	c.(325-327)cctfs	p.P109fs	MTMR11_ENST00000492824.1_5'Flank	NM_005850.4	NP_005841.1	Q15427	SF3B4_HUMAN	splicing factor 3b, subunit 4, 49kDa	109	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)	17	Breast(34;0.0009)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			CATCAATCTCAGGGTCCAGGTT	0.46																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			L35013	CCDS72900.1	1q21.2	2013-02-12	2002-08-29		ENSG00000143368	ENSG00000143368		"""RNA binding motif (RRM) containing"""	10771	protein-coding gene	gene with protein product		605593	"""splicing factor 3b, subunit 4, 49kD"""			7958871	Standard	NM_005850		Approved	SAP49, SF3b49, Hsh49	uc001etk.2	Q15427	OTTHUMG00000012208	ENST00000271628.8:c.326_327delCT	1.37:g.149898647_149898648delAG	ENSP00000271628:p.Pro109fs		Q5SZ63	Frame_Shift_Del	DEL	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom	p.P109fs	ENST00000271628.8	37	c.327_326	CCDS941.1	1																																																																																			SF3B4	-	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom	ENSG00000143368		0.460	SF3B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SF3B4	HGNC	protein_coding	OTTHUMT00000033753.1	131	0.00	0	AG	NM_005850		149898647	149898648	-1	no_errors	ENST00000271628	ensembl	human	known	69_37n	frame_shift_del	558	12.65	82	DEL	0.926:1.000	-
TLR4	7099	genome.wustl.edu	37	9	120475369	120475369	+	Missense_Mutation	SNP	A	A	C			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr9:120475369A>C	ENST00000355622.6	+	3	1064	c.963A>C	c.(961-963)gaA>gaC	p.E321D	TLR4_ENST00000394487.4_Missense_Mutation_p.E281D|TLR4_ENST00000472304.1_3'UTR	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	321					activation of MAPK activity (GO:0000187)|B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|detection of fungus (GO:0016046)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|intestinal epithelial structure maintenance (GO:0060729)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-23 production (GO:0032707)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of tumor necrosis factor production (GO:0032720)|nitric oxide production involved in inflammatory response (GO:0002537)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine production (GO:0032722)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 production (GO:0032732)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070430)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|positive regulation of platelet activation (GO:0010572)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)|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 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)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|lipopolysaccharide receptor complex (GO:0046696)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(66)|ovary(4)|pancreas(1)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	103					Naloxone(DB01183)	TGACTATTGAAAGGGTAAAAG	0.318																																						dbGAP											0													67.0	75.0	72.0					9																	120475369		2203	4299	6502	-	-	-	SO:0001583	missense	0			U88880	CCDS6818.1	9q33.1	2013-01-23			ENSG00000136869	ENSG00000136869		"""CD molecules"""	11850	protein-coding gene	gene with protein product		603030				9435236, 9237759	Standard	NM_138554		Approved	hToll, CD284, TLR-4, ARMD10	uc004bjz.4	O00206	OTTHUMG00000021046	ENST00000355622.6:c.963A>C	9.37:g.120475369A>C	ENSP00000363089:p.Glu321Asp		A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Missense_Mutation	SNP	pirsf_Toll-like_receptor,pfam_TIR_dom,pfam_Leu-rich_rpt,superfamily_TIR_dom,smart_Leu-rich_rpt_typical-subtyp,smart_Cys-rich_flank_reg_C,smart_TIR_dom,pfscan_TIR_dom	p.E321D	ENST00000355622.6	37	c.963	CCDS6818.1	9	.	.	.	.	.	.	.	.	.	.	A	2.185	-0.386573	0.04966	.	.	ENSG00000136869	ENST00000394487;ENST00000355622	T;T	0.23147	1.92;1.92	5.78	-11.6	0.00059	.	2.479630	0.01198	N	0.007506	T	0.10294	0.0252	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.14144	-1.0483	10	0.11485	T	0.65	.	4.7601	0.13104	0.4943:0.3124:0.1129:0.0804	.	321	O00206	TLR4_HUMAN	D	281;321	ENSP00000377997:E281D;ENSP00000363089:E321D	ENSP00000363089:E321D	E	+	3	2	TLR4	119515190	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-8.346000	0.00021	-4.384000	0.00052	-1.392000	0.01152	GAA	TLR4	-	pirsf_Toll-like_receptor	ENSG00000136869		0.318	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TLR4	HGNC	protein_coding	OTTHUMT00000055549.3	51	0.00	0	A	NM_138554		120475369	120475369	+1	no_errors	ENST00000355622	ensembl	human	known	69_37n	missense	30	31.82	14	SNP	0.000	C
TLR8	51311	genome.wustl.edu	37	X	12940143	12940143	+	Missense_Mutation	SNP	G	G	A			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chrX:12940143G>A	ENST00000218032.6	+	2	3071	c.2984G>A	c.(2983-2985)cGg>cAg	p.R995Q	TLR8_ENST00000311912.5_Missense_Mutation_p.R1013Q	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	995	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	CTACGGCAGCGGATCTGTAAG	0.463																																						dbGAP											0													105.0	100.0	101.0					X																	12940143		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"""CD molecules"""	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.2984G>A	X.37:g.12940143G>A	ENSP00000218032:p.Arg995Gln		B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	pfam_Leu-rich_rpt,pfam_TIR_dom,superfamily_TIR_dom,smart_Leu-rich_rpt_typical-subtyp,smart_Cys-rich_flank_reg_C,smart_TIR_dom,pfscan_TIR_dom	p.R995Q	ENST00000218032.6	37	c.2984	CCDS14152.1	X	.	.	.	.	.	.	.	.	.	.	G	19.89	3.911012	0.72983	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.08282	3.11;3.11	5.97	5.11	0.69529	Toll/interleukin-1 receptor homology (TIR) domain (3);	0.000000	0.38605	N	0.001627	T	0.28234	0.0697	M	0.85462	2.755	0.38511	D	0.948475	D;D	0.89917	1.0;1.0	D;D	0.76071	0.987;0.987	T	0.11275	-1.0594	10	0.87932	D	0	.	6.4226	0.21752	0.1519:0.0:0.7001:0.148	.	995;1013	Q9NR97;D1CS70	TLR8_HUMAN;.	Q	995;1013	ENSP00000218032:R995Q;ENSP00000312082:R1013Q	ENSP00000218032:R995Q	R	+	2	0	TLR8	12850064	1.000000	0.71417	0.285000	0.24819	0.866000	0.49608	6.676000	0.74498	1.285000	0.44548	0.600000	0.82982	CGG	TLR8	-	pfam_TIR_dom,superfamily_TIR_dom,smart_TIR_dom,pfscan_TIR_dom	ENSG00000101916		0.463	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	TLR8	HGNC	protein_coding	OTTHUMT00000055784.2	89	0.00	0	G	NM_016610		12940143	12940143	+1	no_errors	ENST00000218032	ensembl	human	known	69_37n	missense	41	29.31	17	SNP	0.941	A
TMEM18	129787	genome.wustl.edu	37	2	676599	676599	+	Intron	SNP	G	G	C			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr2:676599G>C	ENST00000281017.3	-	1	151				AC092159.2_ENST00000445418.1_RNA|TMEM18_ENST00000405941.3_Missense_Mutation_p.P14R|TMEM18_ENST00000355654.2_5'Flank	NM_152834.2	NP_690047.2	Q96B42	TMM18_HUMAN	transmembrane protein 18						cell migration (GO:0016477)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	DNA binding (GO:0003677)			endometrium(1)|large_intestine(1)|lung(7)|ovary(1)	10	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;5.27e-05)|all_epithelial(98;2.11e-06)|Ovarian(717;0.0253)		all cancers(51;1.95e-21)|Epithelial(75;9.47e-21)|OV - Ovarian serous cystadenocarcinoma(76;8.15e-18)|GBM - Glioblastoma multiforme(21;0.0285)		ACGGAGGTGAGGGGAGCACGG	0.647																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			AL137269	CCDS33141.1	2p25.3	2008-02-05			ENSG00000151353	ENSG00000151353			25257	protein-coding gene	gene with protein product		613220				12477932	Standard	NM_152834		Approved	DKFZp434C1714	uc002qwl.3	Q96B42	OTTHUMG00000151381	ENST00000281017.3:c.57+689C>G	2.37:g.676599G>C			D6W4X9|Q8N5H2|Q9NTH3	Missense_Mutation	SNP	NULL	p.P14R	ENST00000281017.3	37	c.41	CCDS33141.1	2	.	.	.	.	.	.	.	.	.	.	G	11.77	1.739160	0.30774	.	.	ENSG00000151353	ENST00000405941	.	.	.	0.799	0.799	0.18667	.	.	.	.	.	T	0.34716	0.0907	.	.	.	0.19300	N	0.999975	.	.	.	.	.	.	T	0.30090	-0.9990	5	0.48119	T	0.1	0.3866	4.8829	0.13688	0.0:0.0:1.0:0.0	.	.	.	.	R	14	.	ENSP00000384347:P14R	P	-	2	0	TMEM18	666599	0.001000	0.12720	0.001000	0.08648	0.028000	0.11728	0.100000	0.15231	0.725000	0.32318	0.313000	0.20887	CCT	TMEM18	-	NULL	ENSG00000151353		0.647	TMEM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TMEM18	HGNC	protein_coding	OTTHUMT00000322427.1	62	0.00	0	G	NM_152834		676599	676599	-1	no_errors	ENST00000405941	ensembl	human	novel	69_37n	missense	103	14.17	17	SNP	0.001	C
TRPM2	7226	genome.wustl.edu	37	21	45821603	45821603	+	Silent	SNP	C	C	T			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr21:45821603C>T	ENST00000397928.1	+	16	2806	c.2361C>T	c.(2359-2361)cgC>cgT	p.R787R	TRPM2_ENST00000300482.5_Silent_p.R787R|TRPM2_ENST00000300481.9_Silent_p.R767R|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Silent_p.R787R	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	787					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)	p.R787R(1)		breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						CCGCGGCCCGCGCCCGTGCCT	0.647																																						dbGAP											1	Substitution - coding silent(1)	lung(1)											141.0	111.0	121.0					21																	45821603		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.2361C>T	21.37:g.45821603C>T			D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Silent	SNP	pfam_Ion_trans_dom,superfamily_NUDIX_hydrolase_dom-like	p.R787	ENST00000397928.1	37	c.2361	CCDS13710.1	21																																																																																			TRPM2	-	NULL	ENSG00000142185		0.647	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TRPM2	HGNC	protein_coding	OTTHUMT00000098086.1	83	0.00	0	C	NM_003307		45821603	45821603	+1	no_errors	ENST00000300482	ensembl	human	known	69_37n	silent	37	53.75	43	SNP	0.000	T
TTN	7273	genome.wustl.edu	37	2	179416362	179416362	+	Frame_Shift_Del	DEL	G	G	-			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr2:179416362delG	ENST00000591111.1	-	285	86566	c.86342delC	c.(86341-86343)ccafs	p.P28781fs	TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Frame_Shift_Del_p.P30422fs|TTN_ENST00000342992.6_Frame_Shift_Del_p.P27854fs|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Del_p.P21549fs|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.P21482fs|TTN_ENST00000460472.2_Frame_Shift_Del_p.P21357fs|TTN-AS1_ENST00000592600.1_RNA			Q8WZ42	TITIN_HUMAN	titin	28781	Fibronectin type-III 109. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTACCTACTGGAGAAACAGC	0.363																																						dbGAP											0													59.0	54.0	55.0					2																	179416362		1837	4083	5920	-	-	-	SO:0001589	frameshift_variant	0			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.86342delC	2.37:g.179416362delG	ENSP00000465570:p.Pro28781fs		A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	pfam_Ig_I-set,pfam_Fibronectin_type3,pfam_Immunoglobulin,pfam_Ig_V-set,pfam_Titin_Z,pfam_PPAK_motif,pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_Fibronectin_type3,superfamily_Calpain_domain_III,superfamily_RNaseH-like_dom,smart_Ig_sub,smart_Ig_sub2,smart_Ig_V-set_subgr,smart_Fibronectin_type3,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Fibronectin_type3,pfscan_Prot_kinase_cat_dom,pfscan_Ig-like	p.P27854fs	ENST00000591111.1	37	c.83561		2																																																																																			TTN	-	superfamily_Fibronectin_type3,superfamily_Calpain_domain_III,superfamily_RNaseH-like_dom,pfscan_Fibronectin_type3	ENSG00000155657		0.363	TTN-019	PUTATIVE	basic	protein_coding	TTN	HGNC	protein_coding	OTTHUMT00000460310.1	40	0.00	0	G	NM_133378		179416362	179416362	-1	no_errors	ENST00000342992	ensembl	human	known	69_37n	frame_shift_del	11	15.38	2	DEL	1.000	-
XDH	7498	genome.wustl.edu	37	2	31573005	31573005	+	Missense_Mutation	SNP	G	G	A			TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr2:31573005G>A	ENST00000379416.3	-	25	2764	c.2716C>T	c.(2716-2718)Ctt>Ttt	p.L906F		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	906					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	TTGGAGGGAAGGTTGGTTTTG	0.562																																					Colon(66;682 1445 30109 40147)	dbGAP											0													98.0	107.0	104.0					2																	31573005		2203	4300	6503	-	-	-	SO:0001583	missense	0			D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"""xanthene dehydrogenase"""			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.2716C>T	2.37:g.31573005G>A	ENSP00000368727:p.Leu906Phe		Q16681|Q16712|Q4PJ16	Missense_Mutation	SNP	pfam_AldOxase/xan_DH_Mopterin-bd,pfam_Mopterin_DH_FAD-bd,pfam_Ald_Oxase/Xan_DH_a/b,pfam_2Fe-2S-bd,pfam_CO_DH_flav_C,pfam_2Fe-2S_ferredoxin-type,superfamily_AldOxase/xan_DH_Mopterin-bd,superfamily_FAD-bd_2,superfamily_Ald_Oxase/Xan_DH_a/b,superfamily_2Fe-2S-bd,superfamily_CO_DH_flav_C,superfamily_2Fe-2S_ferredoxin-type,pirsf_Ald_Oxase/xanthine_DH,pfscan_2Fe-2S_ferredoxin-type,tigrfam_Xanthine_DH_ssu	p.L906F	ENST00000379416.3	37	c.2716	CCDS1775.1	2	.	.	.	.	.	.	.	.	.	.	G	14.66	2.600667	0.46423	.	.	ENSG00000158125	ENST00000379416	T	0.40756	1.02	5.85	3.07	0.35406	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (3);	0.000000	0.85682	D	0.000000	T	0.58736	0.2143	M	0.77406	2.37	0.80722	D	1	D	0.69078	0.997	D	0.74348	0.983	T	0.56306	-0.8001	10	0.59425	D	0.04	.	5.9437	0.19207	0.2773:0.1302:0.5925:0.0	.	906	P47989	XDH_HUMAN	F	906	ENSP00000368727:L906F	ENSP00000368727:L906F	L	-	1	0	XDH	31426509	1.000000	0.71417	0.985000	0.45067	0.060000	0.15804	2.856000	0.48341	0.380000	0.24823	0.650000	0.86243	CTT	XDH	-	pfam_AldOxase/xan_DH_Mopterin-bd,superfamily_AldOxase/xan_DH_Mopterin-bd,pirsf_Ald_Oxase/xanthine_DH	ENSG00000158125		0.562	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	XDH	HGNC	protein_coding	OTTHUMT00000216840.1	52	0.00	0	G	NM_000379		31573005	31573005	-1	no_errors	ENST00000379416	ensembl	human	known	69_37n	missense	73	10.98	9	SNP	1.000	A
ZSCAN5C	649137	genome.wustl.edu	37	19	56717353	56717353	+	Missense_Mutation	SNP	A	A	G	rs10419548	byFrequency	TCGA-OL-A5D8-01A-11D-A27P-09	TCGA-OL-A5D8-10A-01D-A27P-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	a4a09ce0-c9d8-40bf-a595-f164256cabe7	30ff9e09-daf1-4754-8c1e-61bcb8e7a002	g.chr19:56717353A>G	ENST00000534327.1	+	2	220	c.71A>G	c.(70-72)cAg>cGg	p.Q24R	ZSCAN5C_ENST00000376267.1_Missense_Mutation_p.Q24R			A6NGD5	ZSA5C_HUMAN	zinc finger and SCAN domain containing 5C	24			Q -> R (in dbSNP:rs10419548).		regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|lung(6)|stomach(1)	8						GAGCCACCACAGTCCATGCCA	0.507													G|||	2285	0.45627	0.6127	0.402	5008	,	,		18546	0.4702		0.3549	False		,,,				2504	0.3732					dbGAP											0																																										-	-	-	SO:0001583	missense	0					19q13.43	2013-01-08			ENSG00000204532	ENSG00000204532		"""-"", ""Zinc fingers, C2H2-type"""	34294	protein-coding gene	gene with protein product							Standard	NG_012782		Approved	ZNF495C		A6NGD5	OTTHUMG00000167475	ENST00000534327.1:c.71A>G	19.37:g.56717353A>G	ENSP00000435234:p.Gln24Arg			Missense_Mutation	SNP	pfam_Tscrpt_reg_SCAN,pfam_Znf_C2H2,superfamily_Retrov_capsid_C,smart_Tscrpt_reg_SCAN,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Tscrpt_reg_SCAN	p.Q24R	ENST00000534327.1	37	c.71		19	955	0.43727106227106227	287	0.5833333333333334	132	0.36464088397790057	271	0.4737762237762238	265	0.3496042216358839	G	0	-2.584802	0.00128	.	.	ENSG00000204532	ENST00000534327;ENST00000376267	T;T	0.06068	3.35;3.35	1.28	-2.57	0.06248	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.42699	-0.9436	5	0.09084	T	0.74	.	0.5299	0.00626	0.441:0.1817:0.1805:0.1968	rs10419548;rs12609919;rs52837470;rs10419548	.	.	.	R	24	ENSP00000435234:Q24R;ENSP00000365443:Q24R	ENSP00000365443:Q24R	Q	+	2	0	ZSCAN5C	61409165	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.702000	0.00389	-2.591000	0.00456	-1.063000	0.02288	CAG	ZSCAN5C	-	NULL	ENSG00000204532		0.507	ZSCAN5C-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	ZSCAN5C	HGNC	protein_coding	OTTHUMT00000394739.1	37	0.00	0	A	XM_001131980		56717353	56717353	+1	no_errors	ENST00000376267	ensembl	human	known	69_37n	missense	27	12.90	4	SNP	0.000	G
